From michalkoziarski at gmail.com Sat Apr 2 15:56:07 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Sat, 2 Apr 2011 21:56:07 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" Message-ID: Hi, my name is Micha? Koziarski and I would like to participate in this year GSoC on project mentioned in title. I've prepared a short plan and would be glad to hear some opinions about it. I have a few questions too: - do I have to be familiar with BioRuby itself? - in what exactly 'web visualization' consists? Does it simply mean that there should be a way to upload created files, or is it something more? And my current plan, in which I don't mention RoR integration (since I am not sure what it will be about): 1. Getting familiarized with BioRuby objects, mainly with the way they hold data. 2. Deciding with features should be visualized. 3. In case of presence data with different format but same way of visualization, implementing a mechanism converting data to unified format. 4. Writing a module responsible for creating graphical representation of data. 5. Writing a documentation. Any feedback is appreciated. From bonnal at ingm.org Mon Apr 4 05:38:36 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 4 Apr 2011 11:38:36 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: Message-ID: Dear Michal, thank you for your interest in this project. I'd like to know more about you, programming experience and why did you chose this project ? Are you interested to work in bioinformatics ? On 02/apr/2011, at 21.56, Micha? Koziarski wrote: > Hi, my name is Micha? Koziarski and I would like to participate in this year > GSoC on project mentioned in title. I've prepared a short plan and would be > glad to hear some opinions about it. I have a few questions too: > > - do I have to be familiar with BioRuby itself? It would help a bit :-) > - in what exactly 'web visualization' consists? Does it simply mean that > there should be a way to upload created files, or is it something more? The projects tries to "attach" the concept of images to "bio objects" or to results of some kind of "bio pipeline" where/when possible. Most of the time we process data and creates objects but often the final product is an image. For web visualization, we would like to have images that are ready for the web and that can be integrated in a web application easily. This project (in the subject) will use bio-gem and a feature I'm developing which will give to the developer the possibility to create in a very smooth way a Rails' engine for his/her library. > And my current plan, in which I don't mention RoR integration (since I am > not sure what it will be about): Currently I'm using RoR for my intenral projects, I know there are other framework but I'd like to use the most common. Btw RoR is not our main scope here. > 1. Getting familiarized with BioRuby objects, mainly with the way they hold > data. ok > 2. Deciding with features should be visualized. > 3. In case of presence data with different format but same way of > visualization, implementing a mechanism converting data to unified format. yeah here we should spend a bit of time in figuring out similar representation for dataset and results from "bioinformatics analysis" > 4. Writing a module responsible for creating graphical representation of > data. > 5. Writing a documentation. I agree with the initial plan, don't forget the testing phase. > > Any feedback is appreciated. You can use the ML, and also the irc channel, usually we are there. and on thursday @14:00 GMT there is a irc meeting feel free to join. For other BioRuby developer, feel free to post any comment/ideas/suggestion. -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Helius github: https://github.com/helios From jan.aerts at gmail.com Mon Apr 4 08:00:12 2011 From: jan.aerts at gmail.com (Jan Aerts) Date: Mon, 4 Apr 2011 14:00:12 +0200 Subject: [BioRuby] feedback site for Ruby Ensembl API Message-ID: All, We have created a site where you can provide feedback for the Ruby API to the Ensembl database (github.com/jandot/ruby-ensembl-api ; see Bioinformatics 27(7):1013-1014, 2011). Using that site, you can ask for features, vote on features, report bugs, ... See http://rubyensemblapi.uservoice.com jan. From michalkoziarski at gmail.com Mon Apr 4 10:12:48 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Mon, 4 Apr 2011 16:12:48 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: Message-ID: 2011/4/4 Raoul Bonnal > Dear Michal, > thank you for your interest in this project. > I'd like to know more about you, programming experience and why did you > chose this project ? Are you interested to work in bioinformatics ? > I have fairly strong Ruby knowledge, I have been using it for about a year and a half. There were no really big projects there though, the biggest I've got was probably small LAN IM. Nevertheless, I use Ruby on daily basis and I am familiar with most of its, even complex, features. Also, from the beginning of this year I work as a RoR developer. I've worked on a bigger, team project and now I am developing one solo. I've learned a lot here: working with version control systems, developing in team, operating on other people's code, testing... not to mention further developing my Ruby knowledge. Other than that, I know C++ pretty well: it was my first language and I still use it whenever I see fit. I also have some basic Python and C# knowledge. About why I've chosen this project: I find the problem of representing computer data in format readable by humans interesting, partially because it's so significant: we could have the best algorithms, the fastest computers, but the output would be useless if we wouldn't be able to read it. Additionally, I love the idea of writing code for organisation such as OBF: it makes me think that I do have, even slightest, impact on science. I must also admit that working with Ruby is very tempting :) I really enjoy writing Ruby code. I am certainly interested in programming for scientific purposes. To be honest I haven't thought much about in what area exactly, but since I do have some interest in biology that would seem like a logical choice. > > On 02/apr/2011, at 21.56, Micha? Koziarski wrote: > > Hi, my name is Micha? Koziarski and I would like to participate in this > year > GSoC on project mentioned in title. I've prepared a short plan and would be > glad to hear some opinions about it. I have a few questions too: > > - do I have to be familiar with BioRuby itself? > > It would help a bit :-) > Well, then I am starting to getting know it right know. :) > - in what exactly 'web visualization' consists? Does it simply mean that > > there should be a way to upload created files, or is it something more? > > The projects tries to "attach" the concept of images to "bio objects" or to > results of some kind of "bio pipeline" where/when possible. > Most of the time we process data and creates objects but often the final > product is an image. > For web visualization, we would like to have images that are ready for the > web and that can be integrated in a web application easily. > This project (in the subject) will use bio-gem and a feature I'm developing > which will give to the developer the possibility to create in a very smooth > way a Rails' engine for his/her library. > > And my current plan, in which I don't mention RoR integration (since I am > not sure what it will be about): > > Currently I'm using RoR for my intenral projects, I know there are other > framework but I'd like to use the most common. Btw RoR is not our main scope > here. > > 1. Getting familiarized with BioRuby objects, mainly with the way they hold > data. > > ok > > 2. Deciding with features should be visualized. > 3. In case of presence data with different format but same way of > visualization, implementing a mechanism converting data to unified format. > > yeah here we should spend a bit of time in figuring out similar > representation for dataset and results from "bioinformatics analysis" > > 4. Writing a module responsible for creating graphical representation of > data. > 5. Writing a documentation. > > I agree with the initial plan, don't forget the testing phase. > Actually, I was thinking about trying some test-driven development, I am not 100% sure if that would work for this project though. But anyway, yes, I haven't included that in my plan, thank you for pointing that out. I guess it would be the best to do the final testing before writing a documentation, with some smaller scaled testing after each milestone completed. > > > Any feedback is appreciated. > > You can use the ML, and also the irc channel, usually we are there. and on > thursday @14:00 GMT there is a irc meeting feel free to join. > I've joined ML (it stands for mail list, right?) already, and visited the irc a day or two before, unfortunately it seemed no one was online at the time. As for the meeting, I have classes at this time, so I am not sure if I will be able to be there, but for sure I will visit irc if any other questions come to my mind. And thank you for answering my questions, I have much clearer picture now. > > For other BioRuby developer, feel free to post any > comment/ideas/suggestion. > -- > Ra > > linkedin: http://it.linkedin.com/in/raoulbonnal > twitter: http://twitter.com/ilpuccio > skype: ilpuccio > irc.freenode.net: Helius > github: https://github.com/helios > > > > > > > From bonnal at ingm.org Mon Apr 4 11:06:40 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 4 Apr 2011 17:06:40 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: Message-ID: <963BE5B3-B551-43BD-9A9B-D21C01A14568@ingm.org> Hi Michal, thank you for your detailed answer, for me it's fine go ahead with the gsoc procedure. About IRC, if you find us online msg us, sorry I wasn't online during the w.e. Yes ML means mailing-list :-) My nick name on IRC is helios. On 04/apr/2011, at 16.12, Micha? Koziarski wrote: > 2011/4/4 Raoul Bonnal > >> Dear Michal, >> thank you for your interest in this project. >> I'd like to know more about you, programming experience and why did you >> chose this project ? Are you interested to work in bioinformatics ? >> > > I have fairly strong Ruby knowledge, I have been using it for about a year > and a half. There were no really big projects there though, the biggest I've > got was probably small LAN IM. Nevertheless, I use Ruby on daily basis and I > am familiar with most of its, even complex, features. > > Also, from the beginning of this year I work as a RoR developer. I've worked > on a bigger, team project and now I am developing one solo. I've learned a > lot here: working with version control systems, developing in team, > operating on other people's code, testing... not to mention further > developing my Ruby knowledge. > > Other than that, I know C++ pretty well: it was my first language and I > still use it whenever I see fit. I also have some basic Python and C# > knowledge. > > About why I've chosen this project: I find the problem of representing > computer data in format readable by humans interesting, partially because > it's so significant: we could have the best algorithms, the fastest > computers, but the output would be useless if we wouldn't be able to read > it. Additionally, I love the idea of writing code for organisation such as > OBF: it makes me think that I do have, even slightest, impact on science. I > must also admit that working with Ruby is very tempting :) I really enjoy > writing Ruby code. > > I am certainly interested in programming for scientific purposes. To be > honest I haven't thought much about in what area exactly, but since I do > have some interest in biology that would seem like a logical choice. > >> >> On 02/apr/2011, at 21.56, Micha? Koziarski wrote: >> >> Hi, my name is Micha? Koziarski and I would like to participate in this >> year >> GSoC on project mentioned in title. I've prepared a short plan and would be >> glad to hear some opinions about it. I have a few questions too: >> >> - do I have to be familiar with BioRuby itself? >> >> It would help a bit :-) >> > > Well, then I am starting to getting know it right know. :) > >> - in what exactly 'web visualization' consists? Does it simply mean that >> >> there should be a way to upload created files, or is it something more? >> >> The projects tries to "attach" the concept of images to "bio objects" or to >> results of some kind of "bio pipeline" where/when possible. >> Most of the time we process data and creates objects but often the final >> product is an image. >> For web visualization, we would like to have images that are ready for the >> web and that can be integrated in a web application easily. >> This project (in the subject) will use bio-gem and a feature I'm developing >> which will give to the developer the possibility to create in a very smooth >> way a Rails' engine for his/her library. >> >> And my current plan, in which I don't mention RoR integration (since I am >> not sure what it will be about): >> >> Currently I'm using RoR for my intenral projects, I know there are other >> framework but I'd like to use the most common. Btw RoR is not our main scope >> here. >> >> 1. Getting familiarized with BioRuby objects, mainly with the way they hold >> data. >> >> ok >> >> 2. Deciding with features should be visualized. >> 3. In case of presence data with different format but same way of >> visualization, implementing a mechanism converting data to unified format. >> >> yeah here we should spend a bit of time in figuring out similar >> representation for dataset and results from "bioinformatics analysis" >> >> 4. Writing a module responsible for creating graphical representation of >> data. >> 5. Writing a documentation. >> >> I agree with the initial plan, don't forget the testing phase. >> > > Actually, I was thinking about trying some test-driven development, I am not > 100% sure if that would work for this project though. But anyway, yes, I > haven't included that in my plan, thank you for pointing that out. > > I guess it would be the best to do the final testing before writing a > documentation, with some smaller scaled testing after each milestone > completed. > >> >> >> Any feedback is appreciated. >> >> You can use the ML, and also the irc channel, usually we are there. and on >> thursday @14:00 GMT there is a irc meeting feel free to join. >> > > I've joined ML (it stands for mail list, right?) already, and visited the > irc a day or two before, unfortunately it seemed no one was online at the > time. As for the meeting, I have classes at this time, so I am not sure if I > will be able to be there, but for sure I will visit irc if any other > questions come to my mind. > > And thank you for answering my questions, I have much clearer picture now. > > >> >> For other BioRuby developer, feel free to post any >> comment/ideas/suggestion. >> -- >> Ra >> >> linkedin: http://it.linkedin.com/in/raoulbonnal >> twitter: http://twitter.com/ilpuccio >> skype: ilpuccio >> irc.freenode.net: Helius >> github: https://github.com/helios >> >> >> >> >> >> >> > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Helius github: https://github.com/helios From yannick.wurm at unil.ch Mon Apr 4 12:13:39 2011 From: yannick.wurm at unil.ch (Yannick Wurm) Date: Mon, 4 Apr 2011 18:13:39 +0200 Subject: [BioRuby] feedback site for Ruby Ensembl API (Jan Aerts) In-Reply-To: References: Message-ID: <52117FE7-08B9-4A08-AB13-2BA9993E3488@unil.ch> Thanks Jan & congrats for the paper. Now if only ensembl supported more ant genomes.... ------------------------- Ant Genomes & Evolution http://yannick.poulet.org skype://yannickwurm On 4 Apr 2011, at 18:00, bioruby-request at lists.open-bio.org wrote: > All, > > We have created a site where you can provide feedback for the Ruby API to > the Ensembl database (github.com/jandot/ruby-ensembl-api ; see > Bioinformatics 27(7):1013-1014, 2011). Using that site, you can ask for > features, vote on features, report bugs, ... > > See http://rubyensemblapi.uservoice.com > > jan. From michalkoziarski at gmail.com Tue Apr 5 13:24:22 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Tue, 5 Apr 2011 19:24:22 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" Message-ID: I've completed my application. Chris Fields suggested that I should write it up, he hasn't specified what parts exactly though. If you have any advice about it, please let me know. I use some of my answers to questions asked here in the application, I hope that's not a problem: I didn't see much point in rewriting it, since the meaning would be the same. I don't include the first point, about the address, since it's a public ML and I don't think it's important here. I am basing the application on the OBF's template, which I enclose too. 1. Why you are interested in the project you are proposing and are well-suited to undertake it. 2. A summary of your programming experience and skills. 3. Programs or projects you have previously authored or contributed to, in particular those available as open-source, including, if applicable, any past Summer of Code involvement. 4. A project plan for the project you are proposing, even if your proposed project is directly based on one of the proposed project ideas for member projects. 5. Any obligations, vacations, or plans for the summer that may require scheduling during the GSoC work period. 1. I find the problem of representing computer data in format readable by humans interesting, partially because it's so significant: we could have the best algorithms, the fastest computers, but the output would be useless if we wouldn't be able to read it. Additionally, I love the idea of writing code for organisation such as OBF: it makes me think that I do have, even slightest, impact on science. I must also admit that working with Ruby is very tempting, I really enjoy writing Ruby code. 2. I have fairly strong Ruby knowledge, I have been using it for about a year and a half. There were no really big projects there though, the biggest I've got was probably small LAN IM. Nevertheless, I use Ruby on daily basis and I am familiar with most of its, even complex, features. Also, from the beginning of this year I work as a RoR developer. I've worked on a bigger, team project and now I am developing one solo. I've learned a lot here: working with version control systems, developing in team, operating on other people's code, testing... not to mention further developing my Ruby knowledge. Other than that, I know C++ pretty well: it was my first language and I still use it whenever I see fit. I also have some basic Python and C# knowledge. 3. I can't say much more than what I've written in previous paragraph. 4. 1. Getting familiarized with BioRuby objects, mainly with the way they hold data. 2. Deciding with features should be visualized. 3. In case of presence data with different format but same way of visualization, implementing a mechanism converting data to unified format. 4. Writing a module responsible for creating graphical representation of data. 5. Final testing. 6. Writing a documentation. 5. Possibly short vacation (less than one week) around beginning of July. Also, I am from Poland, which means that my summer vacations starts from July. Because of that I won't be able to focus only on the project until than. What I can do, however, is to start coding earlier. I would like to familiarize myself with documentation before bonding period starts (I've already began to do it), and when it does start coding right away. Thanks to that I should have just as much time as if I started in May. Other than that I am all about the project. Also, since as I've told I would probably have to start coding a little earlier, I am trying to slowly browse the documentation. It's a big project though, and I don't know what's important. Do you have any suggestions about that? Are there parts that would be especially relevant to the project? Or maybe even better, are there any easier tasks to complete? I learn best by exercise, so that would be great. I've looked up at github's issues page, but haven't found anything like what I am talking about. Maybe I just didn't know on what I was looking? From cjfields at illinois.edu Tue Apr 5 15:09:10 2011 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 5 Apr 2011 14:09:10 -0500 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: Message-ID: <6916C4A0-739E-4069-A1EE-704ACE5DA5D8@illinois.edu> Micha?, In general, the proposal should answer the questions below, but should also have a rough timeline on how you would go about coding the project, creating deliverables for the community for testing, etc. This should come with the input of your possible mentor for the project or from others in the bioruby community. The timeline is a little problematic, but the OBF mentors can further discuss that. One thing that will cause a problem is that there is a significant amount of time (about one month) for community bonding, so any coding on a significant project in that period will be tricky. chris On Apr 5, 2011, at 12:24 PM, Micha? Koziarski wrote: > I've completed my application. Chris Fields suggested that I should write it > up, he hasn't specified what parts exactly though. If you have any advice > about it, please let me know. > > I use some of my answers to questions asked here in the application, I hope > that's not a problem: I didn't see much point in rewriting it, since the > meaning would be the same. > > I don't include the first point, about the address, since it's a public ML > and I don't think it's important here. > > I am basing the application on the OBF's template, which I enclose too. > > > 1. Why you are interested in the project you are proposing and are > well-suited to undertake it. > 2. A summary of your programming experience and skills. > 3. Programs or projects you have previously authored or contributed to, > in particular those available as open-source, including, if applicable, any > past Summer of Code involvement. > 4. A project plan for the project you are proposing, even if your > proposed project is directly based on one of the proposed project ideas for > member projects. > 5. Any obligations, vacations, or plans for the summer that may require > scheduling during the GSoC work period. > > > > 1. I find the problem of representing computer data in format > readable by humans interesting, partially because it's so significant: we > could have the best algorithms, the fastest computers, but the output would > be useless if we wouldn't be able to read it. Additionally, I love the idea > of writing code for organisation such as OBF: it makes me think that I do > have, even slightest, impact on science. I must also admit that working with > Ruby is very tempting, I really enjoy writing Ruby code. > 2. I have fairly strong Ruby knowledge, I have been using it for > about a year and a half. There were no really big projects there though, the > biggest I've got was probably small LAN IM. Nevertheless, I use Ruby on > daily basis and I am familiar with most of its, even complex, features. > Also, from the beginning of this year I work as a RoR developer. > I've worked on a bigger, team project and now I am developing one solo. I've > learned a lot here: working with version control systems, developing in > team, operating on other people's code, testing... not to mention further > developing my Ruby knowledge. > Other than that, I know C++ pretty well: it was my first language > and I still use it whenever I see fit. I also have some basic Python and C# > knowledge. > 3. I can't say much more than what I've written in previous paragraph. > 4. 1. Getting familiarized with BioRuby objects, mainly with the way they > hold data. > 2. Deciding with features should be visualized. > 3. In case of presence data with different format but same way of > visualization, implementing a mechanism converting data to unified format. > 4. Writing a module responsible for creating graphical representation of > data. > 5. Final testing. > 6. Writing a documentation. > 5. Possibly short vacation (less than one week) around beginning of > July. > Also, I am from Poland, which means that my summer vacations starts > from July. Because of that I won't be able to focus only on the project > until than. What I can do, however, is to start coding earlier. I would like > to familiarize myself with documentation before bonding period starts (I've > already began to do it), and when it does start coding right away. Thanks to > that I should have just as much time as if I started in May. > Other than that I am all about the project. > > > Also, since as I've told I would probably have to start coding a little > earlier, I am trying to slowly browse the documentation. It's a big project > though, and I don't know what's important. Do you have any suggestions about > that? Are there parts that would be especially relevant to the project? Or > maybe even better, are there any easier tasks to complete? I learn best by > exercise, so that would be great. I've looked up at github's issues page, > but haven't found anything like what I am talking about. Maybe I just didn't > know on what I was looking? > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From cmzmasek at yahoo.com Tue Apr 5 15:19:35 2011 From: cmzmasek at yahoo.com (Christian Zmasek) Date: Tue, 5 Apr 2011 12:19:35 -0700 (PDT) Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: Message-ID: <981305.71979.qm@web38404.mail.mud.yahoo.com> Hi, Michal: I think your project plan needs to be much more detailed. It might be best in a format similar to the template/example below: Prior to coding ("community bonding period"): -Familiarize myself with BioRuby code base -Learn about graphics within/from Ruby -Discuss ... with mentors/BioRuby community -... -Learn about git, set up my repository Week 1: Goal: Develop necessary utility classes for ... Anticipated problems: None Weeks 2 and 3: Goal: Develop class to visualize intron/exon structures... Anticipated problems: Such and such might not ... Alternatives: If XYZ turns out not feasible, I plan to ... instead Week X: Goal: Unit tests for ... Week Y: Documentation ... Hope this helps, Christian Zmasek ----- Original Message ---- > From: Micha? Koziarski > To: bioruby at lists.open-bio.org > Sent: Tue, April 5, 2011 10:24:22 AM > Subject: [BioRuby] GSoC - project "Represent bio-objects and related >information with images" > > I've completed my application. Chris Fields suggested that I should write it > up, he hasn't specified what parts exactly though. If you have any advice > about it, please let me know. > > I use some of my answers to questions asked here in the application, I hope > that's not a problem: I didn't see much point in rewriting it, since the > meaning would be the same. > > I don't include the first point, about the address, since it's a public ML > and I don't think it's important here. > > I am basing the application on the OBF's template, which I enclose too. > > > 1. Why you are interested in the project you are proposing and are > well-suited to undertake it. > 2. A summary of your programming experience and skills. > 3. Programs or projects you have previously authored or contributed to, > in particular those available as open-source, including, if applicable, any > past Summer of Code involvement. > 4. A project plan for the project you are proposing, even if your > proposed project is directly based on one of the proposed project ideas for > member projects. > 5. Any obligations, vacations, or plans for the summer that may require > scheduling during the GSoC work period. > > > > 1. I find the problem of representing computer data in format > readable by humans interesting, partially because it's so significant: we > could have the best algorithms, the fastest computers, but the output would > be useless if we wouldn't be able to read it. Additionally, I love the idea > of writing code for organisation such as OBF: it makes me think that I do > have, even slightest, impact on science. I must also admit that working >with > Ruby is very tempting, I really enjoy writing Ruby code. > 2. I have fairly strong Ruby knowledge, I have been using it for > about a year and a half. There were no really big projects there though, >the > biggest I've got was probably small LAN IM. Nevertheless, I use Ruby on > daily basis and I am familiar with most of its, even complex, features. > Also, from the beginning of this year I work as a RoR developer. > I've worked on a bigger, team project and now I am developing one solo. >I've > learned a lot here: working with version control systems, developing in > team, operating on other people's code, testing... not to mention further > developing my Ruby knowledge. > Other than that, I know C++ pretty well: it was my first language > and I still use it whenever I see fit. I also have some basic Python and C# > knowledge. > 3. I can't say much more than what I've written in previous paragraph. > 4. 1. Getting familiarized with BioRuby objects, mainly with the way they > hold data. > 2. Deciding with features should be visualized. > 3. In case of presence data with different format but same way of > visualization, implementing a mechanism converting data to unified format. > 4. Writing a module responsible for creating graphical representation of > data. > 5. Final testing. > 6. Writing a documentation. > 5. Possibly short vacation (less than one week) around beginning of > July. > Also, I am from Poland, which means that my summer vacations starts > from July. Because of that I won't be able to focus only on the project > until than. What I can do, however, is to start coding earlier. I would >like > to familiarize myself with documentation before bonding period starts (I've > already began to do it), and when it does start coding right away. Thanks >to > that I should have just as much time as if I started in May. > Other than that I am all about the project. > > > Also, since as I've told I would probably have to start coding a little > earlier, I am trying to slowly browse the documentation. It's a big project > though, and I don't know what's important. Do you have any suggestions about > that? Are there parts that would be especially relevant to the project? Or > maybe even better, are there any easier tasks to complete? I learn best by > exercise, so that would be great. I've looked up at github's issues page, > but haven't found anything like what I am talking about. Maybe I just didn't > know on what I was looking? > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From michalkoziarski at gmail.com Tue Apr 5 16:37:02 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Tue, 5 Apr 2011 22:37:02 +0200 Subject: [BioRuby] Fwd: GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <981305.71979.qm@web38404.mail.mud.yahoo.com> Message-ID: I have to agree, my plan isn't very specific. But mainly coming up with a timeline is kind of a guesswork: maybe it's just me, I don't like saying anything unless I am certain of it, and there's no way at this point to do this. Anyway, I will prepare what I am able to today, and hopefully catch someone tomorrow on irc to further discuss some specifics. Chris: could you explain why any coding at community bonding period would be hard? I assumed that a big part of it is getting familiar with documentation, and with that done before I would have some more time to code. Of course, it wouldn't be a full-time coding, but I thought that at this point I would have all the knowledge to start writing, so why not to. Maybe I am missing something, in that case tell me please. Christian: yes, it was very helpful, I've read some example plans before, but I couldn't really relate them to my project. Now I have a little clearer picture of what to write. Thanks for that, hopefully tomorrow I will present something in that manner. 2011/4/5 Christian Zmasek > Hi, Michal: > > I think your project plan needs to be much more detailed. > > It might be best in a format similar to the template/example below: > > Prior to coding ("community bonding period"): > -Familiarize myself with BioRuby code base > -Learn about graphics within/from Ruby > -Discuss ... with mentors/BioRuby community > -... > -Learn about git, set up my repository > > > > Week 1: > Goal: Develop necessary utility classes for ... > Anticipated problems: None > > Weeks 2 and 3: > Goal: Develop class to visualize intron/exon structures... > Anticipated problems: Such and such might not ... > Alternatives: If XYZ turns out not feasible, I plan to ... instead > > Week X: > Goal: Unit tests for ... > > > > Week Y: > Documentation ... > > Hope this helps, > > Christian Zmasek > > > > > ----- Original Message ---- > > From: Micha? Koziarski > > To: bioruby at lists.open-bio.org > > Sent: Tue, April 5, 2011 10:24:22 AM > > Subject: [BioRuby] GSoC - project "Represent bio-objects and related > >information with images" > > > > I've completed my application. Chris Fields suggested that I should write > it > > up, he hasn't specified what parts exactly though. If you have any > advice > > about it, please let me know. > > > > I use some of my answers to questions asked here in the application, I > hope > > that's not a problem: I didn't see much point in rewriting it, since the > > meaning would be the same. > > > > I don't include the first point, about the address, since it's a public > ML > > and I don't think it's important here. > > > > I am basing the application on the OBF's template, which I enclose too. > > > > > > 1. Why you are interested in the project you are proposing and are > > well-suited to undertake it. > > 2. A summary of your programming experience and skills. > > 3. Programs or projects you have previously authored or contributed > to, > > in particular those available as open-source, including, if > applicable, > any > > past Summer of Code involvement. > > 4. A project plan for the project you are proposing, even if your > > proposed project is directly based on one of the proposed project > ideas > for > > member projects. > > 5. Any obligations, vacations, or plans for the summer that may > require > > scheduling during the GSoC work period. > > > > > > > > 1. I find the problem of representing computer data in format > > readable by humans interesting, partially because it's so > significant: we > > could have the best algorithms, the fastest computers, but the output > would > > be useless if we wouldn't be able to read it. Additionally, I love > the > idea > > of writing code for organisation such as OBF: it makes me think that > I do > > have, even slightest, impact on science. I must also admit that > working > >with > > Ruby is very tempting, I really enjoy writing Ruby code. > > 2. I have fairly strong Ruby knowledge, I have been using it for > > about a year and a half. There were no really big projects there > though, > >the > > biggest I've got was probably small LAN IM. Nevertheless, I use Ruby > on > > daily basis and I am familiar with most of its, even complex, > features. > > Also, from the beginning of this year I work as a RoR > developer. > > I've worked on a bigger, team project and now I am developing one > solo. > >I've > > learned a lot here: working with version control systems, developing > in > > team, operating on other people's code, testing... not to mention > further > > developing my Ruby knowledge. > > Other than that, I know C++ pretty well: it was my first > language > > and I still use it whenever I see fit. I also have some basic Python > and > C# > > knowledge. > > 3. I can't say much more than what I've written in previous > paragraph. > > 4. 1. Getting familiarized with BioRuby objects, mainly with the way > they > > hold data. > > 2. Deciding with features should be visualized. > > 3. In case of presence data with different format but same way of > > visualization, implementing a mechanism converting data to unified > format. > > 4. Writing a module responsible for creating graphical representation > of > > data. > > 5. Final testing. > > 6. Writing a documentation. > > 5. Possibly short vacation (less than one week) around beginning > of > > July. > > Also, I am from Poland, which means that my summer vacations > starts > > from July. Because of that I won't be able to focus only on the > project > > until than. What I can do, however, is to start coding earlier. I > would > >like > > to familiarize myself with documentation before bonding period starts > (I've > > already began to do it), and when it does start coding right away. > Thanks > >to > > that I should have just as much time as if I started in May. > > Other than that I am all about the project. > > > > > > Also, since as I've told I would probably have to start coding a little > > earlier, I am trying to slowly browse the documentation. It's a big > project > > though, and I don't know what's important. Do you have any suggestions > about > > that? Are there parts that would be especially relevant to the project? > Or > > maybe even better, are there any easier tasks to complete? I learn best > by > > exercise, so that would be great. I've looked up at github's issues > page, > > but haven't found anything like what I am talking about. Maybe I just > didn't > > know on what I was looking? > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > From cjfields at illinois.edu Tue Apr 5 16:56:38 2011 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 5 Apr 2011 15:56:38 -0500 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <981305.71979.qm@web38404.mail.mud.yahoo.com> Message-ID: On Apr 5, 2011, at 3:37 PM, Micha? Koziarski wrote: > I have to agree, my plan isn't very specific. But mainly coming up with a timeline is kind of a guesswork: maybe it's just me, I don't like saying anything unless I am certain of it, and there's no way at this point to do this. Anyway, I will prepare what I am able to today, and hopefully catch someone tomorrow on irc to further discuss some specifics. Don't think of it as a strict timeline as much as an overall plan for development of your project. Timelines for projects are meant to be malleable and change based on what occurs during development, but w/o underlying structure then there is no organization of your priorities. > Chris: could you explain why any coding at community bonding period would be hard? I assumed that a big part of it is getting familiar with documentation, and with that done before I would have some more time to code. Of course, it wouldn't be a full-time coding, but I thought that at this point I would have all the knowledge to start writing, so why not to. Maybe I am missing something, in that case tell me please. In general, little coding occurs during community bonding; the time is spent asking questions on the API, working out final priorities, details on the project, etc with the community (mentor in particular). I'm not sure of your level of experience with BioRuby, but from my experience with BioPerl and past GSoC projects the codebase and API (and documentation, or lack thereof) can be daunting for a beginner. So, mentioning that you will use that period to code b/c of time issues during the scheduled period is a bit premature in my opinion w/o more specifics, but that's really for the BioRuby folks to decide. I think Christian made some more specific notes on what is expected. chris > Christian: yes, it was very helpful, I've read some example plans before, but I couldn't really relate them to my project. Now I have a little clearer picture of what to write. Thanks for that, hopefully tomorrow I will present something in that manner. > > > 2011/4/5 Christian Zmasek > Hi, Michal: > > I think your project plan needs to be much more detailed. > > It might be best in a format similar to the template/example below: > > Prior to coding ("community bonding period"): > -Familiarize myself with BioRuby code base > -Learn about graphics within/from Ruby > -Discuss ... with mentors/BioRuby community > -... > -Learn about git, set up my repository > > > > Week 1: > Goal: Develop necessary utility classes for ... > Anticipated problems: None > > Weeks 2 and 3: > Goal: Develop class to visualize intron/exon structures... > Anticipated problems: Such and such might not ... > Alternatives: If XYZ turns out not feasible, I plan to ... instead > > Week X: > Goal: Unit tests for ... > > > > Week Y: > Documentation ... > > Hope this helps, > > Christian Zmasek > > > > > ----- Original Message ---- > > From: Micha? Koziarski > > To: bioruby at lists.open-bio.org > > Sent: Tue, April 5, 2011 10:24:22 AM > > Subject: [BioRuby] GSoC - project "Represent bio-objects and related > >information with images" > > > > I've completed my application. Chris Fields suggested that I should write it > > up, he hasn't specified what parts exactly though. If you have any advice > > about it, please let me know. > > > > I use some of my answers to questions asked here in the application, I hope > > that's not a problem: I didn't see much point in rewriting it, since the > > meaning would be the same. > > > > I don't include the first point, about the address, since it's a public ML > > and I don't think it's important here. > > > > I am basing the application on the OBF's template, which I enclose too. > > > > > > 1. Why you are interested in the project you are proposing and are > > well-suited to undertake it. > > 2. A summary of your programming experience and skills. > > 3. Programs or projects you have previously authored or contributed to, > > in particular those available as open-source, including, if applicable, > any > > past Summer of Code involvement. > > 4. A project plan for the project you are proposing, even if your > > proposed project is directly based on one of the proposed project ideas > for > > member projects. > > 5. Any obligations, vacations, or plans for the summer that may require > > scheduling during the GSoC work period. > > > > > > > > 1. I find the problem of representing computer data in format > > readable by humans interesting, partially because it's so significant: we > > could have the best algorithms, the fastest computers, but the output > would > > be useless if we wouldn't be able to read it. Additionally, I love the > idea > > of writing code for organisation such as OBF: it makes me think that I do > > have, even slightest, impact on science. I must also admit that working > >with > > Ruby is very tempting, I really enjoy writing Ruby code. > > 2. I have fairly strong Ruby knowledge, I have been using it for > > about a year and a half. There were no really big projects there though, > >the > > biggest I've got was probably small LAN IM. Nevertheless, I use Ruby on > > daily basis and I am familiar with most of its, even complex, features. > > Also, from the beginning of this year I work as a RoR developer. > > I've worked on a bigger, team project and now I am developing one solo. > >I've > > learned a lot here: working with version control systems, developing in > > team, operating on other people's code, testing... not to mention further > > developing my Ruby knowledge. > > Other than that, I know C++ pretty well: it was my first language > > and I still use it whenever I see fit. I also have some basic Python and > C# > > knowledge. > > 3. I can't say much more than what I've written in previous paragraph. > > 4. 1. Getting familiarized with BioRuby objects, mainly with the way they > > hold data. > > 2. Deciding with features should be visualized. > > 3. In case of presence data with different format but same way of > > visualization, implementing a mechanism converting data to unified > format. > > 4. Writing a module responsible for creating graphical representation of > > data. > > 5. Final testing. > > 6. Writing a documentation. > > 5. Possibly short vacation (less than one week) around beginning of > > July. > > Also, I am from Poland, which means that my summer vacations starts > > from July. Because of that I won't be able to focus only on the project > > until than. What I can do, however, is to start coding earlier. I would > >like > > to familiarize myself with documentation before bonding period starts > (I've > > already began to do it), and when it does start coding right away. Thanks > >to > > that I should have just as much time as if I started in May. > > Other than that I am all about the project. > > > > > > Also, since as I've told I would probably have to start coding a little > > earlier, I am trying to slowly browse the documentation. It's a big project > > though, and I don't know what's important. Do you have any suggestions about > > that? Are there parts that would be especially relevant to the project? Or > > maybe even better, are there any easier tasks to complete? I learn best by > > exercise, so that would be great. I've looked up at github's issues page, > > but haven't found anything like what I am talking about. Maybe I just didn't > > know on what I was looking? > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > From ales.guzik at gmail.com Wed Apr 6 05:27:59 2011 From: ales.guzik at gmail.com (=?UTF-8?B?0JDQu9C10YHRjA==?=) Date: Wed, 6 Apr 2011 12:27:59 +0300 Subject: [BioRuby] BioRuby Wrapper for Command line application (GSOC 2011) Message-ID: Hello. My name is Ales and I'd like to implement BioRuby wrapper for command line applications as my Google Summer of Code 2011 project. 1. Your complete contact information, including full name, physical address, preferred email address, and telephone number, plus other pertinent contact information such as IRC handles, etc. Ales Guzik 4th year student at Belarusian State University of Informatics and Radioelectronics. Belarus, Minsk, P.Brovki st. 3-1 46 ales.guzik at gmail.com +375 25 902 8190 (Belarus) +1 650 336 5853 (Google Voice) skype: ales-guzik IRC, twitter, facebook, github etc.: nekotwi 2. Why you are interested in the project you are proposing and are well-suited to undertake it. This project is interesting for me because it requires metaprogramming - thing I most like in ruby and because it's BioRuby - project I wanted to get familiar with long time ago. I use Ruby more than 2 years for most of my university tasks and daily linux scripting. 2 month ago I started working as Ruby on Rails developer. I have pretty good experience in ruby metaprogramming which is needed for this project. 3. A summary of your programming experience and skills. I have well experience in C, know but not heavily used C++ and Qt, long time ago learned some Erlang, have coded some C# at university but dislike it, played a bit with Android/Java programming. Know and sometimes use Scheme(Racket), now learning some Perl 5. Started learning Ruby somewhere in the beginning of 2nd university year and liked it very much. 4. Programs or projects you have previously authored or contributed to, in particular those available as open-source, including, if applicable, any past Summer of Code involvement. I haven't yet contributed to opensource projects (except for some tiny projects by myself) but really want to. 5. A project plan for the project you are proposing, even if your proposed project is directly based on one of the proposed project ideas for member projects. 1) Get familiar with source code, use cases and documentation of BioRuby and BioRuby-ngs 2) Define specs and write rspec tests for this CLI application wrapper 3) Code to make all tests pass 4) Optimize code for processing BIG ammounts of information 5) Refactor 6) Document undocumented parts 6. Any obligations, vacations, or plans for the summer that may require scheduling during the GSoC work period. I work as rails programmer 30 hours a week. It's like 8:00 - 14:00 GMT+2 DST monday - friday, so I can code for my project 14:30 - 22:00 or even more. It will be like this in june and august. In july I'll be at military training. I'll have time and internet access but can't tell my schedule for now. -- Regards, Ales Guzik ------------------------------------------------------------ e-mail: ales.guzik at gmail.com skype: ales-guzik tel: +375 25 9028190 From bonnal at ingm.org Wed Apr 6 05:48:52 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Wed, 6 Apr 2011 11:48:52 +0200 Subject: [BioRuby] BioRuby Wrapper for Command line application (GSOC 2011) In-Reply-To: References: Message-ID: <4B02CC0A-20DE-4A60-93C3-E7EDACC9BA64@ingm.org> Hello Ales, thank you for submitting your proposal, like Michal: I quote here the discussion with Chris and Christian, if you could write a better time line in form of days/weeks with tasks/objectives I think it would be better: this is the quote from Christian and Chris Hi, Michal: I think your project plan needs to be much more detailed. It might be best in a format similar to the template/example below: Prior to coding ("community bonding period"): -Familiarize myself with BioRuby code base -Learn about graphics within/from Ruby -Discuss ... with mentors/BioRuby community -... -Learn about git, set up my repository Week 1: Goal: Develop necessary utility classes for ... Anticipated problems: None Weeks 2 and 3: Goal: Develop class to visualize intron/exon structures... Anticipated problems: Such and such might not ... Alternatives: If XYZ turns out not feasible, I plan to ... instead Week X: Goal: Unit tests for ... Week Y: Documentation ... Hope this helps, Christian Zmasek ---- Micha?, In general, the proposal should answer the questions below, but should also have a rough timeline on how you would go about coding the project, creating deliverables for the community for testing, etc. This should come with the input of your possible mentor for the project or from others in the bioruby community. The timeline is a little problematic, but the OBF mentors can further discuss that. One thing that will cause a problem is that there is a significant amount of time (about one month) for community bonding, so any coding on a significant project in that period will be tricky. chris ----- Original Message ---- > From: Micha? Koziarski > To: bioruby at lists.open-bio.org > Sent: Tue, April 5, 2011 10:24:22 AM > Subject: [BioRuby] GSoC - project "Represent bio-objects and related > information with images" > > I've completed my application. Chris Fields suggested that I should write it > up, he hasn't specified what parts exactly though. If you have any advice > about it, please let me know. > > I use some of my answers to questions asked here in the application, I hope > that's not a problem: I didn't see much point in rewriting it, since the > meaning would be the same. > > I don't include the first point, about the address, since it's a public ML > and I don't think it's important here. > > I am basing the application on the OBF's template, which I enclose too. > > > 1. Why you are interested in the project you are proposing and are > well-suited to undertake it. > 2. A summary of your programming experience and skills. > 3. Programs or projects you have previously authored or contributed to, > in particular those available as open-source, including, if applicable, any > past Summer of Code involvement. > 4. A project plan for the project you are proposing, even if your > proposed project is directly based on one of the proposed project ideas for > member projects. > 5. Any obligations, vacations, or plans for the summer that may require > scheduling during the GSoC work period. > > > > 1. I find the problem of representing computer data in format > readable by humans interesting, partially because it's so significant: we > could have the best algorithms, the fastest computers, but the output would > be useless if we wouldn't be able to read it. Additionally, I love the idea > of writing code for organisation such as OBF: it makes me think that I do > have, even slightest, impact on science. I must also admit that working > with > Ruby is very tempting, I really enjoy writing Ruby code. > 2. I have fairly strong Ruby knowledge, I have been using it for > about a year and a half. There were no really big projects there though, > the > biggest I've got was probably small LAN IM. Nevertheless, I use Ruby on > daily basis and I am familiar with most of its, even complex, features. > Also, from the beginning of this year I work as a RoR developer. > I've worked on a bigger, team project and now I am developing one solo. > I've > learned a lot here: working with version control systems, developing in > team, operating on other people's code, testing... not to mention further > developing my Ruby knowledge. > Other than that, I know C++ pretty well: it was my first language > and I still use it whenever I see fit. I also have some basic Python and C# > knowledge. > 3. I can't say much more than what I've written in previous paragraph. > 4. 1. Getting familiarized with BioRuby objects, mainly with the way they > hold data. > 2. Deciding with features should be visualized. > 3. In case of presence data with different format but same way of > visualization, implementing a mechanism converting data to unified format. > 4. Writing a module responsible for creating graphical representation of > data. > 5. Final testing. > 6. Writing a documentation. > 5. Possibly short vacation (less than one week) around beginning of > July. > Also, I am from Poland, which means that my summer vacations starts > from July. Because of that I won't be able to focus only on the project > until than. What I can do, however, is to start coding earlier. I would > like > to familiarize myself with documentation before bonding period starts (I've > already began to do it), and when it does start coding right away. Thanks > to > that I should have just as much time as if I started in May. > Other than that I am all about the project. > > > Also, since as I've told I would probably have to start coding a little > earlier, I am trying to slowly browse the documentation. It's a big project > though, and I don't know what's important. Do you have any suggestions about > that? Are there parts that would be especially relevant to the project? Or > maybe even better, are there any easier tasks to complete? I learn best by > exercise, so that would be great. I've looked up at github's issues page, > but haven't found anything like what I am talking about. Maybe I just didn't > know on what I was looking? > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > _______________________________________________ BioRuby Project - http://www.bioruby.org/ BioRuby mailing list BioRuby at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioruby On 06/apr/2011, at 11.27, ????? wrote: > Hello. My name is Ales and I'd like to implement BioRuby wrapper for > command line applications as my Google Summer of Code 2011 project. > > > 1. Your complete contact information, including full name, physical > address, preferred email address, and telephone number, plus other > pertinent contact information such as IRC handles, etc. > > Ales Guzik > 4th year student at Belarusian State University of Informatics and > Radioelectronics. > Belarus, Minsk, P.Brovki st. 3-1 46 > ales.guzik at gmail.com > +375 25 902 8190 (Belarus) > +1 650 336 5853 (Google Voice) > skype: ales-guzik > IRC, twitter, facebook, github etc.: nekotwi > > 2. Why you are interested in the project you are proposing and are > well-suited to undertake it. > > This project is interesting for me because it requires metaprogramming > - thing I most like in ruby and > because it's BioRuby - project I wanted to get familiar with long time ago. > I use Ruby more than 2 years for most of my university tasks and daily > linux scripting. 2 month ago I > started working as Ruby on Rails developer. I have pretty good > experience in ruby metaprogramming which > is needed for this project. > > 3. A summary of your programming experience and skills. > > I have well experience in C, know but not heavily used C++ and Qt, > long time ago learned some Erlang, > have coded some C# at university but dislike it, played a bit with > Android/Java programming. > Know and sometimes use Scheme(Racket), now learning some Perl 5. > Started learning Ruby somewhere in the beginning of 2nd university > year and liked it very much. > > 4. Programs or projects you have previously authored or contributed > to, in particular those available as open-source, including, if > applicable, any past Summer of Code involvement. > > I haven't yet contributed to opensource projects (except for some tiny > projects by myself) but really want to. > > 5. A project plan for the project you are proposing, even if your > proposed project is directly based on one of the proposed project > ideas for member projects. > > 1) Get familiar with source code, use cases and documentation of > BioRuby and BioRuby-ngs > 2) Define specs and write rspec tests for this CLI application wrapper > 3) Code to make all tests pass > 4) Optimize code for processing BIG ammounts of information > 5) Refactor > 6) Document undocumented parts > > 6. Any obligations, vacations, or plans for the summer that may > require scheduling during the GSoC work period. > > I work as rails programmer 30 hours a week. It's like 8:00 - 14:00 > GMT+2 DST monday - friday, so I can code for > my project 14:30 - 22:00 or even more. It will be like this in june and august. > In july I'll be at military training. I'll have time and internet > access but can't tell my schedule for now. > > -- > Regards, > Ales Guzik > ------------------------------------------------------------ > e-mail: ales.guzik at gmail.com > skype: ales-guzik > tel: +375 25 9028190 > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Helius github: https://github.com/helios From michalkoziarski at gmail.com Wed Apr 6 14:14:55 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Wed, 6 Apr 2011 20:14:55 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <981305.71979.qm@web38404.mail.mud.yahoo.com> Message-ID: W dniu 5 kwietnia 2011 22:56 u?ytkownik Chris Fields napisa?: > On Apr 5, 2011, at 3:37 PM, Micha? Koziarski wrote: > > > I have to agree, my plan isn't very specific. But mainly coming up with a > timeline is kind of a guesswork: maybe it's just me, I don't like saying > anything unless I am certain of it, and there's no way at this point to do > this. Anyway, I will prepare what I am able to today, and hopefully catch > someone tomorrow on irc to further discuss some specifics. > > Don't think of it as a strict timeline as much as an overall plan for > development of your project. Timelines for projects are meant to be > malleable and change based on what occurs during development, but w/o > underlying structure then there is no organization of your priorities. > I believe that I understand it better now. I attach something more specific. I am still working on it, but there are some questions I would like to ask about what I've completed so far. But first, the timeline: Prior to coding: - Familiarize myself with BioRuby code in general perspective. - Prepare my environment to work with and learn about Rubyvis. - Take a closer look at how BioRuby objects stores data. - Prepare ideas on how to unify that data format. The goal is to create one format that would easily allow to base visualization module on it. If that turn out to be impossible divide objects in as small number of groups as possible and propose formats for each one of them. - Discuss these ideas, decide which one to choose. - Discuss what set of functions user should have access to. - Discuss which features should be visualized, and in which order it should be implemented. - Decide if there are any other tools that could help with developing the project, if so learn about them. - Final preparation for coding: preparing environment, creating git repo. Week 1: Goal: choose one representative type of BioRuby object and develop class that would convert its data to proposed format. That should come along with unit tests. Week 2: Goal: develop graphical module that would create image files based on data in unified format and provide user interface, write unit tests. On this point it should be possible to fully visualize chosen BioRuby object. Weeks 3 to 8: Goal: basing on first weeks work, prepare similar classes for all of the remaining BioRuby objects. Each class should have unit tests. Week 9: Goal: develop mechanism of browsing images in shell. It should include simple search and a way of opening images. Week 10: Goal: write integration tests. Weeks 11 and 12: Goal: write documentation. I would like to be more specific about what should be done from weeks 3 to 8, though. It would be nice to plan some time for every object that needs visualization, but I don't know which that would be exactly. Could you give me a hand with this? And in general, as always I would be happy to hear some feedback. > > > Chris: could you explain why any coding at community bonding period would > be hard? I assumed that a big part of it is getting familiar with > documentation, and with that done before I would have some more time to > code. Of course, it wouldn't be a full-time coding, but I thought that at > this point I would have all the knowledge to start writing, so why not to. > Maybe I am missing something, in that case tell me please. > > In general, little coding occurs during community bonding; the time is > spent asking questions on the API, working out final priorities, details on > the project, etc with the community (mentor in particular). I'm not sure of > your level of experience with BioRuby, but from my experience with BioPerl > and past GSoC projects the codebase and API (and documentation, or lack > thereof) can be daunting for a beginner. So, mentioning that you will use > that period to code b/c of time issues during the scheduled period is a bit > premature in my opinion w/o more specifics, but that's really for the > BioRuby folks to decide. > I do understand your point. However, I didn't mean to spend less time on getting to know the codebase, I just wanted to start doing it earlier. Anyhow, maybe you have some suggestions about how to solve this time issue? It's a matter of coding for one month for about 30 hours a week. I based my proposition on something I read on one of GSoC suggestions page. But yes, you may be right that BioRuby is to big project for such a approach. > > I think Christian made some more specific notes on what is expected. > > chris > > > Christian: yes, it was very helpful, I've read some example plans before, > but I couldn't really relate them to my project. Now I have a little clearer > picture of what to write. Thanks for that, hopefully tomorrow I will present > something in that manner. > > > > > > 2011/4/5 Christian Zmasek > > Hi, Michal: > > > > I think your project plan needs to be much more detailed. > > > > It might be best in a format similar to the template/example below: > > > > Prior to coding ("community bonding period"): > > -Familiarize myself with BioRuby code base > > -Learn about graphics within/from Ruby > > -Discuss ... with mentors/BioRuby community > > -... > > -Learn about git, set up my repository > > > > > > > > Week 1: > > Goal: Develop necessary utility classes for ... > > Anticipated problems: None > > > > Weeks 2 and 3: > > Goal: Develop class to visualize intron/exon structures... > > Anticipated problems: Such and such might not ... > > Alternatives: If XYZ turns out not feasible, I plan to ... instead > > > > Week X: > > Goal: Unit tests for ... > > > > > > > > Week Y: > > Documentation ... > > > > Hope this helps, > > > > Christian Zmasek > > > > > > > > > > ----- Original Message ---- > > > From: Micha? Koziarski > > > To: bioruby at lists.open-bio.org > > > Sent: Tue, April 5, 2011 10:24:22 AM > > > Subject: [BioRuby] GSoC - project "Represent bio-objects and related > > >information with images" > > > > > > I've completed my application. Chris Fields suggested that I should > write it > > > up, he hasn't specified what parts exactly though. If you have any > advice > > > about it, please let me know. > > > > > > I use some of my answers to questions asked here in the application, I > hope > > > that's not a problem: I didn't see much point in rewriting it, since > the > > > meaning would be the same. > > > > > > I don't include the first point, about the address, since it's a > public ML > > > and I don't think it's important here. > > > > > > I am basing the application on the OBF's template, which I enclose > too. > > > > > > > > > 1. Why you are interested in the project you are proposing and are > > > well-suited to undertake it. > > > 2. A summary of your programming experience and skills. > > > 3. Programs or projects you have previously authored or contributed > to, > > > in particular those available as open-source, including, if > applicable, > > any > > > past Summer of Code involvement. > > > 4. A project plan for the project you are proposing, even if your > > > proposed project is directly based on one of the proposed project > ideas > > for > > > member projects. > > > 5. Any obligations, vacations, or plans for the summer that may > require > > > scheduling during the GSoC work period. > > > > > > > > > > > > 1. I find the problem of representing computer data in format > > > readable by humans interesting, partially because it's so > significant: we > > > could have the best algorithms, the fastest computers, but the > output > > would > > > be useless if we wouldn't be able to read it. Additionally, I love > the > > idea > > > of writing code for organisation such as OBF: it makes me think > that I do > > > have, even slightest, impact on science. I must also admit that > working > > >with > > > Ruby is very tempting, I really enjoy writing Ruby code. > > > 2. I have fairly strong Ruby knowledge, I have been using it > for > > > about a year and a half. There were no really big projects there > though, > > >the > > > biggest I've got was probably small LAN IM. Nevertheless, I use > Ruby on > > > daily basis and I am familiar with most of its, even complex, > features. > > > Also, from the beginning of this year I work as a RoR > developer. > > > I've worked on a bigger, team project and now I am developing one > solo. > > >I've > > > learned a lot here: working with version control systems, > developing in > > > team, operating on other people's code, testing... not to mention > further > > > developing my Ruby knowledge. > > > Other than that, I know C++ pretty well: it was my first > language > > > and I still use it whenever I see fit. I also have some basic > Python and > > C# > > > knowledge. > > > 3. I can't say much more than what I've written in previous > paragraph. > > > 4. 1. Getting familiarized with BioRuby objects, mainly with the > way they > > > hold data. > > > 2. Deciding with features should be visualized. > > > 3. In case of presence data with different format but same way of > > > visualization, implementing a mechanism converting data to unified > > format. > > > 4. Writing a module responsible for creating graphical > representation of > > > data. > > > 5. Final testing. > > > 6. Writing a documentation. > > > 5. Possibly short vacation (less than one week) around > beginning of > > > July. > > > Also, I am from Poland, which means that my summer vacations > starts > > > from July. Because of that I won't be able to focus only on the > project > > > until than. What I can do, however, is to start coding earlier. I > would > > >like > > > to familiarize myself with documentation before bonding period > starts > > (I've > > > already began to do it), and when it does start coding right away. > Thanks > > >to > > > that I should have just as much time as if I started in May. > > > Other than that I am all about the project. > > > > > > > > > Also, since as I've told I would probably have to start coding a > little > > > earlier, I am trying to slowly browse the documentation. It's a big > project > > > though, and I don't know what's important. Do you have any suggestions > about > > > that? Are there parts that would be especially relevant to the > project? Or > > > maybe even better, are there any easier tasks to complete? I learn > best by > > > exercise, so that would be great. I've looked up at github's issues > page, > > > but haven't found anything like what I am talking about. Maybe I just > didn't > > > know on what I was looking? > > > _______________________________________________ > > > BioRuby Project - http://www.bioruby.org/ > > > BioRuby mailing list > > > BioRuby at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > > > > From cjfields at illinois.edu Wed Apr 6 14:22:25 2011 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 6 Apr 2011 13:22:25 -0500 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <981305.71979.qm@web38404.mail.mud.yahoo.com> Message-ID: <938AF391-AC73-4558-8902-8954ADC2AE90@illinois.edu> On Apr 6, 2011, at 1:14 PM, Micha? Koziarski wrote: > ... > > Chris: could you explain why any coding at community bonding period would be hard? I assumed that a big part of it is getting familiar with documentation, and with that done before I would have some more time to code. Of course, it wouldn't be a full-time coding, but I thought that at this point I would have all the knowledge to start writing, so why not to. Maybe I am missing something, in that case tell me please. > > In general, little coding occurs during community bonding; the time is spent asking questions on the API, working out final priorities, details on the project, etc with the community (mentor in particular). I'm not sure of your level of experience with BioRuby, but from my experience with BioPerl and past GSoC projects the codebase and API (and documentation, or lack thereof) can be daunting for a beginner. So, mentioning that you will use that period to code b/c of time issues during the scheduled period is a bit premature in my opinion w/o more specifics, but that's really for the BioRuby folks to decide. > > I do understand your point. However, I didn't mean to spend less time on getting to know the codebase, I just wanted to start doing it earlier. Anyhow, maybe you have some suggestions about how to solve this time issue? It's a matter of coding for one month for about 30 hours a week. > > I based my proposition on something I read on one of GSoC suggestions page. But yes, you may be right that BioRuby is to big project for such a approach. Actually I raised this issue on the GSoC mentors list, and the general consensus is that it is up to your specific organization (which in this case means that the OBF mentors, who would rely on the good instincts of the BioRuby mentors), as time isn't the only factor involved; experience, attainable project goals, benefits to the project in general, etc are also important. So, if the BioRuby mentors don't have a problem with this, then I fine as well. -c From cmzmasek at yahoo.com Wed Apr 6 14:48:32 2011 From: cmzmasek at yahoo.com (Christian Zmasek) Date: Wed, 6 Apr 2011 11:48:32 -0700 (PDT) Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <981305.71979.qm@web38404.mail.mud.yahoo.com> Message-ID: <313339.26768.qm@web38403.mail.mud.yahoo.com> Hi, Micha?: You timeline is much better now! I put some comments/question into your text (see below). > Week 1: > Goal: choose one representative type of BioRuby object and develop class > that would convert its data to proposed format. That should come along with > unit tests. This is a good idea -- to deliver a proof of concept first! Did you think about how exactly the image(s) will be produced? Which library (if any) do you plan to use? Also do you plan to produce (interactive) graphics on the fly and/or create (static) image files (such as .png) to be viewed with other software? > Week 2: > Goal: develop graphical module that would create image files based on > data in unified format and provide user interface, write unit tests. > > On this point it should be possible to fully visualize chosen BioRuby > object. > > Weeks 3 to 8: > Goal: basing on first weeks work, prepare similar classes for all of the > remaining BioRuby objects. Each class should have unit tests. > > Week 9: > Goal: develop mechanism of browsing images in shell. It should include > simple search and a way of opening images. > > Week 10: > Goal: write integration tests. > > Weeks 11 and 12: > Goal: write documentation. > > I would like to be more specific about what should be done from weeks 3 to > 8, though. It would be nice to plan some time for every object that needs > visualization, but I don't know which that would be exactly. Could you give > me a hand with this? I think Raoul can answer this better. I guess a good candidate would be sequence objects with features, such as intron/exon, mutations, etc. I have doubts about this "develop mechanism of browsing images in shell. It should include simple search and a way of opening images." What about anticipated problems? Can you propose alternatives for things which might not work as planned? Christian From francesco.strozzi at gmail.com Wed Apr 6 15:02:56 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Wed, 6 Apr 2011 21:02:56 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: <313339.26768.qm@web38403.mail.mud.yahoo.com> References: <981305.71979.qm@web38404.mail.mud.yahoo.com> <313339.26768.qm@web38403.mail.mud.yahoo.com> Message-ID: Hi all, 2011/4/6 Christian Zmasek > Hi, Micha?: > > You timeline is much better now! > > I put some comments/question into your text (see below). > > > > > Week 1: > > Goal: choose one representative type of BioRuby object and develop > class > > that would convert its data to proposed format. That should come along > with > > unit tests. > > > This is a good idea -- to deliver a proof of concept first! > > Did you think about how exactly the image(s) will be produced? > > Which library (if any) do you plan to use? > > > Also do you plan to produce (interactive) graphics on the fly and/or create > (static) image files (such as .png) to be viewed with other software? > > If I can suggest a couple of libraries that should be used for this project I will say: - BioGraphics for sequence/genomic features display http://bio-graphics.rubyforge.org/ - Rubyvis for everything else (a great library and fits perfectly well for web visulisation since it's producing SVG images) http://rubyvis.rubyforge.org/ Cheers -- Francesco From michalkoziarski at gmail.com Wed Apr 6 15:25:10 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Wed, 6 Apr 2011 21:25:10 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: <313339.26768.qm@web38403.mail.mud.yahoo.com> References: <981305.71979.qm@web38404.mail.mud.yahoo.com> <313339.26768.qm@web38403.mail.mud.yahoo.com> Message-ID: 2011/4/6 Christian Zmasek > Hi, Micha?: > > You timeline is much better now! > > I put some comments/question into your text (see below). > > > > > Week 1: > > Goal: choose one representative type of BioRuby object and develop > class > > that would convert its data to proposed format. That should come along > with > > unit tests. > > > This is a good idea -- to deliver a proof of concept first! > > Did you think about how exactly the image(s) will be produced? > I thought about using Rubyvis to produce images. > > Which library (if any) do you plan to use? > I've read a little about the Rubyvis and it seems like a fine solution, so I would like to go with that, but I am open for suggestions. > > > Also do you plan to produce (interactive) graphics on the fly and/or create > (static) image files (such as .png) to be viewed with other software? > I think that since one of the purposes of the project is to prepare images for use in web, they should be static from the beginning. It would be great to create an interactive version too, so that you could modify data on the fly and perhaps change data by modifing a graphic, but I don't think that I would make it in time. > > > > > > Week 2: > > Goal: develop graphical module that would create image files based > on > > data in unified format and provide user interface, write unit tests. > > > > On this point it should be possible to fully visualize chosen > BioRuby > > object. > > > > Weeks 3 to 8: > > Goal: basing on first weeks work, prepare similar classes for all of > the > > remaining BioRuby objects. Each class should have unit tests. > > > > Week 9: > > Goal: develop mechanism of browsing images in shell. It should > include > > simple search and a way of opening images. > > > > Week 10: > > Goal: write integration tests. > > > > Weeks 11 and 12: > > Goal: write documentation. > > > > I would like to be more specific about what should be done from weeks 3 > to > > 8, though. It would be nice to plan some time for every object that > needs > > visualization, but I don't know which that would be exactly. Could you > give > > me a hand with this? > > I think Raoul can answer this better. > > > I guess a good candidate would be sequence objects with features, such as > intron/exon, mutations, etc. > > > I have doubts about this "develop mechanism of browsing images in shell. > It > should include simple search and a way of opening images." > Could you explain why? > > What about anticipated problems? Can you propose alternatives for things > which > might not work as planned? > Yes, I am working on that right now, but strangely I can't come up with many problems to anticipate. Perhaps you have some suggestions about this? Anyway, I will most certainly update that. > > Christian > > From michalkoziarski at gmail.com Wed Apr 6 15:34:07 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Wed, 6 Apr 2011 21:34:07 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <981305.71979.qm@web38404.mail.mud.yahoo.com> <313339.26768.qm@web38403.mail.mud.yahoo.com> Message-ID: Hi Francesco, 2011/4/6 Francesco Strozzi > Hi all, > > 2011/4/6 Christian Zmasek > >> Hi, Micha?: >> >> You timeline is much better now! >> >> I put some comments/question into your text (see below). >> >> >> >> > Week 1: >> > Goal: choose one representative type of BioRuby object and develop >> class >> > that would convert its data to proposed format. That should come along >> with >> > unit tests. >> >> >> This is a good idea -- to deliver a proof of concept first! >> >> Did you think about how exactly the image(s) will be produced? >> >> Which library (if any) do you plan to use? >> >> >> Also do you plan to produce (interactive) graphics on the fly and/or >> create >> (static) image files (such as .png) to be viewed with other software? >> >> > If I can suggest a couple of libraries that should be used for this project > I will say: > > - BioGraphics for sequence/genomic features display > http://bio-graphics.rubyforge.org/ > - Rubyvis for everything else (a great library and fits perfectly well for > web visulisation since it's producing SVG images) > http://rubyvis.rubyforge.org/ > I've read about the Rubyvis before, but not about the BioGraphics. Thanks for that, it seems like a great lib. I am just worried that it could force implementing two separate ways of creating graphics, with other style, convention and so on. > > > Cheers > > > -- > > Francesco > > From bonnal at ingm.org Wed Apr 6 16:16:36 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Wed, 06 Apr 2011 22:16:36 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: <313339.26768.qm@web38403.mail.mud.yahoo.com> Message-ID: <20110406201636.3f58bcc0@mail.ingm.it> Hi Michal, the time line is more detailed now. As Francesco suggested and also reported on our page we suggest RubyVis library, Claudio the coder of the binding offers his help and this is a very good news for us. Week 9: what do you mean for browsing images in shell ? I can't grasp the benefit now, but we can discuss. The main problem is how to control the application which displays the image; for web browsers there are techniques but are not so easy. I'm just thinking to an add-on for this week: if we have different types of data that we can display quite easily on the web(done in the previous weeks) , why not spending this time to enrich the images with controls (bars, check boxes, interaction in general). This part requires a skill in javascript. http://vis.stanford.edu/protovis/ex/cartogram-full.html Or another interesting feature would be: adding layers of information to the standard image. Note: perhaps these ideas are a bit complicate for 1 week but it would be interesting to evaluate the feasibility. I forgot to mention, in some case I think that if there are web services which produce images that services could be used. Consider the possibility to display Venn diagrams Google has one service http://code.google.com/intl/it-IT/apis/chart/docs/gallery/venn_charts.html or another one is http://bioinfogp.cnb.csic.es/tools/venny/index.html. Sets are a kind of data type that in my daily work I have to display with a high frequency, specially when the boss needs to make reports :-) So we arrived to the which bioruby objects we want to display. This is a quite complex question because some are there and other are not. This library as been always sequence/feature centric (please correct me if I'm wrong), because we were used to demand to R tasks more statistics. Main areas are * NGS: display create coverage alignemnt for a region with the possible annotation that are accessible from bioruby * Matrix: display heatmaps, scatter plots, bars ( I wrote a very alpha lib for handling real time PCR and gene expression datasets -not images-) * Sets: a seq could be generated from any kind of analysis, enrichment, annotation, reports ** reports could be meta-objects for instance the results of an allignment or mapping or gene quantification when you need to compare multiple populations or technical replicates * Phylo (i'm not an expert) with the idea to produce high quality images ready to be published. These are a bunch of ideas and words. About tomorrow IRC meeting, @work they scheduled a meeting for (my) afternoon, I'll do my best to be on IRC. Feel free to contact who is around. Regards. _____ From: Christian Zmasek [mailto:cmzmasek at yahoo.com] To: Micha? Koziarski [mailto:michalkoziarski at gmail.com], Chris Fields [mailto:cjfields at illinois.edu], bioruby at lists.open-bio.org Cc: Raoul Bonnal [mailto:bonnalraoul at ingm.it] Sent: Wed, 06 Apr 2011 20:48:32 +0200 Subject: Re: [BioRuby] GSoC - project "Represent bio-objects and related information with images" Hi, Micha?: You timeline is much better now! I put some comments/question into your text (see below). > Week 1: > Goal: choose one representative type of BioRuby object and develop class > that would convert its data to proposed format. That should come along with > unit tests. This is a good idea -- to deliver a proof of concept first! Did you think about how exactly the image(s) will be produced? Which library (if any) do you plan to use? Also do you plan to produce (interactive) graphics on the fly and/or create (static) image files (such as .png) to be viewed with other software? > Week 2: > Goal: develop graphical module that would create image files based on > data in unified format and provide user interface, write unit tests. > > On this point it should be possible to fully visualize chosen BioRuby > object. > > Weeks 3 to 8: > Goal: basing on first weeks work, prepare similar classes for all of the > remaining BioRuby objects. Each class should have unit tests. > > Week 9: > Goal: develop mechanism of browsing images in shell. It should include > simple search and a way of opening images. > > Week 10: > Goal: write integration tests. > > Weeks 11 and 12: > Goal: write documentation. > > I would like to be more specific about what should be done from weeks 3 to > 8, though. It would be nice to plan some time for every object that needs > visualization, but I don't know which that would be exactly. Could you give > me a hand with this? I think Raoul can answer this better. I guess a good candidate would be sequence objects with features, such as intron/exon, mutations, etc. What about anticipated problems? Can you propose alternatives for things which might not work as planned? Christian From michalkoziarski at gmail.com Wed Apr 6 17:06:12 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Wed, 6 Apr 2011 23:06:12 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: <20110406201636.3f58bcc0@mail.ingm.it> References: <313339.26768.qm@web38403.mail.mud.yahoo.com> <20110406201636.3f58bcc0@mail.ingm.it> Message-ID: 2011/4/6 Raoul Bonnal > Hi Michal, > the time line is more detailed now. > As Francesco suggested and also reported on our page we suggest RubyVis > library, Claudio the coder of the binding offers his help and this is a very > good news for us. > > Week 9: what do you mean for browsing images in shell ? I can't grasp the > benefit now, but we can discuss. The main problem is how to control the > application which displays the image; for web browsers there are techniques > but are not so easy. > The idea was to be able to view image right after it's created, not having to juggle with opened folders, terminals or whatever else someone could use for that. I thought that it would be useful and in some cases could save us some mechanic job, but that's not an essential thing for sure. > I'm just thinking to an add-on for this week: if we have different types of > data that we can display quite easily on the web(done in the previous weeks) > , why not spending this time to enrich the images with controls (bars, check > boxes, interaction in general). This part requires a skill in javascript. > http://vis.stanford.edu/protovis/ex/cartogram-full.html > Or another interesting feature would be: adding layers of information to > the standard image. > Note: perhaps these ideas are a bit complicate for 1 week but it would be > interesting to evaluate the feasibility. > I really like the enrichment idea, it's both useful and great looking :) The question is: how exactly should we enrich those images? I think that depending on what exactly we would like to achieve one week could be enough. For example some on-demand displaying (from the set of images only those which we check are currently visible) is not hard to do and quite useful. > > I forgot to mention, in some case I think that if there are web services > which produce images that services could be used. Consider the possibility > to display Venn diagrams Google has one service > http://code.google.com/intl/it-IT/apis/chart/docs/gallery/venn_charts.htmlor another one is > http://bioinfogp.cnb.csic.es/tools/venny/index.html. > Sets are a kind of data type that in my daily work I have to display with a > high frequency, specially when the boss needs to make reports :-) > Again, I am a little worried about the integrity. I mean, of course, if implementing any of those would have to take a significant amount of time than it's probably better not to carry about it so much and spend time developing a new feature, but otherwise it's just unnecessary complicating the code. At least that's my opinion. > > So we arrived to the which bioruby objects we want to display. This is a > quite complex question because some are there and other are not. > This library as been always sequence/feature centric (please correct me if > I'm wrong), because we were used to demand to R tasks more statistics. > Main areas are > * NGS: display create coverage alignemnt for a region with the possible > annotation that are accessible from bioruby > * Matrix: display heatmaps, scatter plots, bars ( I wrote a very alpha lib > for handling real time PCR and gene expression datasets -not images-) > * Sets: a seq could be generated from any kind of analysis, enrichment, > annotation, reports > ** reports could be meta-objects for instance the results of an allignment > or mapping or gene quantification when you need to compare multiple > populations or technical replicates > * Phylo (i'm not an expert) > I will have some additional questions about that tomorrow, right now my brain refuses to work properly. > > with the idea to produce high quality images ready to be published. > > These are a bunch of ideas and words. > About tomorrow IRC meeting, @work they scheduled a meeting for (my) > afternoon, I'll do my best to be on IRC. Feel free to contact who is around. > I've tried that today, no one from BioRuby was around though. I guess that's because I am dropping by too late. > > Regards. > > ------------------------------ > *From:* Christian Zmasek [mailto:cmzmasek at yahoo.com] > *To:* Micha? Koziarski [mailto:michalkoziarski at gmail.com], Chris Fields > [mailto:cjfields at illinois.edu], bioruby at lists.open-bio.org > *Cc:* Raoul Bonnal [mailto:bonnalraoul at ingm.it] > *Sent:* Wed, 06 Apr 2011 20:48:32 +0200 > *Subject:* Re: [BioRuby] GSoC - project "Represent bio-objects and related > information with images" > > > Hi, Micha?: > > You timeline is much better now! > > I put some comments/question into your text (see below). > > > > > Week 1: > > Goal: choose one representative type of BioRuby object and develop class > > that would convert its data to proposed format. That should come along > with > > unit tests. > > > This is a good idea -- to deliver a proof of concept first! > > Did you think about how exactly the image(s) will be produced? > > Which library (if any) do you plan to use? > > > Also do you plan to produce (interactive) graphics on the fly and/or create > > (static) image files (such as .png) to be viewed with other software? > > > > > > Week 2: > > Goal: develop graphical module that would create image files based on > > data in unified format and provide user interface, write unit tests. > > > > On this point it should be possible to fully visualize chosen BioRuby > > object. > > > > Weeks 3 to 8: > > Goal: basing on first weeks work, prepare similar classes for all of the > > remaining BioRuby objects. Each class should have unit tests. > > > > Week 9: > > Goal: develop mechanism of browsing images in shell. It should include > > simple search and a way of opening images. > > > > Week 10: > > Goal: write integration tests. > > > > Weeks 11 and 12: > > Goal: write documentation. > > > > I would like to be more specific about what should be done from weeks 3 > to > > 8, though. It would be nice to plan some time for every object that needs > > visualization, but I don't know which that would be exactly. Could you > give > > me a hand with this? > > I think Raoul can answer this better. > > > I guess a good candidate would be sequence objects with features, such as > intron/exon, mutations, etc. > > > > > What about anticipated problems? Can you propose alternatives for things > which > might not work as planned? > > Christian > > From missy at be.to Thu Apr 7 01:03:30 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Thu, 07 Apr 2011 14:03:30 +0900 Subject: [BioRuby] A new plugin: bio-genomic-interval Message-ID: <4D9D45A2.9070608@be.to> Hi all, I have uploaded a new Bioruby plugin 'bio-genomic-interval'. The Bio::GenomicInterval class is designed to handle genomic intervals such as "chr1:123-456". The class has methods to detect the overlapping status between two intervals. It may help to avoid messy case branching and improve readability of codes. Developmental tools for BioRuby plugin and documents in the BioRuby wiki were very helpful. Thank you all the authors. Please see also the followings: GitHub - https://github.com/misshie/bioruby-genomic-interval RubyGems.org - https://rubygems.org/gems/bio-genomic-interval Sincerely yours, Hiro. -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From francesco.strozzi at gmail.com Thu Apr 7 10:33:10 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Thu, 7 Apr 2011 16:33:10 +0200 Subject: [BioRuby] BioRuby Wrapper for Command line application (GSOC 2011) In-Reply-To: <4B02CC0A-20DE-4A60-93C3-E7EDACC9BA64@ingm.org> References: <4B02CC0A-20DE-4A60-93C3-E7EDACC9BA64@ingm.org> Message-ID: Hi Ales, did you had the chance to update your proposal on BioRuby Wrapper for the GSoC ? Deadline is tomorrow for student application and we think with this proposal we could be able to get some interesting results. But for your application to have a better chance to be considered and evaluated you should provide an updated timeline (even a draft but a bit more detailed) with the activities and tasks broken down into weeks. If you need some help or advise please write here on the Maling List and we will provide our contributions. Cheers Francesco On Wed, Apr 6, 2011 at 11:48, Raoul Bonnal wrote: > Hello Ales, > thank you for submitting your proposal, > like Michal: > I quote here the discussion with Chris and Christian, if you could write a > better time line in form of days/weeks with tasks/objectives I think it > would be better: > > this is the quote from Christian and Chris > > Hi, Michal: > > I think your project plan needs to be much more detailed. > > It might be best in a format similar to the template/example below: > > Prior to coding ("community bonding period"): > -Familiarize myself with BioRuby code base > -Learn about graphics within/from Ruby > -Discuss ... with mentors/BioRuby community > -... > -Learn about git, set up my repository > > > > Week 1: > Goal: Develop necessary utility classes for ... > Anticipated problems: None > > Weeks 2 and 3: > Goal: Develop class to visualize intron/exon structures... > Anticipated problems: Such and such might not ... > Alternatives: If XYZ turns out not feasible, I plan to ... instead > > Week X: > Goal: Unit tests for ... > > > > Week Y: > Documentation ... > > Hope this helps, > > Christian Zmasek > ---- > Micha?, > > In general, the proposal should answer the questions below, but should also > have a rough timeline on how you would go about coding the project, creating > deliverables for the community for testing, etc. This should come with the > input of your possible mentor for the project or from others in the bioruby > community. > > The timeline is a little problematic, but the OBF mentors can further > discuss that. One thing that will cause a problem is that there is a > significant amount of time (about one month) for community bonding, so any > coding on a significant project in that period will be tricky. > > chris > > > > ----- Original Message ---- > > From: Micha? Koziarski > > To: bioruby at lists.open-bio.org > > Sent: Tue, April 5, 2011 10:24:22 AM > > Subject: [BioRuby] GSoC - project "Represent bio-objects and related > > information with images" > > > > I've completed my application. Chris Fields suggested that I should write > it > > up, he hasn't specified what parts exactly though. If you have any > advice > > about it, please let me know. > > > > I use some of my answers to questions asked here in the application, I > hope > > that's not a problem: I didn't see much point in rewriting it, since the > > meaning would be the same. > > > > I don't include the first point, about the address, since it's a public > ML > > and I don't think it's important here. > > > > I am basing the application on the OBF's template, which I enclose too. > > > > > > 1. Why you are interested in the project you are proposing and are > > well-suited to undertake it. > > 2. A summary of your programming experience and skills. > > 3. Programs or projects you have previously authored or contributed > to, > > in particular those available as open-source, including, if > applicable, > any > > past Summer of Code involvement. > > 4. A project plan for the project you are proposing, even if your > > proposed project is directly based on one of the proposed project > ideas > for > > member projects. > > 5. Any obligations, vacations, or plans for the summer that may > require > > scheduling during the GSoC work period. > > > > > > > > 1. I find the problem of representing computer data in format > > readable by humans interesting, partially because it's so significant: > we > > could have the best algorithms, the fastest computers, but the output > would > > be useless if we wouldn't be able to read it. Additionally, I love the > idea > > of writing code for organisation such as OBF: it makes me think that I > do > > have, even slightest, impact on science. I must also admit that > working > > with > > Ruby is very tempting, I really enjoy writing Ruby code. > > 2. I have fairly strong Ruby knowledge, I have been using it for > > about a year and a half. There were no really big projects there > though, > > the > > biggest I've got was probably small LAN IM. Nevertheless, I use Ruby > on > > daily basis and I am familiar with most of its, even complex, > features. > > Also, from the beginning of this year I work as a RoR developer. > > I've worked on a bigger, team project and now I am developing one > solo. > > I've > > learned a lot here: working with version control systems, developing > in > > team, operating on other people's code, testing... not to mention > further > > developing my Ruby knowledge. > > Other than that, I know C++ pretty well: it was my first language > > and I still use it whenever I see fit. I also have some basic Python > and > C# > > knowledge. > > 3. I can't say much more than what I've written in previous paragraph. > > 4. 1. Getting familiarized with BioRuby objects, mainly with the way > they > > hold data. > > 2. Deciding with features should be visualized. > > 3. In case of presence data with different format but same way of > > visualization, implementing a mechanism converting data to unified > format. > > 4. Writing a module responsible for creating graphical representation > of > > data. > > 5. Final testing. > > 6. Writing a documentation. > > 5. Possibly short vacation (less than one week) around beginning > of > > July. > > Also, I am from Poland, which means that my summer vacations > starts > > from July. Because of that I won't be able to focus only on the > project > > until than. What I can do, however, is to start coding earlier. I > would > > like > > to familiarize myself with documentation before bonding period starts > (I've > > already began to do it), and when it does start coding right away. > Thanks > > to > > that I should have just as much time as if I started in May. > > Other than that I am all about the project. > > > > > > Also, since as I've told I would probably have to start coding a little > > earlier, I am trying to slowly browse the documentation. It's a big > project > > though, and I don't know what's important. Do you have any suggestions > about > > that? Are there parts that would be especially relevant to the project? > Or > > maybe even better, are there any easier tasks to complete? I learn best > by > > exercise, so that would be great. I've looked up at github's issues > page, > > but haven't found anything like what I am talking about. Maybe I just > didn't > > know on what I was looking? > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > > On 06/apr/2011, at 11.27, ????? wrote: > > > Hello. My name is Ales and I'd like to implement BioRuby wrapper for > > command line applications as my Google Summer of Code 2011 project. > > > > > > 1. Your complete contact information, including full name, physical > > address, preferred email address, and telephone number, plus other > > pertinent contact information such as IRC handles, etc. > > > > Ales Guzik > > 4th year student at Belarusian State University of Informatics and > > Radioelectronics. > > Belarus, Minsk, P.Brovki st. 3-1 46 > > ales.guzik at gmail.com > > +375 25 902 8190 (Belarus) > > +1 650 336 5853 (Google Voice) > > skype: ales-guzik > > IRC, twitter, facebook, github etc.: nekotwi > > > > 2. Why you are interested in the project you are proposing and are > > well-suited to undertake it. > > > > This project is interesting for me because it requires metaprogramming > > - thing I most like in ruby and > > because it's BioRuby - project I wanted to get familiar with long time > ago. > > I use Ruby more than 2 years for most of my university tasks and daily > > linux scripting. 2 month ago I > > started working as Ruby on Rails developer. I have pretty good > > experience in ruby metaprogramming which > > is needed for this project. > > > > 3. A summary of your programming experience and skills. > > > > I have well experience in C, know but not heavily used C++ and Qt, > > long time ago learned some Erlang, > > have coded some C# at university but dislike it, played a bit with > > Android/Java programming. > > Know and sometimes use Scheme(Racket), now learning some Perl 5. > > Started learning Ruby somewhere in the beginning of 2nd university > > year and liked it very much. > > > > 4. Programs or projects you have previously authored or contributed > > to, in particular those available as open-source, including, if > > applicable, any past Summer of Code involvement. > > > > I haven't yet contributed to opensource projects (except for some tiny > > projects by myself) but really want to. > > > > 5. A project plan for the project you are proposing, even if your > > proposed project is directly based on one of the proposed project > > ideas for member projects. > > > > 1) Get familiar with source code, use cases and documentation of > > BioRuby and BioRuby-ngs > > 2) Define specs and write rspec tests for this CLI application wrapper > > 3) Code to make all tests pass > > 4) Optimize code for processing BIG ammounts of information > > 5) Refactor > > 6) Document undocumented parts > > > > 6. Any obligations, vacations, or plans for the summer that may > > require scheduling during the GSoC work period. > > > > I work as rails programmer 30 hours a week. It's like 8:00 - 14:00 > > GMT+2 DST monday - friday, so I can code for > > my project 14:30 - 22:00 or even more. It will be like this in june and > august. > > In july I'll be at military training. I'll have time and internet > > access but can't tell my schedule for now. > > > > -- > > Regards, > > Ales Guzik > > ------------------------------------------------------------ > > e-mail: ales.guzik at gmail.com > > skype: ales-guzik > > tel: +375 25 9028190 > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > -- > Ra > > linkedin: http://it.linkedin.com/in/raoulbonnal > twitter: http://twitter.com/ilpuccio > skype: ilpuccio > irc.freenode.net: Helius > github: https://github.com/helios > > > > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Francesco From ales.guzik at gmail.com Thu Apr 7 12:24:45 2011 From: ales.guzik at gmail.com (=?UTF-8?B?0JDQu9C10YHRjA==?=) Date: Thu, 7 Apr 2011 19:24:45 +0300 Subject: [BioRuby] BioRuby Wrapper for Command line application (GSOC 2011) In-Reply-To: References: <4B02CC0A-20DE-4A60-93C3-E7EDACC9BA64@ingm.org> Message-ID: Sorry for this dellay. I just wanted to polish timeline and better understand for myself how will I undertake this project. ** Timeline * getting in (4 weeks) 27 apr - 24 may - getting familiar with BioRuby project (2-3 weeks) - getting into bioinformatics basics (at least 1 week) - getting into project goals and project usage (1 week) - reading articles about BioRuby - reading usage documentation - checking out usage examples - getting into source codebase (1 week) - reading source code documentation (4 days) - looking through source code (2 days) - defining coding guidelines (1 evening) - getting into comunity (in parallel with above) - reading mailing list archive (2-3 days) - hanging up on IRC (all the time) - getting familiar with problem (1-2 weeks) - finding examples of applications that will be used with this wrapper - getting familiar with EMBOSS and ACD configuration files - exploring ways to define wrapper configuration * coding-1 (7 weeks) 25 may - 11 july - writing specs (4 weeks) - defining complete API/DSL for end-users (1 week) - defining interface for adding new CLI tools and EMBOSS suites. (1 week) - defining additional specs (1 week) - writing code (3 weeks) - writing code for API generation (1 week) - writing code for interprocess communication and data passing (1-2 week) 0-1 additional week to have for finishing all this stuff. * mid-term evaluation (5 days) 11 july - 15 july At this moment we have complete API/DSL specs and code wich allows us wrapping CLI applications. * coding 2 (4 weeks) 17 july - 16 aug - writing ACD file parser (1-2 weeks) - writing automatic wrapper generation based on ACD files (2-3 weeks) * documentation and refactoring (1 week) 16 aug - 21 aug * final evaluation On Thu, Apr 7, 2011 at 5:33 PM, Francesco Strozzi wrote: > Hi Ales, > did you had the chance to update your proposal on BioRuby Wrapper for the > GSoC ? Deadline is tomorrow for student application and we think with this > proposal we could be able to get some interesting results. But for your > application to have a better chance to be considered and evaluated you > should provide an updated timeline (even a draft but a bit more detailed) > with the activities and tasks broken down into weeks. > If you need some help or advise please write here on the Maling List and we > will provide our contributions. > Cheers > Francesco > > On Wed, Apr 6, 2011 at 11:48, Raoul Bonnal wrote: >> >> Hello Ales, >> ?thank you for submitting your proposal, >> like Michal: >> I quote here the discussion with Chris and Christian, if you could write a >> better time line in form of days/weeks with tasks/objectives I think it >> would be better: >> >> this is the quote from Christian and Chris >> >> Hi, Michal: >> >> I think your project plan needs to be much more detailed. >> >> It might be best in a format similar to the template/example below: >> >> Prior to coding ("community bonding period"): >> -Familiarize myself with BioRuby code base >> -Learn about graphics within/from Ruby >> -Discuss ... with mentors/BioRuby community >> -... >> -Learn about git, set up my repository >> >> >> >> Week 1: >> Goal: Develop necessary utility classes for ... >> Anticipated problems: None >> >> Weeks 2 and 3: >> Goal: Develop class to visualize intron/exon structures... >> Anticipated problems: Such and such might not ... >> Alternatives: If XYZ turns out not feasible, I plan to ... instead >> >> Week X: >> Goal: Unit tests for ... >> >> >> >> Week Y: >> Documentation ... >> >> Hope this helps, >> >> Christian Zmasek >> ---- >> Micha?, >> >> In general, the proposal should answer the questions below, but should >> also have a rough timeline on how you would go about coding the project, >> creating deliverables for the community for testing, etc. This should come >> with the input of your possible mentor for the project or from others in the >> bioruby community. >> >> The timeline is a little problematic, but the OBF mentors can further >> discuss that. ?One thing that will cause a problem is that there is a >> significant amount of time (about one month) for community bonding, so any >> coding on a significant project in that period will be tricky. >> >> chris >> >> >> >> ----- Original Message ---- >> > From: Micha? Koziarski >> > To: bioruby at lists.open-bio.org >> > Sent: Tue, April 5, 2011 10:24:22 AM >> > Subject: [BioRuby] GSoC - project "Represent bio-objects and related >> > information with images" >> > >> > I've completed my application. Chris Fields suggested that I should >> > write ?it >> > up, he hasn't specified what parts exactly though. If you have any >> > ?advice >> > about it, please let me know. >> > >> > I use some of my answers to ?questions asked here in the application, I >> > hope >> > that's not a problem: I ?didn't see much point in rewriting it, since >> > the >> > meaning would be the ?same. >> > >> > I don't include the first point, about the address, since it's a ?public >> > ML >> > and I don't think it's important here. >> > >> > I am basing the ?application on the OBF's template, which I enclose too. >> > >> > >> > ? 1. ?Why you are interested in the project you are proposing and are >> > ? ?well-suited to undertake it. >> > ? 2. A summary of your programming ?experience and skills. >> > ? 3. Programs or projects you have previously ?authored or contributed >> > to, >> > ? in particular those available as ?open-source, including, if >> > applicable, >> any >> > ? past Summer of Code ?involvement. >> > ? 4. A project plan for the project you are proposing, ?even if your >> > ? proposed project is directly based on one of the ?proposed project >> > ideas >> for >> > ? member projects. >> > ? 5. Any ?obligations, vacations, or plans for the summer that may >> > require >> > ? ?scheduling during the GSoC work period. >> > >> > >> > >> > ? 1. ? ? ? I find the problem of representing computer data in format >> > ? ?readable by humans interesting, partially because it's so >> > significant: ?we >> > ? could have the best algorithms, the fastest computers, but the ?output >> would >> > ? be useless if we wouldn't be able to read it. ?Additionally, I love >> > the >> idea >> > ? of writing code for organisation such ?as OBF: it makes me think that >> > I do >> > ? have, even slightest, impact on ?science. I must also admit that >> > working >> > with >> > ? Ruby is very tempting, I ?really enjoy writing Ruby code. >> > ? 2. ? ? ?I have fairly ?strong Ruby knowledge, I have been using it for >> > ? about a year and a ?half. There were no really big projects there >> > though, >> > the >> > ? biggest ?I've got was probably small LAN IM. Nevertheless, I use Ruby >> > on >> > ? daily ?basis and I am familiar with most of its, even complex, >> > features. >> > ? ? ? ? Also, from the beginning of this year I work as a RoR >> > ?developer. >> > ? I've worked on a bigger, team project and now I am ?developing one >> > solo. >> > I've >> > ? learned a lot here: working with version ?control systems, developing >> > in >> > ? team, operating on other people's ?code, testing... not to mention >> > further >> > ? developing my Ruby ?knowledge. >> > ? ? ? ?Other than that, I know C++ pretty ?well: it was my first >> > language >> > ? and I still use it whenever I see fit. ?I also have some basic Python >> > and >> C# >> > ? knowledge. >> > ? 3. I can't ?say much more than what I've written in previous >> > paragraph. >> > ? 4. 1. ?Getting familiarized with BioRuby objects, mainly with the way >> > they >> > ? ?hold data. >> > ? 2. Deciding with features should be visualized. >> > ? ?3. In case of presence data with different format but same way of >> > ? ?visualization, implementing a mechanism converting data to unified >> format. >> > ? 4. Writing a module responsible for creating graphical ?representation >> > of >> > ? data. >> > ? 5. Final testing. >> > ? 6. ?Writing a documentation. >> > ? 5. ? ? ?Possibly short ?vacation (less than one week) around beginning >> > of >> > ? July. >> > ? ? ? ? Also, I am from Poland, which means that my summer ?vacations >> > starts >> > ? from July. Because of that I won't be able to focus ?only on the >> > project >> > ? until than. What I can do, however, is to start ?coding earlier. I >> > would >> > like >> > ? to familiarize myself with documentation ?before bonding period starts >> (I've >> > ? already began to do it), and when ?it does start coding right away. >> > Thanks >> > to >> > ? that I should have just as ?much time as if I started in May. >> > ? ? ? ?Other than that ?I am all about the project. >> > >> > >> > Also, since as I've told I would probably ?have to start coding a little >> > earlier, I am trying to slowly browse the ?documentation. It's a big >> > project >> > though, and I don't know what's important. ?Do you have any suggestions >> > about >> > that? Are there parts that would be ?especially relevant to the project? >> > Or >> > maybe even better, are there any ?easier tasks to complete? I learn best >> > by >> > exercise, so that would be great. ?I've looked up at github's issues >> > page, >> > but haven't found anything like what ?I am talking about. Maybe I just >> > didn't >> > know on what I was ?looking? >> > _______________________________________________ >> > BioRuby Project - ?http://www.bioruby.org/ >> > BioRuby mailing list >> > BioRuby at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/bioruby >> > >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> On 06/apr/2011, at 11.27, ????? wrote: >> >> > Hello. My name is Ales and I'd like to implement BioRuby wrapper for >> > command line applications as my Google Summer of Code 2011 project. >> > >> > >> > 1. Your complete contact information, including full name, physical >> > address, preferred email address, and telephone number, plus other >> > pertinent contact information such as IRC handles, etc. >> > >> > Ales Guzik >> > 4th year student at Belarusian State University of Informatics and >> > Radioelectronics. >> > Belarus, Minsk, P.Brovki st. 3-1 46 >> > ales.guzik at gmail.com >> > +375 25 902 8190 (Belarus) >> > +1 650 336 5853 (Google Voice) >> > skype: ales-guzik >> > IRC, twitter, facebook, github etc.: nekotwi >> > >> > 2. Why you are interested in the project you are proposing and are >> > well-suited to undertake it. >> > >> > This project is interesting for me because it requires metaprogramming >> > - thing I most like in ruby and >> > because it's BioRuby - project I wanted to get familiar with long time >> > ago. >> > I use Ruby more than 2 years for most of my university tasks and daily >> > linux scripting. 2 month ago I >> > started working as Ruby on Rails developer. I have pretty good >> > experience in ruby metaprogramming which >> > is needed for this project. >> > >> > 3. A summary of your programming experience and skills. >> > >> > I have well experience in C, know but not heavily used C++ and Qt, >> > long time ago learned some Erlang, >> > have coded some C# at university but dislike it, played a bit with >> > Android/Java programming. >> > Know and sometimes use Scheme(Racket), now learning some Perl 5. >> > Started learning Ruby somewhere in the beginning of 2nd university >> > year and liked it very much. >> > >> > 4. Programs or projects you have previously authored or contributed >> > to, in particular those available as open-source, including, if >> > applicable, any past Summer of Code involvement. >> > >> > I haven't yet contributed to opensource projects (except for some tiny >> > projects by myself) but really want to. >> > >> > 5. A project plan for the project you are proposing, even if your >> > proposed project is directly based on one of the proposed project >> > ideas for member projects. >> > >> > ?1) Get familiar with source code, use cases and documentation of >> > BioRuby and BioRuby-ngs >> > ?2) Define specs and write rspec tests for this CLI application wrapper >> > ?3) Code to make all tests pass >> > ?4) Optimize code for processing BIG ammounts of information >> > ?5) Refactor >> > ?6) Document undocumented parts >> > >> > 6. Any obligations, vacations, or plans for the summer that may >> > require scheduling during the GSoC work period. >> > >> > I work as rails programmer 30 hours a week. It's like 8:00 - 14:00 >> > GMT+2 DST monday - friday, so I can code for >> > my project 14:30 - 22:00 or even more. It will be like this in june and >> > august. >> > In july I'll be at military training. I'll have time and internet >> > access but can't tell my schedule for now. >> > >> > -- >> > Regards, >> > Ales Guzik >> > ------------------------------------------------------------ >> > e-mail: ales.guzik at gmail.com >> > skype: ales-guzik >> > tel: +375 25 9028190 >> > _______________________________________________ >> > BioRuby Project - http://www.bioruby.org/ >> > BioRuby mailing list >> > BioRuby at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/bioruby >> >> -- >> Ra >> >> linkedin: http://it.linkedin.com/in/raoulbonnal >> twitter: http://twitter.com/ilpuccio >> skype: ilpuccio >> irc.freenode.net: Helius >> github: https://github.com/helios >> >> >> >> >> >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > > > > -- > > Francesco > > -- Regards, Ales Guzik ------------------------------------------------------------ e-mail: ales.guzik at gmail.com skype: ales-guzik tel: +375 25 9028190 From michalkoziarski at gmail.com Thu Apr 7 13:39:25 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Thu, 7 Apr 2011 19:39:25 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: <20110406201636.3f58bcc0@mail.ingm.it> References: <313339.26768.qm@web38403.mail.mud.yahoo.com> <20110406201636.3f58bcc0@mail.ingm.it> Message-ID: 2011/4/6 Raoul Bonnal > Hi Michal, > the time line is more detailed now. > As Francesco suggested and also reported on our page we suggest RubyVis > library, Claudio the coder of the binding offers his help and this is a very > good news for us. > > Week 9: what do you mean for browsing images in shell ? I can't grasp the > benefit now, but we can discuss. The main problem is how to control the > application which displays the image; for web browsers there are techniques > but are not so easy. > I'm just thinking to an add-on for this week: if we have different types of > data that we can display quite easily on the web(done in the previous weeks) > , why not spending this time to enrich the images with controls (bars, check > boxes, interaction in general). This part requires a skill in javascript. > http://vis.stanford.edu/protovis/ex/cartogram-full.html > Or another interesting feature would be: adding layers of information to > the standard image. > Note: perhaps these ideas are a bit complicate for 1 week but it would be > interesting to evaluate the feasibility. > I thought about whether to implement that shell browser or work on images enrichment, and I am quite confused. Generally, I would agree that your idea seems to be better, but right now I can't come up with specific ways of enriching them. I guess it should be more obvious once images itself are created, but then there may be not enough time to implement everything. > > I forgot to mention, in some case I think that if there are web services > which produce images that services could be used. Consider the possibility > to display Venn diagrams Google has one service > http://code.google.com/intl/it-IT/apis/chart/docs/gallery/venn_charts.htmlor another one is > http://bioinfogp.cnb.csic.es/tools/venny/index.html. > Sets are a kind of data type that in my daily work I have to display with a > high frequency, specially when the boss needs to make reports :-) > > So we arrived to the which bioruby objects we want to display. This is a > quite complex question because some are there and other are not. > This library as been always sequence/feature centric (please correct me if > I'm wrong), because we were used to demand to R tasks more statistics. > Main areas are > * NGS: display create coverage alignemnt for a region with the possible > annotation that are accessible from bioruby > * Matrix: display heatmaps, scatter plots, bars ( I wrote a very alpha lib > for handling real time PCR and gene expression datasets -not images-) > Is that lib public now? And if so, could you provide me with repo url? > * Sets: a seq could be generated from any kind of analysis, enrichment, > annotation, reports > ** reports could be meta-objects for instance the results of an allignment > or mapping or gene quantification when you need to compare multiple > populations or technical replicates > * Phylo (i'm not an expert) > That seems to be the most complicated one of those to visualize (or am I wrong?), it would be great to hear some specifics. Out of those, I think that Matrix would be a good place to start. They could be generated only with Rubyvis, and as I believe are used quite often. Would you agree? > with the idea to produce high quality images ready to be published. > > > These are a bunch of ideas and words. > About tomorrow IRC meeting, @work they scheduled a meeting for (my) > afternoon, I'll do my best to be on IRC. Feel free to contact who is around. > > Regards. > > ------------------------------ > *From:* Christian Zmasek [mailto:cmzmasek at yahoo.com] > *To:* Micha? Koziarski [mailto:michalkoziarski at gmail.com], Chris Fields > [mailto:cjfields at illinois.edu], bioruby at lists.open-bio.org > *Cc:* Raoul Bonnal [mailto:bonnalraoul at ingm.it] > *Sent:* Wed, 06 Apr 2011 20:48:32 +0200 > *Subject:* Re: [BioRuby] GSoC - project "Represent bio-objects and related > information with images" > > > Hi, Micha?: > > You timeline is much better now! > > I put some comments/question into your text (see below). > > > > > Week 1: > > Goal: choose one representative type of BioRuby object and develop class > > that would convert its data to proposed format. That should come along > with > > unit tests. > > > This is a good idea -- to deliver a proof of concept first! > > Did you think about how exactly the image(s) will be produced? > > Which library (if any) do you plan to use? > > > Also do you plan to produce (interactive) graphics on the fly and/or create > > (static) image files (such as .png) to be viewed with other software? > > > > > > Week 2: > > Goal: develop graphical module that would create image files based on > > data in unified format and provide user interface, write unit tests. > > > > On this point it should be possible to fully visualize chosen BioRuby > > object. > > > > Weeks 3 to 8: > > Goal: basing on first weeks work, prepare similar classes for all of the > > remaining BioRuby objects. Each class should have unit tests. > > > > Week 9: > > Goal: develop mechanism of browsing images in shell. It should include > > simple search and a way of opening images. > > > > Week 10: > > Goal: write integration tests. > > > > Weeks 11 and 12: > > Goal: write documentation. > > > > I would like to be more specific about what should be done from weeks 3 > to > > 8, though. It would be nice to plan some time for every object that needs > > visualization, but I don't know which that would be exactly. Could you > give > > me a hand with this? > > I think Raoul can answer this better. > > > I guess a good candidate would be sequence objects with features, such as > intron/exon, mutations, etc. > > > > > What about anticipated problems? Can you propose alternatives for things > which > might not work as planned? > > Christian > > From francesco.strozzi at gmail.com Thu Apr 7 14:07:30 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Thu, 7 Apr 2011 20:07:30 +0200 Subject: [BioRuby] BioRuby Wrapper for Command line application (GSOC 2011) In-Reply-To: References: <4B02CC0A-20DE-4A60-93C3-E7EDACC9BA64@ingm.org> Message-ID: Excellent! To me the timeline looks good and the working plan is fine. Anyone else have some comment on this? Cheers Francesco On Thu, Apr 7, 2011 at 18:24, ????? wrote: > Sorry for this dellay. I just wanted to polish timeline and better > understand for myself how will I undertake this project. > > ** Timeline > > * getting in (4 weeks) 27 apr - 24 may > > - getting familiar with BioRuby project (2-3 weeks) > - getting into bioinformatics basics (at least 1 week) > - getting into project goals and project usage (1 week) > - reading articles about BioRuby > - reading usage documentation > - checking out usage examples > - getting into source codebase (1 week) > - reading source code documentation (4 days) > - looking through source code (2 days) > - defining coding guidelines (1 evening) > - getting into comunity (in parallel with above) > - reading mailing list archive (2-3 days) > - hanging up on IRC (all the time) > > - getting familiar with problem (1-2 weeks) > - finding examples of applications that will be used with this wrapper > - getting familiar with EMBOSS and ACD configuration files > - exploring ways to define wrapper configuration > > * coding-1 (7 weeks) 25 may - 11 july > - writing specs (4 weeks) > - defining complete API/DSL for end-users (1 week) > - defining interface for adding new CLI tools and EMBOSS suites. (1 > week) > - defining additional specs (1 week) > - writing code (3 weeks) > - writing code for API generation (1 week) > - writing code for interprocess communication and data passing (1-2 > week) > 0-1 additional week to have for finishing all this stuff. > > * mid-term evaluation (5 days) 11 july - 15 july > At this moment we have complete API/DSL specs and code wich allows > us wrapping CLI applications. > > * coding 2 (4 weeks) 17 july - 16 aug > - writing ACD file parser (1-2 weeks) > - writing automatic wrapper generation based on ACD files (2-3 weeks) > > * documentation and refactoring (1 week) 16 aug - 21 aug > > * final evaluation > > > On Thu, Apr 7, 2011 at 5:33 PM, Francesco Strozzi > wrote: > > Hi Ales, > > did you had the chance to update your proposal on BioRuby Wrapper for the > > GSoC ? Deadline is tomorrow for student application and we think with > this > > proposal we could be able to get some interesting results. But for your > > application to have a better chance to be considered and evaluated you > > should provide an updated timeline (even a draft but a bit more detailed) > > with the activities and tasks broken down into weeks. > > If you need some help or advise please write here on the Maling List and > we > > will provide our contributions. > > Cheers > > Francesco > > > > On Wed, Apr 6, 2011 at 11:48, Raoul Bonnal wrote: > >> > >> Hello Ales, > >> thank you for submitting your proposal, > >> like Michal: > >> I quote here the discussion with Chris and Christian, if you could write > a > >> better time line in form of days/weeks with tasks/objectives I think it > >> would be better: > >> > >> this is the quote from Christian and Chris > >> > >> Hi, Michal: > >> > >> I think your project plan needs to be much more detailed. > >> > >> It might be best in a format similar to the template/example below: > >> > >> Prior to coding ("community bonding period"): > >> -Familiarize myself with BioRuby code base > >> -Learn about graphics within/from Ruby > >> -Discuss ... with mentors/BioRuby community > >> -... > >> -Learn about git, set up my repository > >> > >> > >> > >> Week 1: > >> Goal: Develop necessary utility classes for ... > >> Anticipated problems: None > >> > >> Weeks 2 and 3: > >> Goal: Develop class to visualize intron/exon structures... > >> Anticipated problems: Such and such might not ... > >> Alternatives: If XYZ turns out not feasible, I plan to ... instead > >> > >> Week X: > >> Goal: Unit tests for ... > >> > >> > >> > >> Week Y: > >> Documentation ... > >> > >> Hope this helps, > >> > >> Christian Zmasek > >> ---- > >> Micha?, > >> > >> In general, the proposal should answer the questions below, but should > >> also have a rough timeline on how you would go about coding the project, > >> creating deliverables for the community for testing, etc. This should > come > >> with the input of your possible mentor for the project or from others in > the > >> bioruby community. > >> > >> The timeline is a little problematic, but the OBF mentors can further > >> discuss that. One thing that will cause a problem is that there is a > >> significant amount of time (about one month) for community bonding, so > any > >> coding on a significant project in that period will be tricky. > >> > >> chris > >> > >> > >> > >> ----- Original Message ---- > >> > From: Micha? Koziarski > >> > To: bioruby at lists.open-bio.org > >> > Sent: Tue, April 5, 2011 10:24:22 AM > >> > Subject: [BioRuby] GSoC - project "Represent bio-objects and related > >> > information with images" > >> > > >> > I've completed my application. Chris Fields suggested that I should > >> > write it > >> > up, he hasn't specified what parts exactly though. If you have any > >> > advice > >> > about it, please let me know. > >> > > >> > I use some of my answers to questions asked here in the application, > I > >> > hope > >> > that's not a problem: I didn't see much point in rewriting it, since > >> > the > >> > meaning would be the same. > >> > > >> > I don't include the first point, about the address, since it's a > public > >> > ML > >> > and I don't think it's important here. > >> > > >> > I am basing the application on the OBF's template, which I enclose > too. > >> > > >> > > >> > 1. Why you are interested in the project you are proposing and are > >> > well-suited to undertake it. > >> > 2. A summary of your programming experience and skills. > >> > 3. Programs or projects you have previously authored or contributed > >> > to, > >> > in particular those available as open-source, including, if > >> > applicable, > >> any > >> > past Summer of Code involvement. > >> > 4. A project plan for the project you are proposing, even if your > >> > proposed project is directly based on one of the proposed project > >> > ideas > >> for > >> > member projects. > >> > 5. Any obligations, vacations, or plans for the summer that may > >> > require > >> > scheduling during the GSoC work period. > >> > > >> > > >> > > >> > 1. I find the problem of representing computer data in format > >> > readable by humans interesting, partially because it's so > >> > significant: we > >> > could have the best algorithms, the fastest computers, but the > output > >> would > >> > be useless if we wouldn't be able to read it. Additionally, I love > >> > the > >> idea > >> > of writing code for organisation such as OBF: it makes me think > that > >> > I do > >> > have, even slightest, impact on science. I must also admit that > >> > working > >> > with > >> > Ruby is very tempting, I really enjoy writing Ruby code. > >> > 2. I have fairly strong Ruby knowledge, I have been using it > for > >> > about a year and a half. There were no really big projects there > >> > though, > >> > the > >> > biggest I've got was probably small LAN IM. Nevertheless, I use > Ruby > >> > on > >> > daily basis and I am familiar with most of its, even complex, > >> > features. > >> > Also, from the beginning of this year I work as a RoR > >> > developer. > >> > I've worked on a bigger, team project and now I am developing one > >> > solo. > >> > I've > >> > learned a lot here: working with version control systems, > developing > >> > in > >> > team, operating on other people's code, testing... not to mention > >> > further > >> > developing my Ruby knowledge. > >> > Other than that, I know C++ pretty well: it was my first > >> > language > >> > and I still use it whenever I see fit. I also have some basic > Python > >> > and > >> C# > >> > knowledge. > >> > 3. I can't say much more than what I've written in previous > >> > paragraph. > >> > 4. 1. Getting familiarized with BioRuby objects, mainly with the > way > >> > they > >> > hold data. > >> > 2. Deciding with features should be visualized. > >> > 3. In case of presence data with different format but same way of > >> > visualization, implementing a mechanism converting data to unified > >> format. > >> > 4. Writing a module responsible for creating graphical > representation > >> > of > >> > data. > >> > 5. Final testing. > >> > 6. Writing a documentation. > >> > 5. Possibly short vacation (less than one week) around > beginning > >> > of > >> > July. > >> > Also, I am from Poland, which means that my summer vacations > >> > starts > >> > from July. Because of that I won't be able to focus only on the > >> > project > >> > until than. What I can do, however, is to start coding earlier. I > >> > would > >> > like > >> > to familiarize myself with documentation before bonding period > starts > >> (I've > >> > already began to do it), and when it does start coding right away. > >> > Thanks > >> > to > >> > that I should have just as much time as if I started in May. > >> > Other than that I am all about the project. > >> > > >> > > >> > Also, since as I've told I would probably have to start coding a > little > >> > earlier, I am trying to slowly browse the documentation. It's a big > >> > project > >> > though, and I don't know what's important. Do you have any > suggestions > >> > about > >> > that? Are there parts that would be especially relevant to the > project? > >> > Or > >> > maybe even better, are there any easier tasks to complete? I learn > best > >> > by > >> > exercise, so that would be great. I've looked up at github's issues > >> > page, > >> > but haven't found anything like what I am talking about. Maybe I just > >> > didn't > >> > know on what I was looking? > >> > _______________________________________________ > >> > BioRuby Project - http://www.bioruby.org/ > >> > BioRuby mailing list > >> > BioRuby at lists.open-bio.org > >> > http://lists.open-bio.org/mailman/listinfo/bioruby > >> > > >> > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > >> On 06/apr/2011, at 11.27, ????? wrote: > >> > >> > Hello. My name is Ales and I'd like to implement BioRuby wrapper for > >> > command line applications as my Google Summer of Code 2011 project. > >> > > >> > > >> > 1. Your complete contact information, including full name, physical > >> > address, preferred email address, and telephone number, plus other > >> > pertinent contact information such as IRC handles, etc. > >> > > >> > Ales Guzik > >> > 4th year student at Belarusian State University of Informatics and > >> > Radioelectronics. > >> > Belarus, Minsk, P.Brovki st. 3-1 46 > >> > ales.guzik at gmail.com > >> > +375 25 902 8190 (Belarus) > >> > +1 650 336 5853 (Google Voice) > >> > skype: ales-guzik > >> > IRC, twitter, facebook, github etc.: nekotwi > >> > > >> > 2. Why you are interested in the project you are proposing and are > >> > well-suited to undertake it. > >> > > >> > This project is interesting for me because it requires metaprogramming > >> > - thing I most like in ruby and > >> > because it's BioRuby - project I wanted to get familiar with long time > >> > ago. > >> > I use Ruby more than 2 years for most of my university tasks and daily > >> > linux scripting. 2 month ago I > >> > started working as Ruby on Rails developer. I have pretty good > >> > experience in ruby metaprogramming which > >> > is needed for this project. > >> > > >> > 3. A summary of your programming experience and skills. > >> > > >> > I have well experience in C, know but not heavily used C++ and Qt, > >> > long time ago learned some Erlang, > >> > have coded some C# at university but dislike it, played a bit with > >> > Android/Java programming. > >> > Know and sometimes use Scheme(Racket), now learning some Perl 5. > >> > Started learning Ruby somewhere in the beginning of 2nd university > >> > year and liked it very much. > >> > > >> > 4. Programs or projects you have previously authored or contributed > >> > to, in particular those available as open-source, including, if > >> > applicable, any past Summer of Code involvement. > >> > > >> > I haven't yet contributed to opensource projects (except for some tiny > >> > projects by myself) but really want to. > >> > > >> > 5. A project plan for the project you are proposing, even if your > >> > proposed project is directly based on one of the proposed project > >> > ideas for member projects. > >> > > >> > 1) Get familiar with source code, use cases and documentation of > >> > BioRuby and BioRuby-ngs > >> > 2) Define specs and write rspec tests for this CLI application > wrapper > >> > 3) Code to make all tests pass > >> > 4) Optimize code for processing BIG ammounts of information > >> > 5) Refactor > >> > 6) Document undocumented parts > >> > > >> > 6. Any obligations, vacations, or plans for the summer that may > >> > require scheduling during the GSoC work period. > >> > > >> > I work as rails programmer 30 hours a week. It's like 8:00 - 14:00 > >> > GMT+2 DST monday - friday, so I can code for > >> > my project 14:30 - 22:00 or even more. It will be like this in june > and > >> > august. > >> > In july I'll be at military training. I'll have time and internet > >> > access but can't tell my schedule for now. > >> > > >> > -- > >> > Regards, > >> > Ales Guzik > >> > ------------------------------------------------------------ > >> > e-mail: ales.guzik at gmail.com > >> > skype: ales-guzik > >> > tel: +375 25 9028190 > >> > _______________________________________________ > >> > BioRuby Project - http://www.bioruby.org/ > >> > BioRuby mailing list > >> > BioRuby at lists.open-bio.org > >> > http://lists.open-bio.org/mailman/listinfo/bioruby > >> > >> -- > >> Ra > >> > >> linkedin: http://it.linkedin.com/in/raoulbonnal > >> twitter: http://twitter.com/ilpuccio > >> skype: ilpuccio > >> irc.freenode.net: Helius > >> github: https://github.com/helios > >> > >> > >> > >> > >> > >> > >> > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > > > -- > > > > Francesco > > > > > > > > -- > Regards, > Ales Guzik > ------------------------------------------------------------ > e-mail: ales.guzik at gmail.com > skype: ales-guzik > tel: +375 25 9028190 > -- Francesco From bonnal at ingm.org Thu Apr 7 14:36:29 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 7 Apr 2011 20:36:29 +0200 Subject: [BioRuby] BioRuby Wrapper for Command line application (GSOC 2011) In-Reply-To: References: <4B02CC0A-20DE-4A60-93C3-E7EDACC9BA64@ingm.org> Message-ID: <06B3D501-BB88-4848-B8B2-28C7A05EAB31@ingm.org> it's a detailed time line for sure. Emboss is an example with a structured configuration file for parameters, but we are not bound only to that suite. On 07/apr/2011, at 20.07, Francesco Strozzi wrote: > Excellent! To me the timeline looks good and the working plan is fine. > > Anyone else have some comment on this? > > Cheers > Francesco > > On Thu, Apr 7, 2011 at 18:24, ????? wrote: > Sorry for this dellay. I just wanted to polish timeline and better > understand for myself how will I undertake this project. > > ** Timeline > > * getting in (4 weeks) 27 apr - 24 may > > - getting familiar with BioRuby project (2-3 weeks) > - getting into bioinformatics basics (at least 1 week) > - getting into project goals and project usage (1 week) > - reading articles about BioRuby > - reading usage documentation > - checking out usage examples > - getting into source codebase (1 week) > - reading source code documentation (4 days) > - looking through source code (2 days) > - defining coding guidelines (1 evening) > - getting into comunity (in parallel with above) > - reading mailing list archive (2-3 days) > - hanging up on IRC (all the time) > > - getting familiar with problem (1-2 weeks) > - finding examples of applications that will be used with this wrapper > - getting familiar with EMBOSS and ACD configuration files > - exploring ways to define wrapper configuration > > * coding-1 (7 weeks) 25 may - 11 july > - writing specs (4 weeks) > - defining complete API/DSL for end-users (1 week) > - defining interface for adding new CLI tools and EMBOSS suites. (1 week) > - defining additional specs (1 week) > - writing code (3 weeks) > - writing code for API generation (1 week) > - writing code for interprocess communication and data passing (1-2 week) > 0-1 additional week to have for finishing all this stuff. > > * mid-term evaluation (5 days) 11 july - 15 july > At this moment we have complete API/DSL specs and code wich allows > us wrapping CLI applications. > > * coding 2 (4 weeks) 17 july - 16 aug > - writing ACD file parser (1-2 weeks) > - writing automatic wrapper generation based on ACD files (2-3 weeks) > > * documentation and refactoring (1 week) 16 aug - 21 aug > > * final evaluation > > > On Thu, Apr 7, 2011 at 5:33 PM, Francesco Strozzi > wrote: > > Hi Ales, > > did you had the chance to update your proposal on BioRuby Wrapper for the > > GSoC ? Deadline is tomorrow for student application and we think with this > > proposal we could be able to get some interesting results. But for your > > application to have a better chance to be considered and evaluated you > > should provide an updated timeline (even a draft but a bit more detailed) > > with the activities and tasks broken down into weeks. > > If you need some help or advise please write here on the Maling List and we > > will provide our contributions. > > Cheers > > Francesco > > > > On Wed, Apr 6, 2011 at 11:48, Raoul Bonnal wrote: > >> > >> Hello Ales, > >> thank you for submitting your proposal, > >> like Michal: > >> I quote here the discussion with Chris and Christian, if you could write a > >> better time line in form of days/weeks with tasks/objectives I think it > >> would be better: > >> > >> this is the quote from Christian and Chris > >> > >> Hi, Michal: > >> > >> I think your project plan needs to be much more detailed. > >> > >> It might be best in a format similar to the template/example below: > >> > >> Prior to coding ("community bonding period"): > >> -Familiarize myself with BioRuby code base > >> -Learn about graphics within/from Ruby > >> -Discuss ... with mentors/BioRuby community > >> -... > >> -Learn about git, set up my repository > >> > >> > >> > >> Week 1: > >> Goal: Develop necessary utility classes for ... > >> Anticipated problems: None > >> > >> Weeks 2 and 3: > >> Goal: Develop class to visualize intron/exon structures... > >> Anticipated problems: Such and such might not ... > >> Alternatives: If XYZ turns out not feasible, I plan to ... instead > >> > >> Week X: > >> Goal: Unit tests for ... > >> > >> > >> > >> Week Y: > >> Documentation ... > >> > >> Hope this helps, > >> > >> Christian Zmasek > >> ---- > >> Micha?, > >> > >> In general, the proposal should answer the questions below, but should > >> also have a rough timeline on how you would go about coding the project, > >> creating deliverables for the community for testing, etc. This should come > >> with the input of your possible mentor for the project or from others in the > >> bioruby community. > >> > >> The timeline is a little problematic, but the OBF mentors can further > >> discuss that. One thing that will cause a problem is that there is a > >> significant amount of time (about one month) for community bonding, so any > >> coding on a significant project in that period will be tricky. > >> > >> chris > >> > >> > >> > >> ----- Original Message ---- > >> > From: Micha? Koziarski > >> > To: bioruby at lists.open-bio.org > >> > Sent: Tue, April 5, 2011 10:24:22 AM > >> > Subject: [BioRuby] GSoC - project "Represent bio-objects and related > >> > information with images" > >> > > >> > I've completed my application. Chris Fields suggested that I should > >> > write it > >> > up, he hasn't specified what parts exactly though. If you have any > >> > advice > >> > about it, please let me know. > >> > > >> > I use some of my answers to questions asked here in the application, I > >> > hope > >> > that's not a problem: I didn't see much point in rewriting it, since > >> > the > >> > meaning would be the same. > >> > > >> > I don't include the first point, about the address, since it's a public > >> > ML > >> > and I don't think it's important here. > >> > > >> > I am basing the application on the OBF's template, which I enclose too. > >> > > >> > > >> > 1. Why you are interested in the project you are proposing and are > >> > well-suited to undertake it. > >> > 2. A summary of your programming experience and skills. > >> > 3. Programs or projects you have previously authored or contributed > >> > to, > >> > in particular those available as open-source, including, if > >> > applicable, > >> any > >> > past Summer of Code involvement. > >> > 4. A project plan for the project you are proposing, even if your > >> > proposed project is directly based on one of the proposed project > >> > ideas > >> for > >> > member projects. > >> > 5. Any obligations, vacations, or plans for the summer that may > >> > require > >> > scheduling during the GSoC work period. > >> > > >> > > >> > > >> > 1. I find the problem of representing computer data in format > >> > readable by humans interesting, partially because it's so > >> > significant: we > >> > could have the best algorithms, the fastest computers, but the output > >> would > >> > be useless if we wouldn't be able to read it. Additionally, I love > >> > the > >> idea > >> > of writing code for organisation such as OBF: it makes me think that > >> > I do > >> > have, even slightest, impact on science. I must also admit that > >> > working > >> > with > >> > Ruby is very tempting, I really enjoy writing Ruby code. > >> > 2. I have fairly strong Ruby knowledge, I have been using it for > >> > about a year and a half. There were no really big projects there > >> > though, > >> > the > >> > biggest I've got was probably small LAN IM. Nevertheless, I use Ruby > >> > on > >> > daily basis and I am familiar with most of its, even complex, > >> > features. > >> > Also, from the beginning of this year I work as a RoR > >> > developer. > >> > I've worked on a bigger, team project and now I am developing one > >> > solo. > >> > I've > >> > learned a lot here: working with version control systems, developing > >> > in > >> > team, operating on other people's code, testing... not to mention > >> > further > >> > developing my Ruby knowledge. > >> > Other than that, I know C++ pretty well: it was my first > >> > language > >> > and I still use it whenever I see fit. I also have some basic Python > >> > and > >> C# > >> > knowledge. > >> > 3. I can't say much more than what I've written in previous > >> > paragraph. > >> > 4. 1. Getting familiarized with BioRuby objects, mainly with the way > >> > they > >> > hold data. > >> > 2. Deciding with features should be visualized. > >> > 3. In case of presence data with different format but same way of > >> > visualization, implementing a mechanism converting data to unified > >> format. > >> > 4. Writing a module responsible for creating graphical representation > >> > of > >> > data. > >> > 5. Final testing. > >> > 6. Writing a documentation. > >> > 5. Possibly short vacation (less than one week) around beginning > >> > of > >> > July. > >> > Also, I am from Poland, which means that my summer vacations > >> > starts > >> > from July. Because of that I won't be able to focus only on the > >> > project > >> > until than. What I can do, however, is to start coding earlier. I > >> > would > >> > like > >> > to familiarize myself with documentation before bonding period starts > >> (I've > >> > already began to do it), and when it does start coding right away. > >> > Thanks > >> > to > >> > that I should have just as much time as if I started in May. > >> > Other than that I am all about the project. > >> > > >> > > >> > Also, since as I've told I would probably have to start coding a little > >> > earlier, I am trying to slowly browse the documentation. It's a big > >> > project > >> > though, and I don't know what's important. Do you have any suggestions > >> > about > >> > that? Are there parts that would be especially relevant to the project? > >> > Or > >> > maybe even better, are there any easier tasks to complete? I learn best > >> > by > >> > exercise, so that would be great. I've looked up at github's issues > >> > page, > >> > but haven't found anything like what I am talking about. Maybe I just > >> > didn't > >> > know on what I was looking? > >> > _______________________________________________ > >> > BioRuby Project - http://www.bioruby.org/ > >> > BioRuby mailing list > >> > BioRuby at lists.open-bio.org > >> > http://lists.open-bio.org/mailman/listinfo/bioruby > >> > > >> > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > >> On 06/apr/2011, at 11.27, ????? wrote: > >> > >> > Hello. My name is Ales and I'd like to implement BioRuby wrapper for > >> > command line applications as my Google Summer of Code 2011 project. > >> > > >> > > >> > 1. Your complete contact information, including full name, physical > >> > address, preferred email address, and telephone number, plus other > >> > pertinent contact information such as IRC handles, etc. > >> > > >> > Ales Guzik > >> > 4th year student at Belarusian State University of Informatics and > >> > Radioelectronics. > >> > Belarus, Minsk, P.Brovki st. 3-1 46 > >> > ales.guzik at gmail.com > >> > +375 25 902 8190 (Belarus) > >> > +1 650 336 5853 (Google Voice) > >> > skype: ales-guzik > >> > IRC, twitter, facebook, github etc.: nekotwi > >> > > >> > 2. Why you are interested in the project you are proposing and are > >> > well-suited to undertake it. > >> > > >> > This project is interesting for me because it requires metaprogramming > >> > - thing I most like in ruby and > >> > because it's BioRuby - project I wanted to get familiar with long time > >> > ago. > >> > I use Ruby more than 2 years for most of my university tasks and daily > >> > linux scripting. 2 month ago I > >> > started working as Ruby on Rails developer. I have pretty good > >> > experience in ruby metaprogramming which > >> > is needed for this project. > >> > > >> > 3. A summary of your programming experience and skills. > >> > > >> > I have well experience in C, know but not heavily used C++ and Qt, > >> > long time ago learned some Erlang, > >> > have coded some C# at university but dislike it, played a bit with > >> > Android/Java programming. > >> > Know and sometimes use Scheme(Racket), now learning some Perl 5. > >> > Started learning Ruby somewhere in the beginning of 2nd university > >> > year and liked it very much. > >> > > >> > 4. Programs or projects you have previously authored or contributed > >> > to, in particular those available as open-source, including, if > >> > applicable, any past Summer of Code involvement. > >> > > >> > I haven't yet contributed to opensource projects (except for some tiny > >> > projects by myself) but really want to. > >> > > >> > 5. A project plan for the project you are proposing, even if your > >> > proposed project is directly based on one of the proposed project > >> > ideas for member projects. > >> > > >> > 1) Get familiar with source code, use cases and documentation of > >> > BioRuby and BioRuby-ngs > >> > 2) Define specs and write rspec tests for this CLI application wrapper > >> > 3) Code to make all tests pass > >> > 4) Optimize code for processing BIG ammounts of information > >> > 5) Refactor > >> > 6) Document undocumented parts > >> > > >> > 6. Any obligations, vacations, or plans for the summer that may > >> > require scheduling during the GSoC work period. > >> > > >> > I work as rails programmer 30 hours a week. It's like 8:00 - 14:00 > >> > GMT+2 DST monday - friday, so I can code for > >> > my project 14:30 - 22:00 or even more. It will be like this in june and > >> > august. > >> > In july I'll be at military training. I'll have time and internet > >> > access but can't tell my schedule for now. > >> > > >> > -- > >> > Regards, > >> > Ales Guzik > >> > ------------------------------------------------------------ > >> > e-mail: ales.guzik at gmail.com > >> > skype: ales-guzik > >> > tel: +375 25 9028190 > >> > _______________________________________________ > >> > BioRuby Project - http://www.bioruby.org/ > >> > BioRuby mailing list > >> > BioRuby at lists.open-bio.org > >> > http://lists.open-bio.org/mailman/listinfo/bioruby > >> > >> -- > >> Ra > >> > >> linkedin: http://it.linkedin.com/in/raoulbonnal > >> twitter: http://twitter.com/ilpuccio > >> skype: ilpuccio > >> irc.freenode.net: Helius > >> github: https://github.com/helios > >> > >> > >> > >> > >> > >> > >> > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > > > -- > > > > Francesco > > > > > > > > -- > Regards, > Ales Guzik > ------------------------------------------------------------ > e-mail: ales.guzik at gmail.com > skype: ales-guzik > tel: +375 25 9028190 > > > > -- > > Francesco > -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Helius github: https://github.com/helios From bonnal at ingm.org Thu Apr 7 15:21:43 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 7 Apr 2011 21:21:43 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <313339.26768.qm@web38403.mail.mud.yahoo.com> <20110406201636.3f58bcc0@mail.ingm.it> Message-ID: <84B3BBBA-3E8C-4202-B50F-68948811350D@ingm.org> On 07/apr/2011, at 19.39, Micha? Koziarski wrote: > 2011/4/6 Raoul Bonnal > Hi Michal, > the time line is more detailed now. > As Francesco suggested and also reported on our page we suggest RubyVis library, Claudio the coder of the binding offers his help and this is a very good news for us. > > Week 9: what do you mean for browsing images in shell ? I can't grasp the benefit now, but we can discuss. The main problem is how to control the application which displays the image; for web browsers there are techniques but are not so easy. > I'm just thinking to an add-on for this week: if we have different types of data that we can display quite easily on the web(done in the previous weeks) , why not spending this time to enrich the images with controls (bars, check boxes, interaction in general). This part requires a skill in javascript. http://vis.stanford.edu/protovis/ex/cartogram-full.html > Or another interesting feature would be: adding layers of information to the standard image. > Note: perhaps these ideas are a bit complicate for 1 week but it would be interesting to evaluate the feasibility. > > I thought about whether to implement that shell browser or work on images enrichment, and I am quite confused. Generally, I would agree that your idea seems to be better, but right now I can't come up with specific ways of enriching them. I guess it should be more obvious once images itself are created, but then there may be not enough time to implement everything. Those were just ideas and were not mandatory. I think, as you wrote, when the images will be ready and you'll be more familiar with bioinformatics problems, the enrichment will be more clear. What about the possibility to evaluate how to "fuse"/enrich and image with data coming from slightly different objects ? Like tagging data sets etc... (today american football training, I hope to find inspiration ^_^ ) > > I forgot to mention, in some case I think that if there are web services which produce images that services could be used. Consider the possibility to display Venn diagrams Google has one service http://code.google.com/intl/it-IT/apis/chart/docs/gallery/venn_charts.html or another one is http://bioinfogp.cnb.csic.es/tools/venny/index.html. > Sets are a kind of data type that in my daily work I have to display with a high frequency, specially when the boss needs to make reports :-) > > So we arrived to the which bioruby objects we want to display. This is a quite complex question because some are there and other are not. > This library as been always sequence/feature centric (please correct me if I'm wrong), because we were used to demand to R tasks more statistics. > Main areas are > * NGS: display create coverage alignemnt for a region with the possible annotation that are accessible from bioruby > * Matrix: display heatmaps, scatter plots, bars ( I wrote a very alpha lib for handling real time PCR and gene expression datasets -not images-) > > Is that lib public now? And if so, could you provide me with repo url? Did you mean R? http://www.bioconductor.org/developers/package-guidelines/ this library is voted to bioinformatics + statistic note that Claudio Bustos (RubyVis) has coded another great library for R http://ruby-statsample.rubyforge.org/rserve-client/ and this is for statistics http://ruby-statsample.rubyforge.org/ > > * Sets: a seq could be generated from any kind of analysis, enrichment, annotation, reports > ** reports could be meta-objects for instance the results of an allignment or mapping or gene quantification when you need to compare multiple populations or technical replicates > * Phylo (i'm not an expert) > > That seems to be the most complicated one of those to visualize (or am I wrong?), it would be great to hear some specifics. If you mean phylo, I think Christian is an expert . > > Out of those, I think that Matrix would be a good place to start. They could be generated only with Rubyvis, and as I believe are used quite often. Would you agree? Yeah at low level I think that most of the problems could be reduced to matrices. Another great tool for visualizing data and I love it, coded in perl, is http://mkweb.bcgsc.ca/circos/ we could you is to find inspirations. and http://vizbi.org/2011/Posters/List/?poster=D10 Ciao. > > > with the idea to produce high quality images ready to be published. > > > These are a bunch of ideas and words. > About tomorrow IRC meeting, @work they scheduled a meeting for (my) afternoon, I'll do my best to be on IRC. Feel free to contact who is around. > > Regards. > > From: Christian Zmasek [mailto:cmzmasek at yahoo.com] > To: Micha? Koziarski [mailto:michalkoziarski at gmail.com], Chris Fields [mailto:cjfields at illinois.edu], bioruby at lists.open-bio.org > Cc: Raoul Bonnal [mailto:bonnalraoul at ingm.it] > Sent: Wed, 06 Apr 2011 20:48:32 +0200 > Subject: Re: [BioRuby] GSoC - project "Represent bio-objects and related information with images" > > > Hi, Micha?: > > You timeline is much better now! > > I put some comments/question into your text (see below). > > > > > Week 1: > > Goal: choose one representative type of BioRuby object and develop class > > that would convert its data to proposed format. That should come along with > > unit tests. > > > This is a good idea -- to deliver a proof of concept first! > > Did you think about how exactly the image(s) will be produced? > > Which library (if any) do you plan to use? > > > Also do you plan to produce (interactive) graphics on the fly and/or create > (static) image files (such as .png) to be viewed with other software? > > > > > > Week 2: > > Goal: develop graphical module that would create image files based on > > data in unified format and provide user interface, write unit tests. > > > > On this point it should be possible to fully visualize chosen BioRuby > > object. > > > > Weeks 3 to 8: > > Goal: basing on first weeks work, prepare similar classes for all of the > > remaining BioRuby objects. Each class should have unit tests. > > > > Week 9: > > Goal: develop mechanism of browsing images in shell. It should include > > simple search and a way of opening images. > > > > Week 10: > > Goal: write integration tests. > > > > Weeks 11 and 12: > > Goal: write documentation. > > > > I would like to be more specific about what should be done from weeks 3 to > > 8, though. It would be nice to plan some time for every object that needs > > visualization, but I don't know which that would be exactly. Could you give > > me a hand with this? > > I think Raoul can answer this better. > > > I guess a good candidate would be sequence objects with features, such as > intron/exon, mutations, etc. > > > > > What about anticipated problems? Can you propose alternatives for things which > might not work as planned? > > Christian > > -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Helius github: https://github.com/helios From michalkoziarski at gmail.com Thu Apr 7 16:27:44 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Thu, 7 Apr 2011 22:27:44 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: <84B3BBBA-3E8C-4202-B50F-68948811350D@ingm.org> References: <313339.26768.qm@web38403.mail.mud.yahoo.com> <20110406201636.3f58bcc0@mail.ingm.it> <84B3BBBA-3E8C-4202-B50F-68948811350D@ingm.org> Message-ID: 2011/4/7 Raoul Bonnal > > On 07/apr/2011, at 19.39, Micha? Koziarski wrote: > > 2011/4/6 Raoul Bonnal > >> Hi Michal, >> the time line is more detailed now. >> As Francesco suggested and also reported on our page we suggest RubyVis >> library, Claudio the coder of the binding offers his help and this is a very >> good news for us. >> >> Week 9: what do you mean for browsing images in shell ? I can't grasp the >> benefit now, but we can discuss. The main problem is how to control the >> application which displays the image; for web browsers there are techniques >> but are not so easy. >> > I'm just thinking to an add-on for this week: if we have different types of >> data that we can display quite easily on the web(done in the previous weeks) >> , why not spending this time to enrich the images with controls (bars, check >> boxes, interaction in general). This part requires a skill in javascript. >> http://vis.stanford.edu/protovis/ex/cartogram-full.html >> Or another interesting feature would be: adding layers of information to >> the standard image. >> Note: perhaps these ideas are a bit complicate for 1 week but it would be >> interesting to evaluate the feasibility. >> > > I thought about whether to implement that shell browser or work on images > enrichment, and I am quite confused. Generally, I would agree that your idea > seems to be better, but right now I can't come up with specific ways of > enriching them. I guess it should be more obvious once images itself are > created, but then there may be not enough time to implement everything. > > Those were just ideas and were not mandatory. I think, as you wrote, when > the images will be ready and you'll be more familiar with bioinformatics > problems, the enrichment will be more clear. What about the possibility to > evaluate how to "fuse"/enrich and image with data coming from slightly > different objects ? Like tagging data sets etc... (today american football > training, I hope to find inspiration ^_^ ) > Yeah, I realize that they were not mandatory, I just would like to make the best of this time. Anyway, I guess I will just stick to the file browsing idea for now, and later on reevaulate which one will be better at the time. > > >> I forgot to mention, in some case I think that if there are web services >> which produce images that services could be used. Consider the possibility >> to display Venn diagrams Google has one service >> http://code.google.com/intl/it-IT/apis/chart/docs/gallery/venn_charts.htmlor another one is >> http://bioinfogp.cnb.csic.es/tools/venny/index.html. >> Sets are a kind of data type that in my daily work I have to display with >> a high frequency, specially when the boss needs to make reports :-) >> >> So we arrived to the which bioruby objects we want to display. This is a >> quite complex question because some are there and other are not. >> This library as been always sequence/feature centric (please correct me if >> I'm wrong), because we were used to demand to R tasks more statistics. >> Main areas are >> * NGS: display create coverage alignemnt for a region with the possible >> annotation that are accessible from bioruby >> * Matrix: display heatmaps, scatter plots, bars ( I wrote a very alpha lib >> for handling real time PCR and gene expression datasets -not images-) >> > > Is that lib public now? And if so, could you provide me with repo url? > > Did you mean R? > http://www.bioconductor.org/developers/package-guidelines/ > this library is voted to bioinformatics + statistic > note that Claudio Bustos (RubyVis) has coded another great library for R > http://ruby-statsample.rubyforge.org/rserve-client/ > and this is for statistics http://ruby-statsample.rubyforge.org/ > > Sorry, I wasn't very specific. I ment your lib for handling real time PCR. > > >> * Sets: a seq could be generated from any kind of analysis, enrichment, >> annotation, reports >> ** reports could be meta-objects for instance the results of an >> allignment or mapping or gene quantification when you need to compare >> multiple populations or technical replicates >> * Phylo (i'm not an expert) >> > > That seems to be the most complicated one of those to visualize (or am I > wrong?), it would be great to hear some specifics. > > If you mean phylo, I think Christian is an expert . > Yes, I ment Phylo. > > > Out of those, I think that Matrix would be a good place to start. They > could be generated only with Rubyvis, and as I believe are used quite often. > Would you agree? > > Yeah at low level I think that most of the problems could be reduced to > matrices. > Another great tool for visualizing data and I love it, coded in perl, is > http://mkweb.bcgsc.ca/circos/ we could you is to find inspirations. > and http://vizbi.org/2011/Posters/List/?poster=D10 > Indeed, Circos looks really great. Have you used it? How about the readibility? > > > Ciao. > > > >> with the idea to produce high quality images ready to be published. >> >> >> These are a bunch of ideas and words. >> About tomorrow IRC meeting, @work they scheduled a meeting for (my) >> afternoon, I'll do my best to be on IRC. Feel free to contact who is around. >> >> Regards. >> >> ------------------------------ >> *From:* Christian Zmasek [mailto:cmzmasek at yahoo.com] >> *To:* Micha? Koziarski [mailto:michalkoziarski at gmail.com], Chris Fields >> [mailto:cjfields at illinois.edu], bioruby at lists.open-bio.org >> *Cc:* Raoul Bonnal [mailto:bonnalraoul at ingm.it] >> *Sent:* Wed, 06 Apr 2011 20:48:32 +0200 >> *Subject:* Re: [BioRuby] GSoC - project "Represent bio-objects and >> related information with images" >> >> >> Hi, Micha?: >> >> You timeline is much better now! >> >> I put some comments/question into your text (see below). >> >> >> >> > Week 1: >> > Goal: choose one representative type of BioRuby object and develop class >> > that would convert its data to proposed format. That should come along >> with >> > unit tests. >> >> >> This is a good idea -- to deliver a proof of concept first! >> >> Did you think about how exactly the image(s) will be produced? >> >> Which library (if any) do you plan to use? >> >> >> Also do you plan to produce (interactive) graphics on the fly and/or >> create >> (static) image files (such as .png) to be viewed with other software? >> >> >> >> >> > Week 2: >> > Goal: develop graphical module that would create image files based on >> > data in unified format and provide user interface, write unit tests. >> > >> > On this point it should be possible to fully visualize chosen BioRuby >> > object. >> > >> > Weeks 3 to 8: >> > Goal: basing on first weeks work, prepare similar classes for all of the >> > remaining BioRuby objects. Each class should have unit tests. >> > >> > Week 9: >> > Goal: develop mechanism of browsing images in shell. It should include >> > simple search and a way of opening images. >> > >> > Week 10: >> > Goal: write integration tests. >> > >> > Weeks 11 and 12: >> > Goal: write documentation. >> > >> > I would like to be more specific about what should be done from weeks 3 >> to >> > 8, though. It would be nice to plan some time for every object that >> needs >> > visualization, but I don't know which that would be exactly. Could you >> give >> > me a hand with this? >> >> I think Raoul can answer this better. >> >> >> I guess a good candidate would be sequence objects with features, such as >> intron/exon, mutations, etc. >> >> >> >> >> What about anticipated problems? Can you propose alternatives for things >> which >> might not work as planned? >> >> Christian >> >> > > -- > Ra > > linkedin: http://it.linkedin.com/in/raoulbonnal > twitter: http://twitter.com/ilpuccio > skype: ilpuccio > irc.freenode.net: Helius > github: https://github.com/helios > > > > > > > From bonnal at ingm.org Thu Apr 7 18:26:46 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 8 Apr 2011 00:26:46 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <313339.26768.qm@web38403.mail.mud.yahoo.com> <20110406201636.3f58bcc0@mail.ingm.it> <84B3BBBA-3E8C-4202-B50F-68948811350D@ingm.org> Message-ID: Hi Michal, On 07/apr/2011, at 22.27, Micha? Koziarski wrote: > 2011/4/7 Raoul Bonnal > > On 07/apr/2011, at 19.39, Micha? Koziarski wrote: > >> 2011/4/6 Raoul Bonnal >> Hi Michal, >> the time line is more detailed now. >> As Francesco suggested and also reported on our page we suggest RubyVis library, Claudio the coder of the binding offers his help and this is a very good news for us. >> >> Week 9: what do you mean for browsing images in shell ? I can't grasp the benefit now, but we can discuss. The main problem is how to control the application which displays the image; for web browsers there are techniques but are not so easy. >> I'm just thinking to an add-on for this week: if we have different types of data that we can display quite easily on the web(done in the previous weeks) , why not spending this time to enrich the images with controls (bars, check boxes, interaction in general). This part requires a skill in javascript. http://vis.stanford.edu/protovis/ex/cartogram-full.html >> Or another interesting feature would be: adding layers of information to the standard image. >> Note: perhaps these ideas are a bit complicate for 1 week but it would be interesting to evaluate the feasibility. >> >> I thought about whether to implement that shell browser or work on images enrichment, and I am quite confused. Generally, I would agree that your idea seems to be better, but right now I can't come up with specific ways of enriching them. I guess it should be more obvious once images itself are created, but then there may be not enough time to implement everything. > Those were just ideas and were not mandatory. I think, as you wrote, when the images will be ready and you'll be more familiar with bioinformatics problems, the enrichment will be more clear. What about the possibility to evaluate how to "fuse"/enrich and image with data coming from slightly different objects ? Like tagging data sets etc... (today american football training, I hope to find inspiration ^_^ ) > > Yeah, I realize that they were not mandatory, I just would like to make the best of this time. Anyway, I guess I will just stick to the file browsing idea for now, and later on reevaulate which one will be better at the time. > >> >> I forgot to mention, in some case I think that if there are web services which produce images that services could be used. Consider the possibility to display Venn diagrams Google has one service http://code.google.com/intl/it-IT/apis/chart/docs/gallery/venn_charts.html or another one is http://bioinfogp.cnb.csic.es/tools/venny/index.html. >> Sets are a kind of data type that in my daily work I have to display with a high frequency, specially when the boss needs to make reports :-) >> >> So we arrived to the which bioruby objects we want to display. This is a quite complex question because some are there and other are not. >> This library as been always sequence/feature centric (please correct me if I'm wrong), because we were used to demand to R tasks more statistics. >> Main areas are >> * NGS: display create coverage alignemnt for a region with the possible annotation that are accessible from bioruby >> * Matrix: display heatmaps, scatter plots, bars ( I wrote a very alpha lib for handling real time PCR and gene expression datasets -not images-) >> >> Is that lib public now? And if so, could you provide me with repo url? > Did you mean R? http://www.bioconductor.org/developers/package-guidelines/ > this library is voted to bioinformatics + statistic > note that Claudio Bustos (RubyVis) has coded another great library for R http://ruby-statsample.rubyforge.org/rserve-client/ > and this is for statistics http://ruby-statsample.rubyforge.org/ > > Sorry, I wasn't very specific. I ment your lib for handling real time PCR. It's not yet on github, was/is quite experimental, but is't a good candidate for a new plugins :-D when I'll have time to reopen it, however basically the data are managed like matrices ( in the latest version i was using statsample). >> >> * Sets: a seq could be generated from any kind of analysis, enrichment, annotation, reports >> ** reports could be meta-objects for instance the results of an allignment or mapping or gene quantification when you need to compare multiple populations or technical replicates >> * Phylo (i'm not an expert) >> >> That seems to be the most complicated one of those to visualize (or am I wrong?), it would be great to hear some specifics. > If you mean phylo, I think Christian is an expert . > > Yes, I ment Phylo. Ok wait some hint from Christian. > >> >> Out of those, I think that Matrix would be a good place to start. They could be generated only with Rubyvis, and as I believe are used quite often. Would you agree? > > Yeah at low level I think that most of the problems could be reduced to matrices. > Another great tool for visualizing data and I love it, coded in perl, is http://mkweb.bcgsc.ca/circos/ we could you is to find inspirations. > and http://vizbi.org/2011/Posters/List/?poster=D10 > > Indeed, Circos looks really great. Have you used it? How about the readibility? Yeah for some projects mostly on visualizing feature on circular genome, some time ago I was working on assembling bacterial genome which are circular > > > Ciao. > >> >> >> with the idea to produce high quality images ready to be published. >> >> >> These are a bunch of ideas and words. >> About tomorrow IRC meeting, @work they scheduled a meeting for (my) afternoon, I'll do my best to be on IRC. Feel free to contact who is around. >> >> Regards. >> >> From: Christian Zmasek [mailto:cmzmasek at yahoo.com] >> To: Micha? Koziarski [mailto:michalkoziarski at gmail.com], Chris Fields [mailto:cjfields at illinois.edu], bioruby at lists.open-bio.org >> Cc: Raoul Bonnal [mailto:bonnalraoul at ingm.it] >> Sent: Wed, 06 Apr 2011 20:48:32 +0200 >> Subject: Re: [BioRuby] GSoC - project "Represent bio-objects and related information with images" >> >> >> Hi, Micha?: >> >> You timeline is much better now! >> >> I put some comments/question into your text (see below). >> >> >> >> > Week 1: >> > Goal: choose one representative type of BioRuby object and develop class >> > that would convert its data to proposed format. That should come along with >> > unit tests. >> >> >> This is a good idea -- to deliver a proof of concept first! >> >> Did you think about how exactly the image(s) will be produced? >> >> Which library (if any) do you plan to use? >> >> >> Also do you plan to produce (interactive) graphics on the fly and/or create >> (static) image files (such as .png) to be viewed with other software? >> >> >> >> >> > Week 2: >> > Goal: develop graphical module that would create image files based on >> > data in unified format and provide user interface, write unit tests. >> > >> > On this point it should be possible to fully visualize chosen BioRuby >> > object. >> > >> > Weeks 3 to 8: >> > Goal: basing on first weeks work, prepare similar classes for all of the >> > remaining BioRuby objects. Each class should have unit tests. >> > >> > Week 9: >> > Goal: develop mechanism of browsing images in shell. It should include >> > simple search and a way of opening images. >> > >> > Week 10: >> > Goal: write integration tests. >> > >> > Weeks 11 and 12: >> > Goal: write documentation. >> > >> > I would like to be more specific about what should be done from weeks 3 to >> > 8, though. It would be nice to plan some time for every object that needs >> > visualization, but I don't know which that would be exactly. Could you give >> > me a hand with this? >> >> I think Raoul can answer this better. >> >> >> I guess a good candidate would be sequence objects with features, such as >> intron/exon, mutations, etc. >> >> >> >> >> What about anticipated problems? Can you propose alternatives for things which >> might not work as planned? >> >> Christian >> >> > > > -- > Ra > > linkedin: http://it.linkedin.com/in/raoulbonnal > twitter: http://twitter.com/ilpuccio > skype: ilpuccio > irc.freenode.net: Helius > github: https://github.com/helios > > > > > > > -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Helius github: https://github.com/helios From missy at be.to Thu Apr 21 22:22:49 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Fri, 22 Apr 2011 11:22:49 +0900 Subject: [BioRuby] A new plugin: BioRuby UCSC API Message-ID: <4DB0E679.9080009@be.to> Hi all, I uploaded a new BioRuby plugin 'bio-ucsc-api' to RubyGems.org. RubyGem: https://rubygems.org/gems/bio-ucsc-api GitHub: https://github.com/misshie/bioruby-ucsc-api GitHub-Issues: http://github.com/misshie/bioruby-ucsc-api/issues BioRuby UCSC API is a API for the UCSC genome browser database. The design is based on Ruby-Ensembl-API and Ruby-UCSC-API by Francesco Strozzi and Jan Aerts. Features of Bioruby UCSC API is the followings: * Designed as a BioRuby plugin * Using ActiveRecord as an O/R mapping framework * Using the Bin index system to improve query performance * Automatic conversion of "1-based full-closed intervals" to internal "0-based half-closed intervals" (see also bioruby-genomic-interval) * Supporting non-official MySql hosts (e.g. local servers) * Using Rspec for the testing framework * Trying to support whole hg19 and hg18 databases. Current version is still experimental. I have implemented only tables that I need to use now. Comments, suggestions, and requests are welcome. Sincerely yours, Hiro. -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From pjotr.public14 at thebird.nl Fri Apr 22 02:35:35 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 22 Apr 2011 08:35:35 +0200 Subject: [BioRuby] A new plugin: BioRuby UCSC API In-Reply-To: <4DB0E679.9080009@be.to> References: <4DB0E679.9080009@be.to> Message-ID: <20110422063535.GA32036@thebird.nl> Great stuff :) On Fri, Apr 22, 2011 at 11:22:49AM +0900, MISHIMA, Hiroyuki wrote: > Hi all, > > I uploaded a new BioRuby plugin 'bio-ucsc-api' to RubyGems.org. > > RubyGem: > https://rubygems.org/gems/bio-ucsc-api > > GitHub: > https://github.com/misshie/bioruby-ucsc-api > > GitHub-Issues: > http://github.com/misshie/bioruby-ucsc-api/issues > > BioRuby UCSC API is a API for the UCSC genome browser database. The > design is based on Ruby-Ensembl-API and Ruby-UCSC-API by Francesco > Strozzi and Jan Aerts. > > Features of Bioruby UCSC API is the followings: > * Designed as a BioRuby plugin > * Using ActiveRecord as an O/R mapping framework > * Using the Bin index system to improve query performance > * Automatic conversion of "1-based full-closed intervals" to internal > "0-based half-closed intervals" (see also bioruby-genomic-interval) > * Supporting non-official MySql hosts (e.g. local servers) > * Using Rspec for the testing framework > * Trying to support whole hg19 and hg18 databases. > > Current version is still experimental. I have implemented only tables > that I need to use now. Comments, suggestions, and requests are welcome. > > Sincerely yours, > Hiro. > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From bonnal at ingm.org Fri Apr 22 05:33:17 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 22 Apr 2011 11:33:17 +0200 Subject: [BioRuby] A new plugin: BioRuby UCSC API In-Reply-To: <4DB0E679.9080009@be.to> References: <4DB0E679.9080009@be.to> Message-ID: this is a great plugin. Well done Hiro. We need to update the wiki to make a list of active plugins new etc... On 22/apr/2011, at 04.22, MISHIMA, Hiroyuki wrote: > Hi all, > > I uploaded a new BioRuby plugin 'bio-ucsc-api' to RubyGems.org. > > RubyGem: > https://rubygems.org/gems/bio-ucsc-api > > GitHub: > https://github.com/misshie/bioruby-ucsc-api > > GitHub-Issues: > http://github.com/misshie/bioruby-ucsc-api/issues > > BioRuby UCSC API is a API for the UCSC genome browser database. The > design is based on Ruby-Ensembl-API and Ruby-UCSC-API by Francesco > Strozzi and Jan Aerts. > > Features of Bioruby UCSC API is the followings: > * Designed as a BioRuby plugin > * Using ActiveRecord as an O/R mapping framework > * Using the Bin index system to improve query performance > * Automatic conversion of "1-based full-closed intervals" to internal > "0-based half-closed intervals" (see also bioruby-genomic-interval) > * Supporting non-official MySql hosts (e.g. local servers) > * Using Rspec for the testing framework > * Trying to support whole hg19 and hg18 databases. > > Current version is still experimental. I have implemented only tables > that I need to use now. Comments, suggestions, and requests are welcome. > > Sincerely yours, > Hiro. > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby Raoul Jean Pierre Bonnal __________________________________________________________________ Istituto Nazionale di Genetica Molecolare Via F.Sforza 35 - 20122 - Milano (MI) - Italy Tel Ufficio :+39 02.00660.326 Tel Fax:+39 02.00662.346 E-Mail :bonnal at ingm.org Web site :http://www.ingm.org SOSTIENI LA RICERCA: devolvi il 5 per mille delle imposte alla FONDAZIONE INGM Istituto Nazionale Genetica Molecolare di Milano. Devi solo inserire il codice fiscale della Fondazione - 04175700964 - in tutti i modelli CUD, 730 e UNICO nella sezione relativa al finanziamento per la RICERCA SANITARIA. Please consider the environment before printing this mail note DISCLAIMER : Questa e-mail potrebbe contenere informazioni privilegiate o confidenziali. Se pensa di aver ricevuto questa e-mail per errore, ? pregato di contattare il mittente rispondendo a questa stessa dopodich? ? pregato di cancellarla immediatamente. This e-mail may contain confidential or privileged information. If you think you have received this e-mail in error, please advise the sender by reply e-mail and then delete this e-mail immediately. From jan.aerts at gmail.com Sat Apr 23 05:31:10 2011 From: jan.aerts at gmail.com (Jan Aerts) Date: Sat, 23 Apr 2011 11:31:10 +0200 Subject: [BioRuby] A new plugin: bio-genomic-interval In-Reply-To: <4D9D45A2.9070608@be.to> References: <4D9D45A2.9070608@be.to> Message-ID: Hi Hiro, You might take a look at the Slice class in the ruby-ensembl-api at https://github.com/jandot/ruby-ensembl-api/blob/master/lib/ensembl/core/slice.rb. This has very similar functionality, and might give some additional ideas as well, for example: - Slice#overlaps?(other_slice) => checks whether 2 slices overlap - Slice#within?(other_slice) => checks whether this slices is contained within another slice - Slice#contains?(other_slice) => checks whether this slices contains another slice - Slice#excise(array_of_regions) => takes a slices and removes a certain region, returning an array of smaller slices. For example: # original_slice = Slice.new('chrX',1,10000) # new_slices = original_slice.excise([500..750, 1050..1075]) # new_slices.each do |s| # puts s.display_name # end # # # result: # # chromosome:X:1:499:1 # # chromosome:X:751:1049:1 # # chromosome:X:1076:10000:1 - Slice#sub_slice(start, stop) => creates a truncated version of this slice - Slice#split(length, overlap) => splits a slice into smaller bits (e.g. creates an array of slices of 100bp long), optionally with an overlap between the resultant slices. Just my 2c. (Also: if you have feature requests, ideas or other comments for the ruby-ensembl-api, see rubyensemblapi.userecho.com) jan. On 7 April 2011 07:03, MISHIMA, Hiroyuki wrote: > Hi all, > > I have uploaded a new Bioruby plugin 'bio-genomic-interval'. > > The Bio::GenomicInterval class is designed to handle genomic intervals > such as "chr1:123-456". The class has methods to detect the overlapping > status between two intervals. It may help to avoid messy case branching > and improve readability of codes. > > Developmental tools for BioRuby plugin and documents in the BioRuby wiki > were very helpful. Thank you all the authors. > > Please see also the followings: > GitHub - > https://github.com/misshie/bioruby-genomic-interval > RubyGems.org - > https://rubygems.org/gems/bio-genomic-interval > > Sincerely yours, > Hiro. > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From jan.aerts at gmail.com Sat Apr 23 05:51:15 2011 From: jan.aerts at gmail.com (Jan Aerts) Date: Sat, 23 Apr 2011 11:51:15 +0200 Subject: [BioRuby] help needed to add compara database to ruby-ensembl-api Message-ID: All, Not that long ago we published a Bioinformatics paper describing the Ruby API to the Ensembl database (Bioinformatics 27(7):1013-1014). This API has the same functionality as the Perl API, with some added benefits (e.g. only 1 API for all releases, very little code which makes maintenance a breeze, and a - we believe - more useful implementation of the Slice concept). At the moment, we have however only implemented the core and the variation databases into the codebase. What has to be done: [1] Create full APIs to all tables in the compara database. This will be very straightforward as it only involves a few lines of code due to the ActiveRecord framework. For example: this is the only code needed to create getters and setters for all columns in the exon_transcript table, plus search functionality in that table: class ExonTranscript < DBConnection set_primary_key nil belongs_to :exon belongs_to :transcript end [2] Add additional functionality that cannot be directly derived from the tables themselves. For the core database, this involved for example coordinate transformations and projections; for the variation database, this involved for example consequence prediction for new variations. If you're interested in helping out (even in part), please don't hesitate to contact me at jan.aerts at esat.kuleuven.be. Glory will be bestowed upon you. Project website: http://github.com/jandot/ruby-ensembl-api Feedback (feature requests, questions, bugs, ...): http://rubyensemblapi.userecho.com Thanks, jan. From missy at be.to Sat Apr 23 10:12:11 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Sat, 23 Apr 2011 23:12:11 +0900 Subject: [BioRuby] A new plugin: bio-genomic-interval In-Reply-To: References: <4D9D45A2.9070608@be.to> Message-ID: <4DB2DE3B.7030606@be.to> Hi Jan and BioRuby-ML, Thank you your comment on the bio-genomic-interval library. After I have released bio-genomic-interval, I found Jan's ruby-ucsc-api and the Slice class. The Slice class also plays an important role in the Ruby Ensembl API. In conclusion, I think that it is good to merge my bio-genomic-interval into the Slice class and make a BioRuby plugin like "bio-slice" to share among libraries. To do this, we have to separate ensemble/core/slice.rb into common methods to share and the Ensembl API specific methods. The strong points of the Slice class are including the followings: * Using BioRuby objects such as Bio::Sequence::NA. * Slice#excise, #sub_slice, and #split * A short simple class name (Matz says "Name is important") So far, I use bio-genomic-interval in bio-ucsc-api because bio-genomic-interval has methods to convert between the common "1-based full-closed" and UCSC-internal "0-based half-closed" intervals. This conversion is trivial arithmetic but prevents bugs. Other methods only in GenomicInterval are the followings: #parse (parses UCSC style "chr1:1,234-3,456") #comparison (returns :left_adjacent [i.e. distance <20bp], :left_off, :contains, :left_overlapped etc.) #overlap (returns a distance or an overlap-length between two intervals) #expand (returns a minimum interval containing two intervals), #center (returns a center position) Sincerely yours, Hiro. Jan Aerts wrote (2011/04/23 18:31): > Hi Hiro, > > You might take a look at the Slice class in the ruby-ensembl-api at > https://github.com/jandot/ruby-ensembl-api/blob/master/lib/ensembl/core/slice.rb. > This has very similar functionality, and might give some additional > ideas as well, for example: > > - Slice#overlaps?(other_slice) => checks whether 2 slices overlap > - Slice#within?(other_slice) => checks whether this slices is contained > within another slice > - Slice#contains?(other_slice) => checks whether this slices contains > another slice > - Slice#excise(array_of_regions) => takes a slices and removes a certain > region, returning an array of smaller slices. For example: > > # original_slice = Slice.new('chrX',1,10000) > # new_slices = original_slice.excise([500..750, 1050..1075]) > # new_slices.each do |s| > # puts s.display_name > # end > # > # # result: > # # chromosome:X:1:499:1 > # # chromosome:X:751:1049:1 > # # chromosome:X:1076:10000:1 > > - Slice#sub_slice(start, stop) => creates a truncated version of this slice > - Slice#split(length, overlap) => splits a slice into smaller bits (e.g. > creates an array of slices of 100bp long), optionally with an overlap > between the resultant slices. > > Just my 2c. (Also: if you have feature requests, ideas or other comments > for the ruby-ensembl-api, see rubyensemblapi.userecho.com > ) > > jan. -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From pjotr.public14 at thebird.nl Sat Apr 23 13:22:48 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 23 Apr 2011 19:22:48 +0200 Subject: [BioRuby] A new plugin: bio-genomic-interval In-Reply-To: <4DB2DE3B.7030606@be.to> References: <4D9D45A2.9070608@be.to> <4DB2DE3B.7030606@be.to> Message-ID: <20110423172247.GA7846@thebird.nl> Good thinking. And I am glad to see biogem encourage modular design; that is what we set out to achieve. Pj. On Sat, Apr 23, 2011 at 11:12:11PM +0900, MISHIMA, Hiroyuki wrote: > Hi Jan and BioRuby-ML, > > Thank you your comment on the bio-genomic-interval library. > > After I have released bio-genomic-interval, I found Jan's ruby-ucsc-api > and the Slice class. The Slice class also plays an important role in the > Ruby Ensembl API. > > In conclusion, I think that it is good to merge my bio-genomic-interval > into the Slice class and make a BioRuby plugin like "bio-slice" to share > among libraries. To do this, we have to separate ensemble/core/slice.rb > into common methods to share and the Ensembl API specific methods. > > The strong points of the Slice class are including the followings: > * Using BioRuby objects such as Bio::Sequence::NA. > * Slice#excise, #sub_slice, and #split > * A short simple class name (Matz says "Name is important") > > So far, I use bio-genomic-interval in bio-ucsc-api because > bio-genomic-interval has methods to convert between the common "1-based > full-closed" and UCSC-internal "0-based half-closed" intervals. This > conversion is trivial arithmetic but prevents bugs. > > Other methods only in GenomicInterval are the followings: > #parse (parses UCSC style "chr1:1,234-3,456") > #comparison (returns :left_adjacent [i.e. distance <20bp], :left_off, > :contains, :left_overlapped etc.) > #overlap (returns a distance or an overlap-length between two intervals) > #expand (returns a minimum interval containing two intervals), > #center (returns a center position) > > Sincerely yours, > Hiro. > > Jan Aerts wrote (2011/04/23 18:31): >> Hi Hiro, >> >> You might take a look at the Slice class in the ruby-ensembl-api at >> https://github.com/jandot/ruby-ensembl-api/blob/master/lib/ensembl/core/slice.rb. >> This has very similar functionality, and might give some additional >> ideas as well, for example: >> >> - Slice#overlaps?(other_slice) => checks whether 2 slices overlap >> - Slice#within?(other_slice) => checks whether this slices is contained >> within another slice >> - Slice#contains?(other_slice) => checks whether this slices contains >> another slice >> - Slice#excise(array_of_regions) => takes a slices and removes a certain >> region, returning an array of smaller slices. For example: >> >> # original_slice = Slice.new('chrX',1,10000) >> # new_slices = original_slice.excise([500..750, 1050..1075]) >> # new_slices.each do |s| >> # puts s.display_name >> # end >> # >> # # result: >> # # chromosome:X:1:499:1 >> # # chromosome:X:751:1049:1 >> # # chromosome:X:1076:10000:1 >> >> - Slice#sub_slice(start, stop) => creates a truncated version of this slice >> - Slice#split(length, overlap) => splits a slice into smaller bits (e.g. >> creates an array of slices of 100bp long), optionally with an overlap >> between the resultant slices. >> >> Just my 2c. (Also: if you have feature requests, ideas or other comments >> for the ruby-ensembl-api, see rubyensemblapi.userecho.com >> ) >> >> jan. > > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Mon Apr 25 05:33:28 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 25 Apr 2011 11:33:28 +0200 Subject: [BioRuby] A new plugin: BioRuby UCSC API In-Reply-To: References: <4DB0E679.9080009@be.to> Message-ID: <20110425093328.GA15152@thebird.nl> On Fri, Apr 22, 2011 at 11:33:17AM +0200, Raoul Bonnal wrote: > We need to update the wiki to make a list of active plugins new etc... I have created a new page: http://bioruby.open-bio.org/wiki/BioRuby_Plugins which simply lists current, stable, developed, and maintained plugins. Plugin authors are encouraged to keep the information up-to-date, and add their plugin as soon as it is committed to rubygems. Field names still need consolidation, I propose to use: Bio-BlastXMLParser - a fast (low-memory) parser for BLAST XML output * Install: gem install bio-blastxmlparser * Depends: Ruby >1.9, nokogiri * Documentation: https://github.com/pjotrp/blastxmlparser * Source: https://github.com/pjotrp/blastxmlparser * Rubygem: https://rubygems.org/gems/bio-blastxmlparser * Developer(s): Pjotr Prins I know some people favour standardizing plugin names to bio-plugin, which is probably a good idea on rubygems (so you can search for bio-*). Otherwise, I don't think it is so important. It is more important we start 'blessing' plugins from BioRuby itself. Pj. From michalkoziarski at gmail.com Sat Apr 2 19:56:07 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Sat, 2 Apr 2011 21:56:07 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" Message-ID: Hi, my name is Micha? Koziarski and I would like to participate in this year GSoC on project mentioned in title. I've prepared a short plan and would be glad to hear some opinions about it. I have a few questions too: - do I have to be familiar with BioRuby itself? - in what exactly 'web visualization' consists? Does it simply mean that there should be a way to upload created files, or is it something more? And my current plan, in which I don't mention RoR integration (since I am not sure what it will be about): 1. Getting familiarized with BioRuby objects, mainly with the way they hold data. 2. Deciding with features should be visualized. 3. In case of presence data with different format but same way of visualization, implementing a mechanism converting data to unified format. 4. Writing a module responsible for creating graphical representation of data. 5. Writing a documentation. Any feedback is appreciated. From bonnal at ingm.org Mon Apr 4 09:38:36 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 4 Apr 2011 11:38:36 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: Message-ID: Dear Michal, thank you for your interest in this project. I'd like to know more about you, programming experience and why did you chose this project ? Are you interested to work in bioinformatics ? On 02/apr/2011, at 21.56, Micha? Koziarski wrote: > Hi, my name is Micha? Koziarski and I would like to participate in this year > GSoC on project mentioned in title. I've prepared a short plan and would be > glad to hear some opinions about it. I have a few questions too: > > - do I have to be familiar with BioRuby itself? It would help a bit :-) > - in what exactly 'web visualization' consists? Does it simply mean that > there should be a way to upload created files, or is it something more? The projects tries to "attach" the concept of images to "bio objects" or to results of some kind of "bio pipeline" where/when possible. Most of the time we process data and creates objects but often the final product is an image. For web visualization, we would like to have images that are ready for the web and that can be integrated in a web application easily. This project (in the subject) will use bio-gem and a feature I'm developing which will give to the developer the possibility to create in a very smooth way a Rails' engine for his/her library. > And my current plan, in which I don't mention RoR integration (since I am > not sure what it will be about): Currently I'm using RoR for my intenral projects, I know there are other framework but I'd like to use the most common. Btw RoR is not our main scope here. > 1. Getting familiarized with BioRuby objects, mainly with the way they hold > data. ok > 2. Deciding with features should be visualized. > 3. In case of presence data with different format but same way of > visualization, implementing a mechanism converting data to unified format. yeah here we should spend a bit of time in figuring out similar representation for dataset and results from "bioinformatics analysis" > 4. Writing a module responsible for creating graphical representation of > data. > 5. Writing a documentation. I agree with the initial plan, don't forget the testing phase. > > Any feedback is appreciated. You can use the ML, and also the irc channel, usually we are there. and on thursday @14:00 GMT there is a irc meeting feel free to join. For other BioRuby developer, feel free to post any comment/ideas/suggestion. -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Helius github: https://github.com/helios From jan.aerts at gmail.com Mon Apr 4 12:00:12 2011 From: jan.aerts at gmail.com (Jan Aerts) Date: Mon, 4 Apr 2011 14:00:12 +0200 Subject: [BioRuby] feedback site for Ruby Ensembl API Message-ID: All, We have created a site where you can provide feedback for the Ruby API to the Ensembl database (github.com/jandot/ruby-ensembl-api ; see Bioinformatics 27(7):1013-1014, 2011). Using that site, you can ask for features, vote on features, report bugs, ... See http://rubyensemblapi.uservoice.com jan. From michalkoziarski at gmail.com Mon Apr 4 14:12:48 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Mon, 4 Apr 2011 16:12:48 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: Message-ID: 2011/4/4 Raoul Bonnal > Dear Michal, > thank you for your interest in this project. > I'd like to know more about you, programming experience and why did you > chose this project ? Are you interested to work in bioinformatics ? > I have fairly strong Ruby knowledge, I have been using it for about a year and a half. There were no really big projects there though, the biggest I've got was probably small LAN IM. Nevertheless, I use Ruby on daily basis and I am familiar with most of its, even complex, features. Also, from the beginning of this year I work as a RoR developer. I've worked on a bigger, team project and now I am developing one solo. I've learned a lot here: working with version control systems, developing in team, operating on other people's code, testing... not to mention further developing my Ruby knowledge. Other than that, I know C++ pretty well: it was my first language and I still use it whenever I see fit. I also have some basic Python and C# knowledge. About why I've chosen this project: I find the problem of representing computer data in format readable by humans interesting, partially because it's so significant: we could have the best algorithms, the fastest computers, but the output would be useless if we wouldn't be able to read it. Additionally, I love the idea of writing code for organisation such as OBF: it makes me think that I do have, even slightest, impact on science. I must also admit that working with Ruby is very tempting :) I really enjoy writing Ruby code. I am certainly interested in programming for scientific purposes. To be honest I haven't thought much about in what area exactly, but since I do have some interest in biology that would seem like a logical choice. > > On 02/apr/2011, at 21.56, Micha? Koziarski wrote: > > Hi, my name is Micha? Koziarski and I would like to participate in this > year > GSoC on project mentioned in title. I've prepared a short plan and would be > glad to hear some opinions about it. I have a few questions too: > > - do I have to be familiar with BioRuby itself? > > It would help a bit :-) > Well, then I am starting to getting know it right know. :) > - in what exactly 'web visualization' consists? Does it simply mean that > > there should be a way to upload created files, or is it something more? > > The projects tries to "attach" the concept of images to "bio objects" or to > results of some kind of "bio pipeline" where/when possible. > Most of the time we process data and creates objects but often the final > product is an image. > For web visualization, we would like to have images that are ready for the > web and that can be integrated in a web application easily. > This project (in the subject) will use bio-gem and a feature I'm developing > which will give to the developer the possibility to create in a very smooth > way a Rails' engine for his/her library. > > And my current plan, in which I don't mention RoR integration (since I am > not sure what it will be about): > > Currently I'm using RoR for my intenral projects, I know there are other > framework but I'd like to use the most common. Btw RoR is not our main scope > here. > > 1. Getting familiarized with BioRuby objects, mainly with the way they hold > data. > > ok > > 2. Deciding with features should be visualized. > 3. In case of presence data with different format but same way of > visualization, implementing a mechanism converting data to unified format. > > yeah here we should spend a bit of time in figuring out similar > representation for dataset and results from "bioinformatics analysis" > > 4. Writing a module responsible for creating graphical representation of > data. > 5. Writing a documentation. > > I agree with the initial plan, don't forget the testing phase. > Actually, I was thinking about trying some test-driven development, I am not 100% sure if that would work for this project though. But anyway, yes, I haven't included that in my plan, thank you for pointing that out. I guess it would be the best to do the final testing before writing a documentation, with some smaller scaled testing after each milestone completed. > > > Any feedback is appreciated. > > You can use the ML, and also the irc channel, usually we are there. and on > thursday @14:00 GMT there is a irc meeting feel free to join. > I've joined ML (it stands for mail list, right?) already, and visited the irc a day or two before, unfortunately it seemed no one was online at the time. As for the meeting, I have classes at this time, so I am not sure if I will be able to be there, but for sure I will visit irc if any other questions come to my mind. And thank you for answering my questions, I have much clearer picture now. > > For other BioRuby developer, feel free to post any > comment/ideas/suggestion. > -- > Ra > > linkedin: http://it.linkedin.com/in/raoulbonnal > twitter: http://twitter.com/ilpuccio > skype: ilpuccio > irc.freenode.net: Helius > github: https://github.com/helios > > > > > > > From bonnal at ingm.org Mon Apr 4 15:06:40 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 4 Apr 2011 17:06:40 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: Message-ID: <963BE5B3-B551-43BD-9A9B-D21C01A14568@ingm.org> Hi Michal, thank you for your detailed answer, for me it's fine go ahead with the gsoc procedure. About IRC, if you find us online msg us, sorry I wasn't online during the w.e. Yes ML means mailing-list :-) My nick name on IRC is helios. On 04/apr/2011, at 16.12, Micha? Koziarski wrote: > 2011/4/4 Raoul Bonnal > >> Dear Michal, >> thank you for your interest in this project. >> I'd like to know more about you, programming experience and why did you >> chose this project ? Are you interested to work in bioinformatics ? >> > > I have fairly strong Ruby knowledge, I have been using it for about a year > and a half. There were no really big projects there though, the biggest I've > got was probably small LAN IM. Nevertheless, I use Ruby on daily basis and I > am familiar with most of its, even complex, features. > > Also, from the beginning of this year I work as a RoR developer. I've worked > on a bigger, team project and now I am developing one solo. I've learned a > lot here: working with version control systems, developing in team, > operating on other people's code, testing... not to mention further > developing my Ruby knowledge. > > Other than that, I know C++ pretty well: it was my first language and I > still use it whenever I see fit. I also have some basic Python and C# > knowledge. > > About why I've chosen this project: I find the problem of representing > computer data in format readable by humans interesting, partially because > it's so significant: we could have the best algorithms, the fastest > computers, but the output would be useless if we wouldn't be able to read > it. Additionally, I love the idea of writing code for organisation such as > OBF: it makes me think that I do have, even slightest, impact on science. I > must also admit that working with Ruby is very tempting :) I really enjoy > writing Ruby code. > > I am certainly interested in programming for scientific purposes. To be > honest I haven't thought much about in what area exactly, but since I do > have some interest in biology that would seem like a logical choice. > >> >> On 02/apr/2011, at 21.56, Micha? Koziarski wrote: >> >> Hi, my name is Micha? Koziarski and I would like to participate in this >> year >> GSoC on project mentioned in title. I've prepared a short plan and would be >> glad to hear some opinions about it. I have a few questions too: >> >> - do I have to be familiar with BioRuby itself? >> >> It would help a bit :-) >> > > Well, then I am starting to getting know it right know. :) > >> - in what exactly 'web visualization' consists? Does it simply mean that >> >> there should be a way to upload created files, or is it something more? >> >> The projects tries to "attach" the concept of images to "bio objects" or to >> results of some kind of "bio pipeline" where/when possible. >> Most of the time we process data and creates objects but often the final >> product is an image. >> For web visualization, we would like to have images that are ready for the >> web and that can be integrated in a web application easily. >> This project (in the subject) will use bio-gem and a feature I'm developing >> which will give to the developer the possibility to create in a very smooth >> way a Rails' engine for his/her library. >> >> And my current plan, in which I don't mention RoR integration (since I am >> not sure what it will be about): >> >> Currently I'm using RoR for my intenral projects, I know there are other >> framework but I'd like to use the most common. Btw RoR is not our main scope >> here. >> >> 1. Getting familiarized with BioRuby objects, mainly with the way they hold >> data. >> >> ok >> >> 2. Deciding with features should be visualized. >> 3. In case of presence data with different format but same way of >> visualization, implementing a mechanism converting data to unified format. >> >> yeah here we should spend a bit of time in figuring out similar >> representation for dataset and results from "bioinformatics analysis" >> >> 4. Writing a module responsible for creating graphical representation of >> data. >> 5. Writing a documentation. >> >> I agree with the initial plan, don't forget the testing phase. >> > > Actually, I was thinking about trying some test-driven development, I am not > 100% sure if that would work for this project though. But anyway, yes, I > haven't included that in my plan, thank you for pointing that out. > > I guess it would be the best to do the final testing before writing a > documentation, with some smaller scaled testing after each milestone > completed. > >> >> >> Any feedback is appreciated. >> >> You can use the ML, and also the irc channel, usually we are there. and on >> thursday @14:00 GMT there is a irc meeting feel free to join. >> > > I've joined ML (it stands for mail list, right?) already, and visited the > irc a day or two before, unfortunately it seemed no one was online at the > time. As for the meeting, I have classes at this time, so I am not sure if I > will be able to be there, but for sure I will visit irc if any other > questions come to my mind. > > And thank you for answering my questions, I have much clearer picture now. > > >> >> For other BioRuby developer, feel free to post any >> comment/ideas/suggestion. >> -- >> Ra >> >> linkedin: http://it.linkedin.com/in/raoulbonnal >> twitter: http://twitter.com/ilpuccio >> skype: ilpuccio >> irc.freenode.net: Helius >> github: https://github.com/helios >> >> >> >> >> >> >> > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Helius github: https://github.com/helios From yannick.wurm at unil.ch Mon Apr 4 16:13:39 2011 From: yannick.wurm at unil.ch (Yannick Wurm) Date: Mon, 4 Apr 2011 18:13:39 +0200 Subject: [BioRuby] feedback site for Ruby Ensembl API (Jan Aerts) In-Reply-To: References: Message-ID: <52117FE7-08B9-4A08-AB13-2BA9993E3488@unil.ch> Thanks Jan & congrats for the paper. Now if only ensembl supported more ant genomes.... ------------------------- Ant Genomes & Evolution http://yannick.poulet.org skype://yannickwurm On 4 Apr 2011, at 18:00, bioruby-request at lists.open-bio.org wrote: > All, > > We have created a site where you can provide feedback for the Ruby API to > the Ensembl database (github.com/jandot/ruby-ensembl-api ; see > Bioinformatics 27(7):1013-1014, 2011). Using that site, you can ask for > features, vote on features, report bugs, ... > > See http://rubyensemblapi.uservoice.com > > jan. From michalkoziarski at gmail.com Tue Apr 5 17:24:22 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Tue, 5 Apr 2011 19:24:22 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" Message-ID: I've completed my application. Chris Fields suggested that I should write it up, he hasn't specified what parts exactly though. If you have any advice about it, please let me know. I use some of my answers to questions asked here in the application, I hope that's not a problem: I didn't see much point in rewriting it, since the meaning would be the same. I don't include the first point, about the address, since it's a public ML and I don't think it's important here. I am basing the application on the OBF's template, which I enclose too. 1. Why you are interested in the project you are proposing and are well-suited to undertake it. 2. A summary of your programming experience and skills. 3. Programs or projects you have previously authored or contributed to, in particular those available as open-source, including, if applicable, any past Summer of Code involvement. 4. A project plan for the project you are proposing, even if your proposed project is directly based on one of the proposed project ideas for member projects. 5. Any obligations, vacations, or plans for the summer that may require scheduling during the GSoC work period. 1. I find the problem of representing computer data in format readable by humans interesting, partially because it's so significant: we could have the best algorithms, the fastest computers, but the output would be useless if we wouldn't be able to read it. Additionally, I love the idea of writing code for organisation such as OBF: it makes me think that I do have, even slightest, impact on science. I must also admit that working with Ruby is very tempting, I really enjoy writing Ruby code. 2. I have fairly strong Ruby knowledge, I have been using it for about a year and a half. There were no really big projects there though, the biggest I've got was probably small LAN IM. Nevertheless, I use Ruby on daily basis and I am familiar with most of its, even complex, features. Also, from the beginning of this year I work as a RoR developer. I've worked on a bigger, team project and now I am developing one solo. I've learned a lot here: working with version control systems, developing in team, operating on other people's code, testing... not to mention further developing my Ruby knowledge. Other than that, I know C++ pretty well: it was my first language and I still use it whenever I see fit. I also have some basic Python and C# knowledge. 3. I can't say much more than what I've written in previous paragraph. 4. 1. Getting familiarized with BioRuby objects, mainly with the way they hold data. 2. Deciding with features should be visualized. 3. In case of presence data with different format but same way of visualization, implementing a mechanism converting data to unified format. 4. Writing a module responsible for creating graphical representation of data. 5. Final testing. 6. Writing a documentation. 5. Possibly short vacation (less than one week) around beginning of July. Also, I am from Poland, which means that my summer vacations starts from July. Because of that I won't be able to focus only on the project until than. What I can do, however, is to start coding earlier. I would like to familiarize myself with documentation before bonding period starts (I've already began to do it), and when it does start coding right away. Thanks to that I should have just as much time as if I started in May. Other than that I am all about the project. Also, since as I've told I would probably have to start coding a little earlier, I am trying to slowly browse the documentation. It's a big project though, and I don't know what's important. Do you have any suggestions about that? Are there parts that would be especially relevant to the project? Or maybe even better, are there any easier tasks to complete? I learn best by exercise, so that would be great. I've looked up at github's issues page, but haven't found anything like what I am talking about. Maybe I just didn't know on what I was looking? From cjfields at illinois.edu Tue Apr 5 19:09:10 2011 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 5 Apr 2011 14:09:10 -0500 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: Message-ID: <6916C4A0-739E-4069-A1EE-704ACE5DA5D8@illinois.edu> Micha?, In general, the proposal should answer the questions below, but should also have a rough timeline on how you would go about coding the project, creating deliverables for the community for testing, etc. This should come with the input of your possible mentor for the project or from others in the bioruby community. The timeline is a little problematic, but the OBF mentors can further discuss that. One thing that will cause a problem is that there is a significant amount of time (about one month) for community bonding, so any coding on a significant project in that period will be tricky. chris On Apr 5, 2011, at 12:24 PM, Micha? Koziarski wrote: > I've completed my application. Chris Fields suggested that I should write it > up, he hasn't specified what parts exactly though. If you have any advice > about it, please let me know. > > I use some of my answers to questions asked here in the application, I hope > that's not a problem: I didn't see much point in rewriting it, since the > meaning would be the same. > > I don't include the first point, about the address, since it's a public ML > and I don't think it's important here. > > I am basing the application on the OBF's template, which I enclose too. > > > 1. Why you are interested in the project you are proposing and are > well-suited to undertake it. > 2. A summary of your programming experience and skills. > 3. Programs or projects you have previously authored or contributed to, > in particular those available as open-source, including, if applicable, any > past Summer of Code involvement. > 4. A project plan for the project you are proposing, even if your > proposed project is directly based on one of the proposed project ideas for > member projects. > 5. Any obligations, vacations, or plans for the summer that may require > scheduling during the GSoC work period. > > > > 1. I find the problem of representing computer data in format > readable by humans interesting, partially because it's so significant: we > could have the best algorithms, the fastest computers, but the output would > be useless if we wouldn't be able to read it. Additionally, I love the idea > of writing code for organisation such as OBF: it makes me think that I do > have, even slightest, impact on science. I must also admit that working with > Ruby is very tempting, I really enjoy writing Ruby code. > 2. I have fairly strong Ruby knowledge, I have been using it for > about a year and a half. There were no really big projects there though, the > biggest I've got was probably small LAN IM. Nevertheless, I use Ruby on > daily basis and I am familiar with most of its, even complex, features. > Also, from the beginning of this year I work as a RoR developer. > I've worked on a bigger, team project and now I am developing one solo. I've > learned a lot here: working with version control systems, developing in > team, operating on other people's code, testing... not to mention further > developing my Ruby knowledge. > Other than that, I know C++ pretty well: it was my first language > and I still use it whenever I see fit. I also have some basic Python and C# > knowledge. > 3. I can't say much more than what I've written in previous paragraph. > 4. 1. Getting familiarized with BioRuby objects, mainly with the way they > hold data. > 2. Deciding with features should be visualized. > 3. In case of presence data with different format but same way of > visualization, implementing a mechanism converting data to unified format. > 4. Writing a module responsible for creating graphical representation of > data. > 5. Final testing. > 6. Writing a documentation. > 5. Possibly short vacation (less than one week) around beginning of > July. > Also, I am from Poland, which means that my summer vacations starts > from July. Because of that I won't be able to focus only on the project > until than. What I can do, however, is to start coding earlier. I would like > to familiarize myself with documentation before bonding period starts (I've > already began to do it), and when it does start coding right away. Thanks to > that I should have just as much time as if I started in May. > Other than that I am all about the project. > > > Also, since as I've told I would probably have to start coding a little > earlier, I am trying to slowly browse the documentation. It's a big project > though, and I don't know what's important. Do you have any suggestions about > that? Are there parts that would be especially relevant to the project? Or > maybe even better, are there any easier tasks to complete? I learn best by > exercise, so that would be great. I've looked up at github's issues page, > but haven't found anything like what I am talking about. Maybe I just didn't > know on what I was looking? > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From cmzmasek at yahoo.com Tue Apr 5 19:19:35 2011 From: cmzmasek at yahoo.com (Christian Zmasek) Date: Tue, 5 Apr 2011 12:19:35 -0700 (PDT) Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: Message-ID: <981305.71979.qm@web38404.mail.mud.yahoo.com> Hi, Michal: I think your project plan needs to be much more detailed. It might be best in a format similar to the template/example below: Prior to coding ("community bonding period"): -Familiarize myself with BioRuby code base -Learn about graphics within/from Ruby -Discuss ... with mentors/BioRuby community -... -Learn about git, set up my repository Week 1: Goal: Develop necessary utility classes for ... Anticipated problems: None Weeks 2 and 3: Goal: Develop class to visualize intron/exon structures... Anticipated problems: Such and such might not ... Alternatives: If XYZ turns out not feasible, I plan to ... instead Week X: Goal: Unit tests for ... Week Y: Documentation ... Hope this helps, Christian Zmasek ----- Original Message ---- > From: Micha? Koziarski > To: bioruby at lists.open-bio.org > Sent: Tue, April 5, 2011 10:24:22 AM > Subject: [BioRuby] GSoC - project "Represent bio-objects and related >information with images" > > I've completed my application. Chris Fields suggested that I should write it > up, he hasn't specified what parts exactly though. If you have any advice > about it, please let me know. > > I use some of my answers to questions asked here in the application, I hope > that's not a problem: I didn't see much point in rewriting it, since the > meaning would be the same. > > I don't include the first point, about the address, since it's a public ML > and I don't think it's important here. > > I am basing the application on the OBF's template, which I enclose too. > > > 1. Why you are interested in the project you are proposing and are > well-suited to undertake it. > 2. A summary of your programming experience and skills. > 3. Programs or projects you have previously authored or contributed to, > in particular those available as open-source, including, if applicable, any > past Summer of Code involvement. > 4. A project plan for the project you are proposing, even if your > proposed project is directly based on one of the proposed project ideas for > member projects. > 5. Any obligations, vacations, or plans for the summer that may require > scheduling during the GSoC work period. > > > > 1. I find the problem of representing computer data in format > readable by humans interesting, partially because it's so significant: we > could have the best algorithms, the fastest computers, but the output would > be useless if we wouldn't be able to read it. Additionally, I love the idea > of writing code for organisation such as OBF: it makes me think that I do > have, even slightest, impact on science. I must also admit that working >with > Ruby is very tempting, I really enjoy writing Ruby code. > 2. I have fairly strong Ruby knowledge, I have been using it for > about a year and a half. There were no really big projects there though, >the > biggest I've got was probably small LAN IM. Nevertheless, I use Ruby on > daily basis and I am familiar with most of its, even complex, features. > Also, from the beginning of this year I work as a RoR developer. > I've worked on a bigger, team project and now I am developing one solo. >I've > learned a lot here: working with version control systems, developing in > team, operating on other people's code, testing... not to mention further > developing my Ruby knowledge. > Other than that, I know C++ pretty well: it was my first language > and I still use it whenever I see fit. I also have some basic Python and C# > knowledge. > 3. I can't say much more than what I've written in previous paragraph. > 4. 1. Getting familiarized with BioRuby objects, mainly with the way they > hold data. > 2. Deciding with features should be visualized. > 3. In case of presence data with different format but same way of > visualization, implementing a mechanism converting data to unified format. > 4. Writing a module responsible for creating graphical representation of > data. > 5. Final testing. > 6. Writing a documentation. > 5. Possibly short vacation (less than one week) around beginning of > July. > Also, I am from Poland, which means that my summer vacations starts > from July. Because of that I won't be able to focus only on the project > until than. What I can do, however, is to start coding earlier. I would >like > to familiarize myself with documentation before bonding period starts (I've > already began to do it), and when it does start coding right away. Thanks >to > that I should have just as much time as if I started in May. > Other than that I am all about the project. > > > Also, since as I've told I would probably have to start coding a little > earlier, I am trying to slowly browse the documentation. It's a big project > though, and I don't know what's important. Do you have any suggestions about > that? Are there parts that would be especially relevant to the project? Or > maybe even better, are there any easier tasks to complete? I learn best by > exercise, so that would be great. I've looked up at github's issues page, > but haven't found anything like what I am talking about. Maybe I just didn't > know on what I was looking? > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From michalkoziarski at gmail.com Tue Apr 5 20:37:02 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Tue, 5 Apr 2011 22:37:02 +0200 Subject: [BioRuby] Fwd: GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <981305.71979.qm@web38404.mail.mud.yahoo.com> Message-ID: I have to agree, my plan isn't very specific. But mainly coming up with a timeline is kind of a guesswork: maybe it's just me, I don't like saying anything unless I am certain of it, and there's no way at this point to do this. Anyway, I will prepare what I am able to today, and hopefully catch someone tomorrow on irc to further discuss some specifics. Chris: could you explain why any coding at community bonding period would be hard? I assumed that a big part of it is getting familiar with documentation, and with that done before I would have some more time to code. Of course, it wouldn't be a full-time coding, but I thought that at this point I would have all the knowledge to start writing, so why not to. Maybe I am missing something, in that case tell me please. Christian: yes, it was very helpful, I've read some example plans before, but I couldn't really relate them to my project. Now I have a little clearer picture of what to write. Thanks for that, hopefully tomorrow I will present something in that manner. 2011/4/5 Christian Zmasek > Hi, Michal: > > I think your project plan needs to be much more detailed. > > It might be best in a format similar to the template/example below: > > Prior to coding ("community bonding period"): > -Familiarize myself with BioRuby code base > -Learn about graphics within/from Ruby > -Discuss ... with mentors/BioRuby community > -... > -Learn about git, set up my repository > > > > Week 1: > Goal: Develop necessary utility classes for ... > Anticipated problems: None > > Weeks 2 and 3: > Goal: Develop class to visualize intron/exon structures... > Anticipated problems: Such and such might not ... > Alternatives: If XYZ turns out not feasible, I plan to ... instead > > Week X: > Goal: Unit tests for ... > > > > Week Y: > Documentation ... > > Hope this helps, > > Christian Zmasek > > > > > ----- Original Message ---- > > From: Micha? Koziarski > > To: bioruby at lists.open-bio.org > > Sent: Tue, April 5, 2011 10:24:22 AM > > Subject: [BioRuby] GSoC - project "Represent bio-objects and related > >information with images" > > > > I've completed my application. Chris Fields suggested that I should write > it > > up, he hasn't specified what parts exactly though. If you have any > advice > > about it, please let me know. > > > > I use some of my answers to questions asked here in the application, I > hope > > that's not a problem: I didn't see much point in rewriting it, since the > > meaning would be the same. > > > > I don't include the first point, about the address, since it's a public > ML > > and I don't think it's important here. > > > > I am basing the application on the OBF's template, which I enclose too. > > > > > > 1. Why you are interested in the project you are proposing and are > > well-suited to undertake it. > > 2. A summary of your programming experience and skills. > > 3. Programs or projects you have previously authored or contributed > to, > > in particular those available as open-source, including, if > applicable, > any > > past Summer of Code involvement. > > 4. A project plan for the project you are proposing, even if your > > proposed project is directly based on one of the proposed project > ideas > for > > member projects. > > 5. Any obligations, vacations, or plans for the summer that may > require > > scheduling during the GSoC work period. > > > > > > > > 1. I find the problem of representing computer data in format > > readable by humans interesting, partially because it's so > significant: we > > could have the best algorithms, the fastest computers, but the output > would > > be useless if we wouldn't be able to read it. Additionally, I love > the > idea > > of writing code for organisation such as OBF: it makes me think that > I do > > have, even slightest, impact on science. I must also admit that > working > >with > > Ruby is very tempting, I really enjoy writing Ruby code. > > 2. I have fairly strong Ruby knowledge, I have been using it for > > about a year and a half. There were no really big projects there > though, > >the > > biggest I've got was probably small LAN IM. Nevertheless, I use Ruby > on > > daily basis and I am familiar with most of its, even complex, > features. > > Also, from the beginning of this year I work as a RoR > developer. > > I've worked on a bigger, team project and now I am developing one > solo. > >I've > > learned a lot here: working with version control systems, developing > in > > team, operating on other people's code, testing... not to mention > further > > developing my Ruby knowledge. > > Other than that, I know C++ pretty well: it was my first > language > > and I still use it whenever I see fit. I also have some basic Python > and > C# > > knowledge. > > 3. I can't say much more than what I've written in previous > paragraph. > > 4. 1. Getting familiarized with BioRuby objects, mainly with the way > they > > hold data. > > 2. Deciding with features should be visualized. > > 3. In case of presence data with different format but same way of > > visualization, implementing a mechanism converting data to unified > format. > > 4. Writing a module responsible for creating graphical representation > of > > data. > > 5. Final testing. > > 6. Writing a documentation. > > 5. Possibly short vacation (less than one week) around beginning > of > > July. > > Also, I am from Poland, which means that my summer vacations > starts > > from July. Because of that I won't be able to focus only on the > project > > until than. What I can do, however, is to start coding earlier. I > would > >like > > to familiarize myself with documentation before bonding period starts > (I've > > already began to do it), and when it does start coding right away. > Thanks > >to > > that I should have just as much time as if I started in May. > > Other than that I am all about the project. > > > > > > Also, since as I've told I would probably have to start coding a little > > earlier, I am trying to slowly browse the documentation. It's a big > project > > though, and I don't know what's important. Do you have any suggestions > about > > that? Are there parts that would be especially relevant to the project? > Or > > maybe even better, are there any easier tasks to complete? I learn best > by > > exercise, so that would be great. I've looked up at github's issues > page, > > but haven't found anything like what I am talking about. Maybe I just > didn't > > know on what I was looking? > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > From cjfields at illinois.edu Tue Apr 5 20:56:38 2011 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 5 Apr 2011 15:56:38 -0500 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <981305.71979.qm@web38404.mail.mud.yahoo.com> Message-ID: On Apr 5, 2011, at 3:37 PM, Micha? Koziarski wrote: > I have to agree, my plan isn't very specific. But mainly coming up with a timeline is kind of a guesswork: maybe it's just me, I don't like saying anything unless I am certain of it, and there's no way at this point to do this. Anyway, I will prepare what I am able to today, and hopefully catch someone tomorrow on irc to further discuss some specifics. Don't think of it as a strict timeline as much as an overall plan for development of your project. Timelines for projects are meant to be malleable and change based on what occurs during development, but w/o underlying structure then there is no organization of your priorities. > Chris: could you explain why any coding at community bonding period would be hard? I assumed that a big part of it is getting familiar with documentation, and with that done before I would have some more time to code. Of course, it wouldn't be a full-time coding, but I thought that at this point I would have all the knowledge to start writing, so why not to. Maybe I am missing something, in that case tell me please. In general, little coding occurs during community bonding; the time is spent asking questions on the API, working out final priorities, details on the project, etc with the community (mentor in particular). I'm not sure of your level of experience with BioRuby, but from my experience with BioPerl and past GSoC projects the codebase and API (and documentation, or lack thereof) can be daunting for a beginner. So, mentioning that you will use that period to code b/c of time issues during the scheduled period is a bit premature in my opinion w/o more specifics, but that's really for the BioRuby folks to decide. I think Christian made some more specific notes on what is expected. chris > Christian: yes, it was very helpful, I've read some example plans before, but I couldn't really relate them to my project. Now I have a little clearer picture of what to write. Thanks for that, hopefully tomorrow I will present something in that manner. > > > 2011/4/5 Christian Zmasek > Hi, Michal: > > I think your project plan needs to be much more detailed. > > It might be best in a format similar to the template/example below: > > Prior to coding ("community bonding period"): > -Familiarize myself with BioRuby code base > -Learn about graphics within/from Ruby > -Discuss ... with mentors/BioRuby community > -... > -Learn about git, set up my repository > > > > Week 1: > Goal: Develop necessary utility classes for ... > Anticipated problems: None > > Weeks 2 and 3: > Goal: Develop class to visualize intron/exon structures... > Anticipated problems: Such and such might not ... > Alternatives: If XYZ turns out not feasible, I plan to ... instead > > Week X: > Goal: Unit tests for ... > > > > Week Y: > Documentation ... > > Hope this helps, > > Christian Zmasek > > > > > ----- Original Message ---- > > From: Micha? Koziarski > > To: bioruby at lists.open-bio.org > > Sent: Tue, April 5, 2011 10:24:22 AM > > Subject: [BioRuby] GSoC - project "Represent bio-objects and related > >information with images" > > > > I've completed my application. Chris Fields suggested that I should write it > > up, he hasn't specified what parts exactly though. If you have any advice > > about it, please let me know. > > > > I use some of my answers to questions asked here in the application, I hope > > that's not a problem: I didn't see much point in rewriting it, since the > > meaning would be the same. > > > > I don't include the first point, about the address, since it's a public ML > > and I don't think it's important here. > > > > I am basing the application on the OBF's template, which I enclose too. > > > > > > 1. Why you are interested in the project you are proposing and are > > well-suited to undertake it. > > 2. A summary of your programming experience and skills. > > 3. Programs or projects you have previously authored or contributed to, > > in particular those available as open-source, including, if applicable, > any > > past Summer of Code involvement. > > 4. A project plan for the project you are proposing, even if your > > proposed project is directly based on one of the proposed project ideas > for > > member projects. > > 5. Any obligations, vacations, or plans for the summer that may require > > scheduling during the GSoC work period. > > > > > > > > 1. I find the problem of representing computer data in format > > readable by humans interesting, partially because it's so significant: we > > could have the best algorithms, the fastest computers, but the output > would > > be useless if we wouldn't be able to read it. Additionally, I love the > idea > > of writing code for organisation such as OBF: it makes me think that I do > > have, even slightest, impact on science. I must also admit that working > >with > > Ruby is very tempting, I really enjoy writing Ruby code. > > 2. I have fairly strong Ruby knowledge, I have been using it for > > about a year and a half. There were no really big projects there though, > >the > > biggest I've got was probably small LAN IM. Nevertheless, I use Ruby on > > daily basis and I am familiar with most of its, even complex, features. > > Also, from the beginning of this year I work as a RoR developer. > > I've worked on a bigger, team project and now I am developing one solo. > >I've > > learned a lot here: working with version control systems, developing in > > team, operating on other people's code, testing... not to mention further > > developing my Ruby knowledge. > > Other than that, I know C++ pretty well: it was my first language > > and I still use it whenever I see fit. I also have some basic Python and > C# > > knowledge. > > 3. I can't say much more than what I've written in previous paragraph. > > 4. 1. Getting familiarized with BioRuby objects, mainly with the way they > > hold data. > > 2. Deciding with features should be visualized. > > 3. In case of presence data with different format but same way of > > visualization, implementing a mechanism converting data to unified > format. > > 4. Writing a module responsible for creating graphical representation of > > data. > > 5. Final testing. > > 6. Writing a documentation. > > 5. Possibly short vacation (less than one week) around beginning of > > July. > > Also, I am from Poland, which means that my summer vacations starts > > from July. Because of that I won't be able to focus only on the project > > until than. What I can do, however, is to start coding earlier. I would > >like > > to familiarize myself with documentation before bonding period starts > (I've > > already began to do it), and when it does start coding right away. Thanks > >to > > that I should have just as much time as if I started in May. > > Other than that I am all about the project. > > > > > > Also, since as I've told I would probably have to start coding a little > > earlier, I am trying to slowly browse the documentation. It's a big project > > though, and I don't know what's important. Do you have any suggestions about > > that? Are there parts that would be especially relevant to the project? Or > > maybe even better, are there any easier tasks to complete? I learn best by > > exercise, so that would be great. I've looked up at github's issues page, > > but haven't found anything like what I am talking about. Maybe I just didn't > > know on what I was looking? > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > From ales.guzik at gmail.com Wed Apr 6 09:27:59 2011 From: ales.guzik at gmail.com (=?UTF-8?B?0JDQu9C10YHRjA==?=) Date: Wed, 6 Apr 2011 12:27:59 +0300 Subject: [BioRuby] BioRuby Wrapper for Command line application (GSOC 2011) Message-ID: Hello. My name is Ales and I'd like to implement BioRuby wrapper for command line applications as my Google Summer of Code 2011 project. 1. Your complete contact information, including full name, physical address, preferred email address, and telephone number, plus other pertinent contact information such as IRC handles, etc. Ales Guzik 4th year student at Belarusian State University of Informatics and Radioelectronics. Belarus, Minsk, P.Brovki st. 3-1 46 ales.guzik at gmail.com +375 25 902 8190 (Belarus) +1 650 336 5853 (Google Voice) skype: ales-guzik IRC, twitter, facebook, github etc.: nekotwi 2. Why you are interested in the project you are proposing and are well-suited to undertake it. This project is interesting for me because it requires metaprogramming - thing I most like in ruby and because it's BioRuby - project I wanted to get familiar with long time ago. I use Ruby more than 2 years for most of my university tasks and daily linux scripting. 2 month ago I started working as Ruby on Rails developer. I have pretty good experience in ruby metaprogramming which is needed for this project. 3. A summary of your programming experience and skills. I have well experience in C, know but not heavily used C++ and Qt, long time ago learned some Erlang, have coded some C# at university but dislike it, played a bit with Android/Java programming. Know and sometimes use Scheme(Racket), now learning some Perl 5. Started learning Ruby somewhere in the beginning of 2nd university year and liked it very much. 4. Programs or projects you have previously authored or contributed to, in particular those available as open-source, including, if applicable, any past Summer of Code involvement. I haven't yet contributed to opensource projects (except for some tiny projects by myself) but really want to. 5. A project plan for the project you are proposing, even if your proposed project is directly based on one of the proposed project ideas for member projects. 1) Get familiar with source code, use cases and documentation of BioRuby and BioRuby-ngs 2) Define specs and write rspec tests for this CLI application wrapper 3) Code to make all tests pass 4) Optimize code for processing BIG ammounts of information 5) Refactor 6) Document undocumented parts 6. Any obligations, vacations, or plans for the summer that may require scheduling during the GSoC work period. I work as rails programmer 30 hours a week. It's like 8:00 - 14:00 GMT+2 DST monday - friday, so I can code for my project 14:30 - 22:00 or even more. It will be like this in june and august. In july I'll be at military training. I'll have time and internet access but can't tell my schedule for now. -- Regards, Ales Guzik ------------------------------------------------------------ e-mail: ales.guzik at gmail.com skype: ales-guzik tel: +375 25 9028190 From bonnal at ingm.org Wed Apr 6 09:48:52 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Wed, 6 Apr 2011 11:48:52 +0200 Subject: [BioRuby] BioRuby Wrapper for Command line application (GSOC 2011) In-Reply-To: References: Message-ID: <4B02CC0A-20DE-4A60-93C3-E7EDACC9BA64@ingm.org> Hello Ales, thank you for submitting your proposal, like Michal: I quote here the discussion with Chris and Christian, if you could write a better time line in form of days/weeks with tasks/objectives I think it would be better: this is the quote from Christian and Chris Hi, Michal: I think your project plan needs to be much more detailed. It might be best in a format similar to the template/example below: Prior to coding ("community bonding period"): -Familiarize myself with BioRuby code base -Learn about graphics within/from Ruby -Discuss ... with mentors/BioRuby community -... -Learn about git, set up my repository Week 1: Goal: Develop necessary utility classes for ... Anticipated problems: None Weeks 2 and 3: Goal: Develop class to visualize intron/exon structures... Anticipated problems: Such and such might not ... Alternatives: If XYZ turns out not feasible, I plan to ... instead Week X: Goal: Unit tests for ... Week Y: Documentation ... Hope this helps, Christian Zmasek ---- Micha?, In general, the proposal should answer the questions below, but should also have a rough timeline on how you would go about coding the project, creating deliverables for the community for testing, etc. This should come with the input of your possible mentor for the project or from others in the bioruby community. The timeline is a little problematic, but the OBF mentors can further discuss that. One thing that will cause a problem is that there is a significant amount of time (about one month) for community bonding, so any coding on a significant project in that period will be tricky. chris ----- Original Message ---- > From: Micha? Koziarski > To: bioruby at lists.open-bio.org > Sent: Tue, April 5, 2011 10:24:22 AM > Subject: [BioRuby] GSoC - project "Represent bio-objects and related > information with images" > > I've completed my application. Chris Fields suggested that I should write it > up, he hasn't specified what parts exactly though. If you have any advice > about it, please let me know. > > I use some of my answers to questions asked here in the application, I hope > that's not a problem: I didn't see much point in rewriting it, since the > meaning would be the same. > > I don't include the first point, about the address, since it's a public ML > and I don't think it's important here. > > I am basing the application on the OBF's template, which I enclose too. > > > 1. Why you are interested in the project you are proposing and are > well-suited to undertake it. > 2. A summary of your programming experience and skills. > 3. Programs or projects you have previously authored or contributed to, > in particular those available as open-source, including, if applicable, any > past Summer of Code involvement. > 4. A project plan for the project you are proposing, even if your > proposed project is directly based on one of the proposed project ideas for > member projects. > 5. Any obligations, vacations, or plans for the summer that may require > scheduling during the GSoC work period. > > > > 1. I find the problem of representing computer data in format > readable by humans interesting, partially because it's so significant: we > could have the best algorithms, the fastest computers, but the output would > be useless if we wouldn't be able to read it. Additionally, I love the idea > of writing code for organisation such as OBF: it makes me think that I do > have, even slightest, impact on science. I must also admit that working > with > Ruby is very tempting, I really enjoy writing Ruby code. > 2. I have fairly strong Ruby knowledge, I have been using it for > about a year and a half. There were no really big projects there though, > the > biggest I've got was probably small LAN IM. Nevertheless, I use Ruby on > daily basis and I am familiar with most of its, even complex, features. > Also, from the beginning of this year I work as a RoR developer. > I've worked on a bigger, team project and now I am developing one solo. > I've > learned a lot here: working with version control systems, developing in > team, operating on other people's code, testing... not to mention further > developing my Ruby knowledge. > Other than that, I know C++ pretty well: it was my first language > and I still use it whenever I see fit. I also have some basic Python and C# > knowledge. > 3. I can't say much more than what I've written in previous paragraph. > 4. 1. Getting familiarized with BioRuby objects, mainly with the way they > hold data. > 2. Deciding with features should be visualized. > 3. In case of presence data with different format but same way of > visualization, implementing a mechanism converting data to unified format. > 4. Writing a module responsible for creating graphical representation of > data. > 5. Final testing. > 6. Writing a documentation. > 5. Possibly short vacation (less than one week) around beginning of > July. > Also, I am from Poland, which means that my summer vacations starts > from July. Because of that I won't be able to focus only on the project > until than. What I can do, however, is to start coding earlier. I would > like > to familiarize myself with documentation before bonding period starts (I've > already began to do it), and when it does start coding right away. Thanks > to > that I should have just as much time as if I started in May. > Other than that I am all about the project. > > > Also, since as I've told I would probably have to start coding a little > earlier, I am trying to slowly browse the documentation. It's a big project > though, and I don't know what's important. Do you have any suggestions about > that? Are there parts that would be especially relevant to the project? Or > maybe even better, are there any easier tasks to complete? I learn best by > exercise, so that would be great. I've looked up at github's issues page, > but haven't found anything like what I am talking about. Maybe I just didn't > know on what I was looking? > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > _______________________________________________ BioRuby Project - http://www.bioruby.org/ BioRuby mailing list BioRuby at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioruby On 06/apr/2011, at 11.27, ????? wrote: > Hello. My name is Ales and I'd like to implement BioRuby wrapper for > command line applications as my Google Summer of Code 2011 project. > > > 1. Your complete contact information, including full name, physical > address, preferred email address, and telephone number, plus other > pertinent contact information such as IRC handles, etc. > > Ales Guzik > 4th year student at Belarusian State University of Informatics and > Radioelectronics. > Belarus, Minsk, P.Brovki st. 3-1 46 > ales.guzik at gmail.com > +375 25 902 8190 (Belarus) > +1 650 336 5853 (Google Voice) > skype: ales-guzik > IRC, twitter, facebook, github etc.: nekotwi > > 2. Why you are interested in the project you are proposing and are > well-suited to undertake it. > > This project is interesting for me because it requires metaprogramming > - thing I most like in ruby and > because it's BioRuby - project I wanted to get familiar with long time ago. > I use Ruby more than 2 years for most of my university tasks and daily > linux scripting. 2 month ago I > started working as Ruby on Rails developer. I have pretty good > experience in ruby metaprogramming which > is needed for this project. > > 3. A summary of your programming experience and skills. > > I have well experience in C, know but not heavily used C++ and Qt, > long time ago learned some Erlang, > have coded some C# at university but dislike it, played a bit with > Android/Java programming. > Know and sometimes use Scheme(Racket), now learning some Perl 5. > Started learning Ruby somewhere in the beginning of 2nd university > year and liked it very much. > > 4. Programs or projects you have previously authored or contributed > to, in particular those available as open-source, including, if > applicable, any past Summer of Code involvement. > > I haven't yet contributed to opensource projects (except for some tiny > projects by myself) but really want to. > > 5. A project plan for the project you are proposing, even if your > proposed project is directly based on one of the proposed project > ideas for member projects. > > 1) Get familiar with source code, use cases and documentation of > BioRuby and BioRuby-ngs > 2) Define specs and write rspec tests for this CLI application wrapper > 3) Code to make all tests pass > 4) Optimize code for processing BIG ammounts of information > 5) Refactor > 6) Document undocumented parts > > 6. Any obligations, vacations, or plans for the summer that may > require scheduling during the GSoC work period. > > I work as rails programmer 30 hours a week. It's like 8:00 - 14:00 > GMT+2 DST monday - friday, so I can code for > my project 14:30 - 22:00 or even more. It will be like this in june and august. > In july I'll be at military training. I'll have time and internet > access but can't tell my schedule for now. > > -- > Regards, > Ales Guzik > ------------------------------------------------------------ > e-mail: ales.guzik at gmail.com > skype: ales-guzik > tel: +375 25 9028190 > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Helius github: https://github.com/helios From michalkoziarski at gmail.com Wed Apr 6 18:14:55 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Wed, 6 Apr 2011 20:14:55 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <981305.71979.qm@web38404.mail.mud.yahoo.com> Message-ID: W dniu 5 kwietnia 2011 22:56 u?ytkownik Chris Fields napisa?: > On Apr 5, 2011, at 3:37 PM, Micha? Koziarski wrote: > > > I have to agree, my plan isn't very specific. But mainly coming up with a > timeline is kind of a guesswork: maybe it's just me, I don't like saying > anything unless I am certain of it, and there's no way at this point to do > this. Anyway, I will prepare what I am able to today, and hopefully catch > someone tomorrow on irc to further discuss some specifics. > > Don't think of it as a strict timeline as much as an overall plan for > development of your project. Timelines for projects are meant to be > malleable and change based on what occurs during development, but w/o > underlying structure then there is no organization of your priorities. > I believe that I understand it better now. I attach something more specific. I am still working on it, but there are some questions I would like to ask about what I've completed so far. But first, the timeline: Prior to coding: - Familiarize myself with BioRuby code in general perspective. - Prepare my environment to work with and learn about Rubyvis. - Take a closer look at how BioRuby objects stores data. - Prepare ideas on how to unify that data format. The goal is to create one format that would easily allow to base visualization module on it. If that turn out to be impossible divide objects in as small number of groups as possible and propose formats for each one of them. - Discuss these ideas, decide which one to choose. - Discuss what set of functions user should have access to. - Discuss which features should be visualized, and in which order it should be implemented. - Decide if there are any other tools that could help with developing the project, if so learn about them. - Final preparation for coding: preparing environment, creating git repo. Week 1: Goal: choose one representative type of BioRuby object and develop class that would convert its data to proposed format. That should come along with unit tests. Week 2: Goal: develop graphical module that would create image files based on data in unified format and provide user interface, write unit tests. On this point it should be possible to fully visualize chosen BioRuby object. Weeks 3 to 8: Goal: basing on first weeks work, prepare similar classes for all of the remaining BioRuby objects. Each class should have unit tests. Week 9: Goal: develop mechanism of browsing images in shell. It should include simple search and a way of opening images. Week 10: Goal: write integration tests. Weeks 11 and 12: Goal: write documentation. I would like to be more specific about what should be done from weeks 3 to 8, though. It would be nice to plan some time for every object that needs visualization, but I don't know which that would be exactly. Could you give me a hand with this? And in general, as always I would be happy to hear some feedback. > > > Chris: could you explain why any coding at community bonding period would > be hard? I assumed that a big part of it is getting familiar with > documentation, and with that done before I would have some more time to > code. Of course, it wouldn't be a full-time coding, but I thought that at > this point I would have all the knowledge to start writing, so why not to. > Maybe I am missing something, in that case tell me please. > > In general, little coding occurs during community bonding; the time is > spent asking questions on the API, working out final priorities, details on > the project, etc with the community (mentor in particular). I'm not sure of > your level of experience with BioRuby, but from my experience with BioPerl > and past GSoC projects the codebase and API (and documentation, or lack > thereof) can be daunting for a beginner. So, mentioning that you will use > that period to code b/c of time issues during the scheduled period is a bit > premature in my opinion w/o more specifics, but that's really for the > BioRuby folks to decide. > I do understand your point. However, I didn't mean to spend less time on getting to know the codebase, I just wanted to start doing it earlier. Anyhow, maybe you have some suggestions about how to solve this time issue? It's a matter of coding for one month for about 30 hours a week. I based my proposition on something I read on one of GSoC suggestions page. But yes, you may be right that BioRuby is to big project for such a approach. > > I think Christian made some more specific notes on what is expected. > > chris > > > Christian: yes, it was very helpful, I've read some example plans before, > but I couldn't really relate them to my project. Now I have a little clearer > picture of what to write. Thanks for that, hopefully tomorrow I will present > something in that manner. > > > > > > 2011/4/5 Christian Zmasek > > Hi, Michal: > > > > I think your project plan needs to be much more detailed. > > > > It might be best in a format similar to the template/example below: > > > > Prior to coding ("community bonding period"): > > -Familiarize myself with BioRuby code base > > -Learn about graphics within/from Ruby > > -Discuss ... with mentors/BioRuby community > > -... > > -Learn about git, set up my repository > > > > > > > > Week 1: > > Goal: Develop necessary utility classes for ... > > Anticipated problems: None > > > > Weeks 2 and 3: > > Goal: Develop class to visualize intron/exon structures... > > Anticipated problems: Such and such might not ... > > Alternatives: If XYZ turns out not feasible, I plan to ... instead > > > > Week X: > > Goal: Unit tests for ... > > > > > > > > Week Y: > > Documentation ... > > > > Hope this helps, > > > > Christian Zmasek > > > > > > > > > > ----- Original Message ---- > > > From: Micha? Koziarski > > > To: bioruby at lists.open-bio.org > > > Sent: Tue, April 5, 2011 10:24:22 AM > > > Subject: [BioRuby] GSoC - project "Represent bio-objects and related > > >information with images" > > > > > > I've completed my application. Chris Fields suggested that I should > write it > > > up, he hasn't specified what parts exactly though. If you have any > advice > > > about it, please let me know. > > > > > > I use some of my answers to questions asked here in the application, I > hope > > > that's not a problem: I didn't see much point in rewriting it, since > the > > > meaning would be the same. > > > > > > I don't include the first point, about the address, since it's a > public ML > > > and I don't think it's important here. > > > > > > I am basing the application on the OBF's template, which I enclose > too. > > > > > > > > > 1. Why you are interested in the project you are proposing and are > > > well-suited to undertake it. > > > 2. A summary of your programming experience and skills. > > > 3. Programs or projects you have previously authored or contributed > to, > > > in particular those available as open-source, including, if > applicable, > > any > > > past Summer of Code involvement. > > > 4. A project plan for the project you are proposing, even if your > > > proposed project is directly based on one of the proposed project > ideas > > for > > > member projects. > > > 5. Any obligations, vacations, or plans for the summer that may > require > > > scheduling during the GSoC work period. > > > > > > > > > > > > 1. I find the problem of representing computer data in format > > > readable by humans interesting, partially because it's so > significant: we > > > could have the best algorithms, the fastest computers, but the > output > > would > > > be useless if we wouldn't be able to read it. Additionally, I love > the > > idea > > > of writing code for organisation such as OBF: it makes me think > that I do > > > have, even slightest, impact on science. I must also admit that > working > > >with > > > Ruby is very tempting, I really enjoy writing Ruby code. > > > 2. I have fairly strong Ruby knowledge, I have been using it > for > > > about a year and a half. There were no really big projects there > though, > > >the > > > biggest I've got was probably small LAN IM. Nevertheless, I use > Ruby on > > > daily basis and I am familiar with most of its, even complex, > features. > > > Also, from the beginning of this year I work as a RoR > developer. > > > I've worked on a bigger, team project and now I am developing one > solo. > > >I've > > > learned a lot here: working with version control systems, > developing in > > > team, operating on other people's code, testing... not to mention > further > > > developing my Ruby knowledge. > > > Other than that, I know C++ pretty well: it was my first > language > > > and I still use it whenever I see fit. I also have some basic > Python and > > C# > > > knowledge. > > > 3. I can't say much more than what I've written in previous > paragraph. > > > 4. 1. Getting familiarized with BioRuby objects, mainly with the > way they > > > hold data. > > > 2. Deciding with features should be visualized. > > > 3. In case of presence data with different format but same way of > > > visualization, implementing a mechanism converting data to unified > > format. > > > 4. Writing a module responsible for creating graphical > representation of > > > data. > > > 5. Final testing. > > > 6. Writing a documentation. > > > 5. Possibly short vacation (less than one week) around > beginning of > > > July. > > > Also, I am from Poland, which means that my summer vacations > starts > > > from July. Because of that I won't be able to focus only on the > project > > > until than. What I can do, however, is to start coding earlier. I > would > > >like > > > to familiarize myself with documentation before bonding period > starts > > (I've > > > already began to do it), and when it does start coding right away. > Thanks > > >to > > > that I should have just as much time as if I started in May. > > > Other than that I am all about the project. > > > > > > > > > Also, since as I've told I would probably have to start coding a > little > > > earlier, I am trying to slowly browse the documentation. It's a big > project > > > though, and I don't know what's important. Do you have any suggestions > about > > > that? Are there parts that would be especially relevant to the > project? Or > > > maybe even better, are there any easier tasks to complete? I learn > best by > > > exercise, so that would be great. I've looked up at github's issues > page, > > > but haven't found anything like what I am talking about. Maybe I just > didn't > > > know on what I was looking? > > > _______________________________________________ > > > BioRuby Project - http://www.bioruby.org/ > > > BioRuby mailing list > > > BioRuby at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > > > > From cjfields at illinois.edu Wed Apr 6 18:22:25 2011 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 6 Apr 2011 13:22:25 -0500 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <981305.71979.qm@web38404.mail.mud.yahoo.com> Message-ID: <938AF391-AC73-4558-8902-8954ADC2AE90@illinois.edu> On Apr 6, 2011, at 1:14 PM, Micha? Koziarski wrote: > ... > > Chris: could you explain why any coding at community bonding period would be hard? I assumed that a big part of it is getting familiar with documentation, and with that done before I would have some more time to code. Of course, it wouldn't be a full-time coding, but I thought that at this point I would have all the knowledge to start writing, so why not to. Maybe I am missing something, in that case tell me please. > > In general, little coding occurs during community bonding; the time is spent asking questions on the API, working out final priorities, details on the project, etc with the community (mentor in particular). I'm not sure of your level of experience with BioRuby, but from my experience with BioPerl and past GSoC projects the codebase and API (and documentation, or lack thereof) can be daunting for a beginner. So, mentioning that you will use that period to code b/c of time issues during the scheduled period is a bit premature in my opinion w/o more specifics, but that's really for the BioRuby folks to decide. > > I do understand your point. However, I didn't mean to spend less time on getting to know the codebase, I just wanted to start doing it earlier. Anyhow, maybe you have some suggestions about how to solve this time issue? It's a matter of coding for one month for about 30 hours a week. > > I based my proposition on something I read on one of GSoC suggestions page. But yes, you may be right that BioRuby is to big project for such a approach. Actually I raised this issue on the GSoC mentors list, and the general consensus is that it is up to your specific organization (which in this case means that the OBF mentors, who would rely on the good instincts of the BioRuby mentors), as time isn't the only factor involved; experience, attainable project goals, benefits to the project in general, etc are also important. So, if the BioRuby mentors don't have a problem with this, then I fine as well. -c From cmzmasek at yahoo.com Wed Apr 6 18:48:32 2011 From: cmzmasek at yahoo.com (Christian Zmasek) Date: Wed, 6 Apr 2011 11:48:32 -0700 (PDT) Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <981305.71979.qm@web38404.mail.mud.yahoo.com> Message-ID: <313339.26768.qm@web38403.mail.mud.yahoo.com> Hi, Micha?: You timeline is much better now! I put some comments/question into your text (see below). > Week 1: > Goal: choose one representative type of BioRuby object and develop class > that would convert its data to proposed format. That should come along with > unit tests. This is a good idea -- to deliver a proof of concept first! Did you think about how exactly the image(s) will be produced? Which library (if any) do you plan to use? Also do you plan to produce (interactive) graphics on the fly and/or create (static) image files (such as .png) to be viewed with other software? > Week 2: > Goal: develop graphical module that would create image files based on > data in unified format and provide user interface, write unit tests. > > On this point it should be possible to fully visualize chosen BioRuby > object. > > Weeks 3 to 8: > Goal: basing on first weeks work, prepare similar classes for all of the > remaining BioRuby objects. Each class should have unit tests. > > Week 9: > Goal: develop mechanism of browsing images in shell. It should include > simple search and a way of opening images. > > Week 10: > Goal: write integration tests. > > Weeks 11 and 12: > Goal: write documentation. > > I would like to be more specific about what should be done from weeks 3 to > 8, though. It would be nice to plan some time for every object that needs > visualization, but I don't know which that would be exactly. Could you give > me a hand with this? I think Raoul can answer this better. I guess a good candidate would be sequence objects with features, such as intron/exon, mutations, etc. I have doubts about this "develop mechanism of browsing images in shell. It should include simple search and a way of opening images." What about anticipated problems? Can you propose alternatives for things which might not work as planned? Christian From francesco.strozzi at gmail.com Wed Apr 6 19:02:56 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Wed, 6 Apr 2011 21:02:56 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: <313339.26768.qm@web38403.mail.mud.yahoo.com> References: <981305.71979.qm@web38404.mail.mud.yahoo.com> <313339.26768.qm@web38403.mail.mud.yahoo.com> Message-ID: Hi all, 2011/4/6 Christian Zmasek > Hi, Micha?: > > You timeline is much better now! > > I put some comments/question into your text (see below). > > > > > Week 1: > > Goal: choose one representative type of BioRuby object and develop > class > > that would convert its data to proposed format. That should come along > with > > unit tests. > > > This is a good idea -- to deliver a proof of concept first! > > Did you think about how exactly the image(s) will be produced? > > Which library (if any) do you plan to use? > > > Also do you plan to produce (interactive) graphics on the fly and/or create > (static) image files (such as .png) to be viewed with other software? > > If I can suggest a couple of libraries that should be used for this project I will say: - BioGraphics for sequence/genomic features display http://bio-graphics.rubyforge.org/ - Rubyvis for everything else (a great library and fits perfectly well for web visulisation since it's producing SVG images) http://rubyvis.rubyforge.org/ Cheers -- Francesco From michalkoziarski at gmail.com Wed Apr 6 19:25:10 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Wed, 6 Apr 2011 21:25:10 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: <313339.26768.qm@web38403.mail.mud.yahoo.com> References: <981305.71979.qm@web38404.mail.mud.yahoo.com> <313339.26768.qm@web38403.mail.mud.yahoo.com> Message-ID: 2011/4/6 Christian Zmasek > Hi, Micha?: > > You timeline is much better now! > > I put some comments/question into your text (see below). > > > > > Week 1: > > Goal: choose one representative type of BioRuby object and develop > class > > that would convert its data to proposed format. That should come along > with > > unit tests. > > > This is a good idea -- to deliver a proof of concept first! > > Did you think about how exactly the image(s) will be produced? > I thought about using Rubyvis to produce images. > > Which library (if any) do you plan to use? > I've read a little about the Rubyvis and it seems like a fine solution, so I would like to go with that, but I am open for suggestions. > > > Also do you plan to produce (interactive) graphics on the fly and/or create > (static) image files (such as .png) to be viewed with other software? > I think that since one of the purposes of the project is to prepare images for use in web, they should be static from the beginning. It would be great to create an interactive version too, so that you could modify data on the fly and perhaps change data by modifing a graphic, but I don't think that I would make it in time. > > > > > > Week 2: > > Goal: develop graphical module that would create image files based > on > > data in unified format and provide user interface, write unit tests. > > > > On this point it should be possible to fully visualize chosen > BioRuby > > object. > > > > Weeks 3 to 8: > > Goal: basing on first weeks work, prepare similar classes for all of > the > > remaining BioRuby objects. Each class should have unit tests. > > > > Week 9: > > Goal: develop mechanism of browsing images in shell. It should > include > > simple search and a way of opening images. > > > > Week 10: > > Goal: write integration tests. > > > > Weeks 11 and 12: > > Goal: write documentation. > > > > I would like to be more specific about what should be done from weeks 3 > to > > 8, though. It would be nice to plan some time for every object that > needs > > visualization, but I don't know which that would be exactly. Could you > give > > me a hand with this? > > I think Raoul can answer this better. > > > I guess a good candidate would be sequence objects with features, such as > intron/exon, mutations, etc. > > > I have doubts about this "develop mechanism of browsing images in shell. > It > should include simple search and a way of opening images." > Could you explain why? > > What about anticipated problems? Can you propose alternatives for things > which > might not work as planned? > Yes, I am working on that right now, but strangely I can't come up with many problems to anticipate. Perhaps you have some suggestions about this? Anyway, I will most certainly update that. > > Christian > > From michalkoziarski at gmail.com Wed Apr 6 19:34:07 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Wed, 6 Apr 2011 21:34:07 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <981305.71979.qm@web38404.mail.mud.yahoo.com> <313339.26768.qm@web38403.mail.mud.yahoo.com> Message-ID: Hi Francesco, 2011/4/6 Francesco Strozzi > Hi all, > > 2011/4/6 Christian Zmasek > >> Hi, Micha?: >> >> You timeline is much better now! >> >> I put some comments/question into your text (see below). >> >> >> >> > Week 1: >> > Goal: choose one representative type of BioRuby object and develop >> class >> > that would convert its data to proposed format. That should come along >> with >> > unit tests. >> >> >> This is a good idea -- to deliver a proof of concept first! >> >> Did you think about how exactly the image(s) will be produced? >> >> Which library (if any) do you plan to use? >> >> >> Also do you plan to produce (interactive) graphics on the fly and/or >> create >> (static) image files (such as .png) to be viewed with other software? >> >> > If I can suggest a couple of libraries that should be used for this project > I will say: > > - BioGraphics for sequence/genomic features display > http://bio-graphics.rubyforge.org/ > - Rubyvis for everything else (a great library and fits perfectly well for > web visulisation since it's producing SVG images) > http://rubyvis.rubyforge.org/ > I've read about the Rubyvis before, but not about the BioGraphics. Thanks for that, it seems like a great lib. I am just worried that it could force implementing two separate ways of creating graphics, with other style, convention and so on. > > > Cheers > > > -- > > Francesco > > From bonnal at ingm.org Wed Apr 6 20:16:36 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Wed, 06 Apr 2011 22:16:36 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: <313339.26768.qm@web38403.mail.mud.yahoo.com> Message-ID: <20110406201636.3f58bcc0@mail.ingm.it> Hi Michal, the time line is more detailed now. As Francesco suggested and also reported on our page we suggest RubyVis library, Claudio the coder of the binding offers his help and this is a very good news for us. Week 9: what do you mean for browsing images in shell ? I can't grasp the benefit now, but we can discuss. The main problem is how to control the application which displays the image; for web browsers there are techniques but are not so easy. I'm just thinking to an add-on for this week: if we have different types of data that we can display quite easily on the web(done in the previous weeks) , why not spending this time to enrich the images with controls (bars, check boxes, interaction in general). This part requires a skill in javascript. http://vis.stanford.edu/protovis/ex/cartogram-full.html Or another interesting feature would be: adding layers of information to the standard image. Note: perhaps these ideas are a bit complicate for 1 week but it would be interesting to evaluate the feasibility. I forgot to mention, in some case I think that if there are web services which produce images that services could be used. Consider the possibility to display Venn diagrams Google has one service http://code.google.com/intl/it-IT/apis/chart/docs/gallery/venn_charts.html or another one is http://bioinfogp.cnb.csic.es/tools/venny/index.html. Sets are a kind of data type that in my daily work I have to display with a high frequency, specially when the boss needs to make reports :-) So we arrived to the which bioruby objects we want to display. This is a quite complex question because some are there and other are not. This library as been always sequence/feature centric (please correct me if I'm wrong), because we were used to demand to R tasks more statistics. Main areas are * NGS: display create coverage alignemnt for a region with the possible annotation that are accessible from bioruby * Matrix: display heatmaps, scatter plots, bars ( I wrote a very alpha lib for handling real time PCR and gene expression datasets -not images-) * Sets: a seq could be generated from any kind of analysis, enrichment, annotation, reports ** reports could be meta-objects for instance the results of an allignment or mapping or gene quantification when you need to compare multiple populations or technical replicates * Phylo (i'm not an expert) with the idea to produce high quality images ready to be published. These are a bunch of ideas and words. About tomorrow IRC meeting, @work they scheduled a meeting for (my) afternoon, I'll do my best to be on IRC. Feel free to contact who is around. Regards. _____ From: Christian Zmasek [mailto:cmzmasek at yahoo.com] To: Micha? Koziarski [mailto:michalkoziarski at gmail.com], Chris Fields [mailto:cjfields at illinois.edu], bioruby at lists.open-bio.org Cc: Raoul Bonnal [mailto:bonnalraoul at ingm.it] Sent: Wed, 06 Apr 2011 20:48:32 +0200 Subject: Re: [BioRuby] GSoC - project "Represent bio-objects and related information with images" Hi, Micha?: You timeline is much better now! I put some comments/question into your text (see below). > Week 1: > Goal: choose one representative type of BioRuby object and develop class > that would convert its data to proposed format. That should come along with > unit tests. This is a good idea -- to deliver a proof of concept first! Did you think about how exactly the image(s) will be produced? Which library (if any) do you plan to use? Also do you plan to produce (interactive) graphics on the fly and/or create (static) image files (such as .png) to be viewed with other software? > Week 2: > Goal: develop graphical module that would create image files based on > data in unified format and provide user interface, write unit tests. > > On this point it should be possible to fully visualize chosen BioRuby > object. > > Weeks 3 to 8: > Goal: basing on first weeks work, prepare similar classes for all of the > remaining BioRuby objects. Each class should have unit tests. > > Week 9: > Goal: develop mechanism of browsing images in shell. It should include > simple search and a way of opening images. > > Week 10: > Goal: write integration tests. > > Weeks 11 and 12: > Goal: write documentation. > > I would like to be more specific about what should be done from weeks 3 to > 8, though. It would be nice to plan some time for every object that needs > visualization, but I don't know which that would be exactly. Could you give > me a hand with this? I think Raoul can answer this better. I guess a good candidate would be sequence objects with features, such as intron/exon, mutations, etc. What about anticipated problems? Can you propose alternatives for things which might not work as planned? Christian From michalkoziarski at gmail.com Wed Apr 6 21:06:12 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Wed, 6 Apr 2011 23:06:12 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: <20110406201636.3f58bcc0@mail.ingm.it> References: <313339.26768.qm@web38403.mail.mud.yahoo.com> <20110406201636.3f58bcc0@mail.ingm.it> Message-ID: 2011/4/6 Raoul Bonnal > Hi Michal, > the time line is more detailed now. > As Francesco suggested and also reported on our page we suggest RubyVis > library, Claudio the coder of the binding offers his help and this is a very > good news for us. > > Week 9: what do you mean for browsing images in shell ? I can't grasp the > benefit now, but we can discuss. The main problem is how to control the > application which displays the image; for web browsers there are techniques > but are not so easy. > The idea was to be able to view image right after it's created, not having to juggle with opened folders, terminals or whatever else someone could use for that. I thought that it would be useful and in some cases could save us some mechanic job, but that's not an essential thing for sure. > I'm just thinking to an add-on for this week: if we have different types of > data that we can display quite easily on the web(done in the previous weeks) > , why not spending this time to enrich the images with controls (bars, check > boxes, interaction in general). This part requires a skill in javascript. > http://vis.stanford.edu/protovis/ex/cartogram-full.html > Or another interesting feature would be: adding layers of information to > the standard image. > Note: perhaps these ideas are a bit complicate for 1 week but it would be > interesting to evaluate the feasibility. > I really like the enrichment idea, it's both useful and great looking :) The question is: how exactly should we enrich those images? I think that depending on what exactly we would like to achieve one week could be enough. For example some on-demand displaying (from the set of images only those which we check are currently visible) is not hard to do and quite useful. > > I forgot to mention, in some case I think that if there are web services > which produce images that services could be used. Consider the possibility > to display Venn diagrams Google has one service > http://code.google.com/intl/it-IT/apis/chart/docs/gallery/venn_charts.htmlor another one is > http://bioinfogp.cnb.csic.es/tools/venny/index.html. > Sets are a kind of data type that in my daily work I have to display with a > high frequency, specially when the boss needs to make reports :-) > Again, I am a little worried about the integrity. I mean, of course, if implementing any of those would have to take a significant amount of time than it's probably better not to carry about it so much and spend time developing a new feature, but otherwise it's just unnecessary complicating the code. At least that's my opinion. > > So we arrived to the which bioruby objects we want to display. This is a > quite complex question because some are there and other are not. > This library as been always sequence/feature centric (please correct me if > I'm wrong), because we were used to demand to R tasks more statistics. > Main areas are > * NGS: display create coverage alignemnt for a region with the possible > annotation that are accessible from bioruby > * Matrix: display heatmaps, scatter plots, bars ( I wrote a very alpha lib > for handling real time PCR and gene expression datasets -not images-) > * Sets: a seq could be generated from any kind of analysis, enrichment, > annotation, reports > ** reports could be meta-objects for instance the results of an allignment > or mapping or gene quantification when you need to compare multiple > populations or technical replicates > * Phylo (i'm not an expert) > I will have some additional questions about that tomorrow, right now my brain refuses to work properly. > > with the idea to produce high quality images ready to be published. > > These are a bunch of ideas and words. > About tomorrow IRC meeting, @work they scheduled a meeting for (my) > afternoon, I'll do my best to be on IRC. Feel free to contact who is around. > I've tried that today, no one from BioRuby was around though. I guess that's because I am dropping by too late. > > Regards. > > ------------------------------ > *From:* Christian Zmasek [mailto:cmzmasek at yahoo.com] > *To:* Micha? Koziarski [mailto:michalkoziarski at gmail.com], Chris Fields > [mailto:cjfields at illinois.edu], bioruby at lists.open-bio.org > *Cc:* Raoul Bonnal [mailto:bonnalraoul at ingm.it] > *Sent:* Wed, 06 Apr 2011 20:48:32 +0200 > *Subject:* Re: [BioRuby] GSoC - project "Represent bio-objects and related > information with images" > > > Hi, Micha?: > > You timeline is much better now! > > I put some comments/question into your text (see below). > > > > > Week 1: > > Goal: choose one representative type of BioRuby object and develop class > > that would convert its data to proposed format. That should come along > with > > unit tests. > > > This is a good idea -- to deliver a proof of concept first! > > Did you think about how exactly the image(s) will be produced? > > Which library (if any) do you plan to use? > > > Also do you plan to produce (interactive) graphics on the fly and/or create > > (static) image files (such as .png) to be viewed with other software? > > > > > > Week 2: > > Goal: develop graphical module that would create image files based on > > data in unified format and provide user interface, write unit tests. > > > > On this point it should be possible to fully visualize chosen BioRuby > > object. > > > > Weeks 3 to 8: > > Goal: basing on first weeks work, prepare similar classes for all of the > > remaining BioRuby objects. Each class should have unit tests. > > > > Week 9: > > Goal: develop mechanism of browsing images in shell. It should include > > simple search and a way of opening images. > > > > Week 10: > > Goal: write integration tests. > > > > Weeks 11 and 12: > > Goal: write documentation. > > > > I would like to be more specific about what should be done from weeks 3 > to > > 8, though. It would be nice to plan some time for every object that needs > > visualization, but I don't know which that would be exactly. Could you > give > > me a hand with this? > > I think Raoul can answer this better. > > > I guess a good candidate would be sequence objects with features, such as > intron/exon, mutations, etc. > > > > > What about anticipated problems? Can you propose alternatives for things > which > might not work as planned? > > Christian > > From missy at be.to Thu Apr 7 05:03:30 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Thu, 07 Apr 2011 14:03:30 +0900 Subject: [BioRuby] A new plugin: bio-genomic-interval Message-ID: <4D9D45A2.9070608@be.to> Hi all, I have uploaded a new Bioruby plugin 'bio-genomic-interval'. The Bio::GenomicInterval class is designed to handle genomic intervals such as "chr1:123-456". The class has methods to detect the overlapping status between two intervals. It may help to avoid messy case branching and improve readability of codes. Developmental tools for BioRuby plugin and documents in the BioRuby wiki were very helpful. Thank you all the authors. Please see also the followings: GitHub - https://github.com/misshie/bioruby-genomic-interval RubyGems.org - https://rubygems.org/gems/bio-genomic-interval Sincerely yours, Hiro. -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From francesco.strozzi at gmail.com Thu Apr 7 14:33:10 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Thu, 7 Apr 2011 16:33:10 +0200 Subject: [BioRuby] BioRuby Wrapper for Command line application (GSOC 2011) In-Reply-To: <4B02CC0A-20DE-4A60-93C3-E7EDACC9BA64@ingm.org> References: <4B02CC0A-20DE-4A60-93C3-E7EDACC9BA64@ingm.org> Message-ID: Hi Ales, did you had the chance to update your proposal on BioRuby Wrapper for the GSoC ? Deadline is tomorrow for student application and we think with this proposal we could be able to get some interesting results. But for your application to have a better chance to be considered and evaluated you should provide an updated timeline (even a draft but a bit more detailed) with the activities and tasks broken down into weeks. If you need some help or advise please write here on the Maling List and we will provide our contributions. Cheers Francesco On Wed, Apr 6, 2011 at 11:48, Raoul Bonnal wrote: > Hello Ales, > thank you for submitting your proposal, > like Michal: > I quote here the discussion with Chris and Christian, if you could write a > better time line in form of days/weeks with tasks/objectives I think it > would be better: > > this is the quote from Christian and Chris > > Hi, Michal: > > I think your project plan needs to be much more detailed. > > It might be best in a format similar to the template/example below: > > Prior to coding ("community bonding period"): > -Familiarize myself with BioRuby code base > -Learn about graphics within/from Ruby > -Discuss ... with mentors/BioRuby community > -... > -Learn about git, set up my repository > > > > Week 1: > Goal: Develop necessary utility classes for ... > Anticipated problems: None > > Weeks 2 and 3: > Goal: Develop class to visualize intron/exon structures... > Anticipated problems: Such and such might not ... > Alternatives: If XYZ turns out not feasible, I plan to ... instead > > Week X: > Goal: Unit tests for ... > > > > Week Y: > Documentation ... > > Hope this helps, > > Christian Zmasek > ---- > Micha?, > > In general, the proposal should answer the questions below, but should also > have a rough timeline on how you would go about coding the project, creating > deliverables for the community for testing, etc. This should come with the > input of your possible mentor for the project or from others in the bioruby > community. > > The timeline is a little problematic, but the OBF mentors can further > discuss that. One thing that will cause a problem is that there is a > significant amount of time (about one month) for community bonding, so any > coding on a significant project in that period will be tricky. > > chris > > > > ----- Original Message ---- > > From: Micha? Koziarski > > To: bioruby at lists.open-bio.org > > Sent: Tue, April 5, 2011 10:24:22 AM > > Subject: [BioRuby] GSoC - project "Represent bio-objects and related > > information with images" > > > > I've completed my application. Chris Fields suggested that I should write > it > > up, he hasn't specified what parts exactly though. If you have any > advice > > about it, please let me know. > > > > I use some of my answers to questions asked here in the application, I > hope > > that's not a problem: I didn't see much point in rewriting it, since the > > meaning would be the same. > > > > I don't include the first point, about the address, since it's a public > ML > > and I don't think it's important here. > > > > I am basing the application on the OBF's template, which I enclose too. > > > > > > 1. Why you are interested in the project you are proposing and are > > well-suited to undertake it. > > 2. A summary of your programming experience and skills. > > 3. Programs or projects you have previously authored or contributed > to, > > in particular those available as open-source, including, if > applicable, > any > > past Summer of Code involvement. > > 4. A project plan for the project you are proposing, even if your > > proposed project is directly based on one of the proposed project > ideas > for > > member projects. > > 5. Any obligations, vacations, or plans for the summer that may > require > > scheduling during the GSoC work period. > > > > > > > > 1. I find the problem of representing computer data in format > > readable by humans interesting, partially because it's so significant: > we > > could have the best algorithms, the fastest computers, but the output > would > > be useless if we wouldn't be able to read it. Additionally, I love the > idea > > of writing code for organisation such as OBF: it makes me think that I > do > > have, even slightest, impact on science. I must also admit that > working > > with > > Ruby is very tempting, I really enjoy writing Ruby code. > > 2. I have fairly strong Ruby knowledge, I have been using it for > > about a year and a half. There were no really big projects there > though, > > the > > biggest I've got was probably small LAN IM. Nevertheless, I use Ruby > on > > daily basis and I am familiar with most of its, even complex, > features. > > Also, from the beginning of this year I work as a RoR developer. > > I've worked on a bigger, team project and now I am developing one > solo. > > I've > > learned a lot here: working with version control systems, developing > in > > team, operating on other people's code, testing... not to mention > further > > developing my Ruby knowledge. > > Other than that, I know C++ pretty well: it was my first language > > and I still use it whenever I see fit. I also have some basic Python > and > C# > > knowledge. > > 3. I can't say much more than what I've written in previous paragraph. > > 4. 1. Getting familiarized with BioRuby objects, mainly with the way > they > > hold data. > > 2. Deciding with features should be visualized. > > 3. In case of presence data with different format but same way of > > visualization, implementing a mechanism converting data to unified > format. > > 4. Writing a module responsible for creating graphical representation > of > > data. > > 5. Final testing. > > 6. Writing a documentation. > > 5. Possibly short vacation (less than one week) around beginning > of > > July. > > Also, I am from Poland, which means that my summer vacations > starts > > from July. Because of that I won't be able to focus only on the > project > > until than. What I can do, however, is to start coding earlier. I > would > > like > > to familiarize myself with documentation before bonding period starts > (I've > > already began to do it), and when it does start coding right away. > Thanks > > to > > that I should have just as much time as if I started in May. > > Other than that I am all about the project. > > > > > > Also, since as I've told I would probably have to start coding a little > > earlier, I am trying to slowly browse the documentation. It's a big > project > > though, and I don't know what's important. Do you have any suggestions > about > > that? Are there parts that would be especially relevant to the project? > Or > > maybe even better, are there any easier tasks to complete? I learn best > by > > exercise, so that would be great. I've looked up at github's issues > page, > > but haven't found anything like what I am talking about. Maybe I just > didn't > > know on what I was looking? > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > > On 06/apr/2011, at 11.27, ????? wrote: > > > Hello. My name is Ales and I'd like to implement BioRuby wrapper for > > command line applications as my Google Summer of Code 2011 project. > > > > > > 1. Your complete contact information, including full name, physical > > address, preferred email address, and telephone number, plus other > > pertinent contact information such as IRC handles, etc. > > > > Ales Guzik > > 4th year student at Belarusian State University of Informatics and > > Radioelectronics. > > Belarus, Minsk, P.Brovki st. 3-1 46 > > ales.guzik at gmail.com > > +375 25 902 8190 (Belarus) > > +1 650 336 5853 (Google Voice) > > skype: ales-guzik > > IRC, twitter, facebook, github etc.: nekotwi > > > > 2. Why you are interested in the project you are proposing and are > > well-suited to undertake it. > > > > This project is interesting for me because it requires metaprogramming > > - thing I most like in ruby and > > because it's BioRuby - project I wanted to get familiar with long time > ago. > > I use Ruby more than 2 years for most of my university tasks and daily > > linux scripting. 2 month ago I > > started working as Ruby on Rails developer. I have pretty good > > experience in ruby metaprogramming which > > is needed for this project. > > > > 3. A summary of your programming experience and skills. > > > > I have well experience in C, know but not heavily used C++ and Qt, > > long time ago learned some Erlang, > > have coded some C# at university but dislike it, played a bit with > > Android/Java programming. > > Know and sometimes use Scheme(Racket), now learning some Perl 5. > > Started learning Ruby somewhere in the beginning of 2nd university > > year and liked it very much. > > > > 4. Programs or projects you have previously authored or contributed > > to, in particular those available as open-source, including, if > > applicable, any past Summer of Code involvement. > > > > I haven't yet contributed to opensource projects (except for some tiny > > projects by myself) but really want to. > > > > 5. A project plan for the project you are proposing, even if your > > proposed project is directly based on one of the proposed project > > ideas for member projects. > > > > 1) Get familiar with source code, use cases and documentation of > > BioRuby and BioRuby-ngs > > 2) Define specs and write rspec tests for this CLI application wrapper > > 3) Code to make all tests pass > > 4) Optimize code for processing BIG ammounts of information > > 5) Refactor > > 6) Document undocumented parts > > > > 6. Any obligations, vacations, or plans for the summer that may > > require scheduling during the GSoC work period. > > > > I work as rails programmer 30 hours a week. It's like 8:00 - 14:00 > > GMT+2 DST monday - friday, so I can code for > > my project 14:30 - 22:00 or even more. It will be like this in june and > august. > > In july I'll be at military training. I'll have time and internet > > access but can't tell my schedule for now. > > > > -- > > Regards, > > Ales Guzik > > ------------------------------------------------------------ > > e-mail: ales.guzik at gmail.com > > skype: ales-guzik > > tel: +375 25 9028190 > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > -- > Ra > > linkedin: http://it.linkedin.com/in/raoulbonnal > twitter: http://twitter.com/ilpuccio > skype: ilpuccio > irc.freenode.net: Helius > github: https://github.com/helios > > > > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Francesco From ales.guzik at gmail.com Thu Apr 7 16:24:45 2011 From: ales.guzik at gmail.com (=?UTF-8?B?0JDQu9C10YHRjA==?=) Date: Thu, 7 Apr 2011 19:24:45 +0300 Subject: [BioRuby] BioRuby Wrapper for Command line application (GSOC 2011) In-Reply-To: References: <4B02CC0A-20DE-4A60-93C3-E7EDACC9BA64@ingm.org> Message-ID: Sorry for this dellay. I just wanted to polish timeline and better understand for myself how will I undertake this project. ** Timeline * getting in (4 weeks) 27 apr - 24 may - getting familiar with BioRuby project (2-3 weeks) - getting into bioinformatics basics (at least 1 week) - getting into project goals and project usage (1 week) - reading articles about BioRuby - reading usage documentation - checking out usage examples - getting into source codebase (1 week) - reading source code documentation (4 days) - looking through source code (2 days) - defining coding guidelines (1 evening) - getting into comunity (in parallel with above) - reading mailing list archive (2-3 days) - hanging up on IRC (all the time) - getting familiar with problem (1-2 weeks) - finding examples of applications that will be used with this wrapper - getting familiar with EMBOSS and ACD configuration files - exploring ways to define wrapper configuration * coding-1 (7 weeks) 25 may - 11 july - writing specs (4 weeks) - defining complete API/DSL for end-users (1 week) - defining interface for adding new CLI tools and EMBOSS suites. (1 week) - defining additional specs (1 week) - writing code (3 weeks) - writing code for API generation (1 week) - writing code for interprocess communication and data passing (1-2 week) 0-1 additional week to have for finishing all this stuff. * mid-term evaluation (5 days) 11 july - 15 july At this moment we have complete API/DSL specs and code wich allows us wrapping CLI applications. * coding 2 (4 weeks) 17 july - 16 aug - writing ACD file parser (1-2 weeks) - writing automatic wrapper generation based on ACD files (2-3 weeks) * documentation and refactoring (1 week) 16 aug - 21 aug * final evaluation On Thu, Apr 7, 2011 at 5:33 PM, Francesco Strozzi wrote: > Hi Ales, > did you had the chance to update your proposal on BioRuby Wrapper for the > GSoC ? Deadline is tomorrow for student application and we think with this > proposal we could be able to get some interesting results. But for your > application to have a better chance to be considered and evaluated you > should provide an updated timeline (even a draft but a bit more detailed) > with the activities and tasks broken down into weeks. > If you need some help or advise please write here on the Maling List and we > will provide our contributions. > Cheers > Francesco > > On Wed, Apr 6, 2011 at 11:48, Raoul Bonnal wrote: >> >> Hello Ales, >> ?thank you for submitting your proposal, >> like Michal: >> I quote here the discussion with Chris and Christian, if you could write a >> better time line in form of days/weeks with tasks/objectives I think it >> would be better: >> >> this is the quote from Christian and Chris >> >> Hi, Michal: >> >> I think your project plan needs to be much more detailed. >> >> It might be best in a format similar to the template/example below: >> >> Prior to coding ("community bonding period"): >> -Familiarize myself with BioRuby code base >> -Learn about graphics within/from Ruby >> -Discuss ... with mentors/BioRuby community >> -... >> -Learn about git, set up my repository >> >> >> >> Week 1: >> Goal: Develop necessary utility classes for ... >> Anticipated problems: None >> >> Weeks 2 and 3: >> Goal: Develop class to visualize intron/exon structures... >> Anticipated problems: Such and such might not ... >> Alternatives: If XYZ turns out not feasible, I plan to ... instead >> >> Week X: >> Goal: Unit tests for ... >> >> >> >> Week Y: >> Documentation ... >> >> Hope this helps, >> >> Christian Zmasek >> ---- >> Micha?, >> >> In general, the proposal should answer the questions below, but should >> also have a rough timeline on how you would go about coding the project, >> creating deliverables for the community for testing, etc. This should come >> with the input of your possible mentor for the project or from others in the >> bioruby community. >> >> The timeline is a little problematic, but the OBF mentors can further >> discuss that. ?One thing that will cause a problem is that there is a >> significant amount of time (about one month) for community bonding, so any >> coding on a significant project in that period will be tricky. >> >> chris >> >> >> >> ----- Original Message ---- >> > From: Micha? Koziarski >> > To: bioruby at lists.open-bio.org >> > Sent: Tue, April 5, 2011 10:24:22 AM >> > Subject: [BioRuby] GSoC - project "Represent bio-objects and related >> > information with images" >> > >> > I've completed my application. Chris Fields suggested that I should >> > write ?it >> > up, he hasn't specified what parts exactly though. If you have any >> > ?advice >> > about it, please let me know. >> > >> > I use some of my answers to ?questions asked here in the application, I >> > hope >> > that's not a problem: I ?didn't see much point in rewriting it, since >> > the >> > meaning would be the ?same. >> > >> > I don't include the first point, about the address, since it's a ?public >> > ML >> > and I don't think it's important here. >> > >> > I am basing the ?application on the OBF's template, which I enclose too. >> > >> > >> > ? 1. ?Why you are interested in the project you are proposing and are >> > ? ?well-suited to undertake it. >> > ? 2. A summary of your programming ?experience and skills. >> > ? 3. Programs or projects you have previously ?authored or contributed >> > to, >> > ? in particular those available as ?open-source, including, if >> > applicable, >> any >> > ? past Summer of Code ?involvement. >> > ? 4. A project plan for the project you are proposing, ?even if your >> > ? proposed project is directly based on one of the ?proposed project >> > ideas >> for >> > ? member projects. >> > ? 5. Any ?obligations, vacations, or plans for the summer that may >> > require >> > ? ?scheduling during the GSoC work period. >> > >> > >> > >> > ? 1. ? ? ? I find the problem of representing computer data in format >> > ? ?readable by humans interesting, partially because it's so >> > significant: ?we >> > ? could have the best algorithms, the fastest computers, but the ?output >> would >> > ? be useless if we wouldn't be able to read it. ?Additionally, I love >> > the >> idea >> > ? of writing code for organisation such ?as OBF: it makes me think that >> > I do >> > ? have, even slightest, impact on ?science. I must also admit that >> > working >> > with >> > ? Ruby is very tempting, I ?really enjoy writing Ruby code. >> > ? 2. ? ? ?I have fairly ?strong Ruby knowledge, I have been using it for >> > ? about a year and a ?half. There were no really big projects there >> > though, >> > the >> > ? biggest ?I've got was probably small LAN IM. Nevertheless, I use Ruby >> > on >> > ? daily ?basis and I am familiar with most of its, even complex, >> > features. >> > ? ? ? ? Also, from the beginning of this year I work as a RoR >> > ?developer. >> > ? I've worked on a bigger, team project and now I am ?developing one >> > solo. >> > I've >> > ? learned a lot here: working with version ?control systems, developing >> > in >> > ? team, operating on other people's ?code, testing... not to mention >> > further >> > ? developing my Ruby ?knowledge. >> > ? ? ? ?Other than that, I know C++ pretty ?well: it was my first >> > language >> > ? and I still use it whenever I see fit. ?I also have some basic Python >> > and >> C# >> > ? knowledge. >> > ? 3. I can't ?say much more than what I've written in previous >> > paragraph. >> > ? 4. 1. ?Getting familiarized with BioRuby objects, mainly with the way >> > they >> > ? ?hold data. >> > ? 2. Deciding with features should be visualized. >> > ? ?3. In case of presence data with different format but same way of >> > ? ?visualization, implementing a mechanism converting data to unified >> format. >> > ? 4. Writing a module responsible for creating graphical ?representation >> > of >> > ? data. >> > ? 5. Final testing. >> > ? 6. ?Writing a documentation. >> > ? 5. ? ? ?Possibly short ?vacation (less than one week) around beginning >> > of >> > ? July. >> > ? ? ? ? Also, I am from Poland, which means that my summer ?vacations >> > starts >> > ? from July. Because of that I won't be able to focus ?only on the >> > project >> > ? until than. What I can do, however, is to start ?coding earlier. I >> > would >> > like >> > ? to familiarize myself with documentation ?before bonding period starts >> (I've >> > ? already began to do it), and when ?it does start coding right away. >> > Thanks >> > to >> > ? that I should have just as ?much time as if I started in May. >> > ? ? ? ?Other than that ?I am all about the project. >> > >> > >> > Also, since as I've told I would probably ?have to start coding a little >> > earlier, I am trying to slowly browse the ?documentation. It's a big >> > project >> > though, and I don't know what's important. ?Do you have any suggestions >> > about >> > that? Are there parts that would be ?especially relevant to the project? >> > Or >> > maybe even better, are there any ?easier tasks to complete? I learn best >> > by >> > exercise, so that would be great. ?I've looked up at github's issues >> > page, >> > but haven't found anything like what ?I am talking about. Maybe I just >> > didn't >> > know on what I was ?looking? >> > _______________________________________________ >> > BioRuby Project - ?http://www.bioruby.org/ >> > BioRuby mailing list >> > BioRuby at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/bioruby >> > >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> On 06/apr/2011, at 11.27, ????? wrote: >> >> > Hello. My name is Ales and I'd like to implement BioRuby wrapper for >> > command line applications as my Google Summer of Code 2011 project. >> > >> > >> > 1. Your complete contact information, including full name, physical >> > address, preferred email address, and telephone number, plus other >> > pertinent contact information such as IRC handles, etc. >> > >> > Ales Guzik >> > 4th year student at Belarusian State University of Informatics and >> > Radioelectronics. >> > Belarus, Minsk, P.Brovki st. 3-1 46 >> > ales.guzik at gmail.com >> > +375 25 902 8190 (Belarus) >> > +1 650 336 5853 (Google Voice) >> > skype: ales-guzik >> > IRC, twitter, facebook, github etc.: nekotwi >> > >> > 2. Why you are interested in the project you are proposing and are >> > well-suited to undertake it. >> > >> > This project is interesting for me because it requires metaprogramming >> > - thing I most like in ruby and >> > because it's BioRuby - project I wanted to get familiar with long time >> > ago. >> > I use Ruby more than 2 years for most of my university tasks and daily >> > linux scripting. 2 month ago I >> > started working as Ruby on Rails developer. I have pretty good >> > experience in ruby metaprogramming which >> > is needed for this project. >> > >> > 3. A summary of your programming experience and skills. >> > >> > I have well experience in C, know but not heavily used C++ and Qt, >> > long time ago learned some Erlang, >> > have coded some C# at university but dislike it, played a bit with >> > Android/Java programming. >> > Know and sometimes use Scheme(Racket), now learning some Perl 5. >> > Started learning Ruby somewhere in the beginning of 2nd university >> > year and liked it very much. >> > >> > 4. Programs or projects you have previously authored or contributed >> > to, in particular those available as open-source, including, if >> > applicable, any past Summer of Code involvement. >> > >> > I haven't yet contributed to opensource projects (except for some tiny >> > projects by myself) but really want to. >> > >> > 5. A project plan for the project you are proposing, even if your >> > proposed project is directly based on one of the proposed project >> > ideas for member projects. >> > >> > ?1) Get familiar with source code, use cases and documentation of >> > BioRuby and BioRuby-ngs >> > ?2) Define specs and write rspec tests for this CLI application wrapper >> > ?3) Code to make all tests pass >> > ?4) Optimize code for processing BIG ammounts of information >> > ?5) Refactor >> > ?6) Document undocumented parts >> > >> > 6. Any obligations, vacations, or plans for the summer that may >> > require scheduling during the GSoC work period. >> > >> > I work as rails programmer 30 hours a week. It's like 8:00 - 14:00 >> > GMT+2 DST monday - friday, so I can code for >> > my project 14:30 - 22:00 or even more. It will be like this in june and >> > august. >> > In july I'll be at military training. I'll have time and internet >> > access but can't tell my schedule for now. >> > >> > -- >> > Regards, >> > Ales Guzik >> > ------------------------------------------------------------ >> > e-mail: ales.guzik at gmail.com >> > skype: ales-guzik >> > tel: +375 25 9028190 >> > _______________________________________________ >> > BioRuby Project - http://www.bioruby.org/ >> > BioRuby mailing list >> > BioRuby at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/bioruby >> >> -- >> Ra >> >> linkedin: http://it.linkedin.com/in/raoulbonnal >> twitter: http://twitter.com/ilpuccio >> skype: ilpuccio >> irc.freenode.net: Helius >> github: https://github.com/helios >> >> >> >> >> >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > > > > -- > > Francesco > > -- Regards, Ales Guzik ------------------------------------------------------------ e-mail: ales.guzik at gmail.com skype: ales-guzik tel: +375 25 9028190 From michalkoziarski at gmail.com Thu Apr 7 17:39:25 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Thu, 7 Apr 2011 19:39:25 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: <20110406201636.3f58bcc0@mail.ingm.it> References: <313339.26768.qm@web38403.mail.mud.yahoo.com> <20110406201636.3f58bcc0@mail.ingm.it> Message-ID: 2011/4/6 Raoul Bonnal > Hi Michal, > the time line is more detailed now. > As Francesco suggested and also reported on our page we suggest RubyVis > library, Claudio the coder of the binding offers his help and this is a very > good news for us. > > Week 9: what do you mean for browsing images in shell ? I can't grasp the > benefit now, but we can discuss. The main problem is how to control the > application which displays the image; for web browsers there are techniques > but are not so easy. > I'm just thinking to an add-on for this week: if we have different types of > data that we can display quite easily on the web(done in the previous weeks) > , why not spending this time to enrich the images with controls (bars, check > boxes, interaction in general). This part requires a skill in javascript. > http://vis.stanford.edu/protovis/ex/cartogram-full.html > Or another interesting feature would be: adding layers of information to > the standard image. > Note: perhaps these ideas are a bit complicate for 1 week but it would be > interesting to evaluate the feasibility. > I thought about whether to implement that shell browser or work on images enrichment, and I am quite confused. Generally, I would agree that your idea seems to be better, but right now I can't come up with specific ways of enriching them. I guess it should be more obvious once images itself are created, but then there may be not enough time to implement everything. > > I forgot to mention, in some case I think that if there are web services > which produce images that services could be used. Consider the possibility > to display Venn diagrams Google has one service > http://code.google.com/intl/it-IT/apis/chart/docs/gallery/venn_charts.htmlor another one is > http://bioinfogp.cnb.csic.es/tools/venny/index.html. > Sets are a kind of data type that in my daily work I have to display with a > high frequency, specially when the boss needs to make reports :-) > > So we arrived to the which bioruby objects we want to display. This is a > quite complex question because some are there and other are not. > This library as been always sequence/feature centric (please correct me if > I'm wrong), because we were used to demand to R tasks more statistics. > Main areas are > * NGS: display create coverage alignemnt for a region with the possible > annotation that are accessible from bioruby > * Matrix: display heatmaps, scatter plots, bars ( I wrote a very alpha lib > for handling real time PCR and gene expression datasets -not images-) > Is that lib public now? And if so, could you provide me with repo url? > * Sets: a seq could be generated from any kind of analysis, enrichment, > annotation, reports > ** reports could be meta-objects for instance the results of an allignment > or mapping or gene quantification when you need to compare multiple > populations or technical replicates > * Phylo (i'm not an expert) > That seems to be the most complicated one of those to visualize (or am I wrong?), it would be great to hear some specifics. Out of those, I think that Matrix would be a good place to start. They could be generated only with Rubyvis, and as I believe are used quite often. Would you agree? > with the idea to produce high quality images ready to be published. > > > These are a bunch of ideas and words. > About tomorrow IRC meeting, @work they scheduled a meeting for (my) > afternoon, I'll do my best to be on IRC. Feel free to contact who is around. > > Regards. > > ------------------------------ > *From:* Christian Zmasek [mailto:cmzmasek at yahoo.com] > *To:* Micha? Koziarski [mailto:michalkoziarski at gmail.com], Chris Fields > [mailto:cjfields at illinois.edu], bioruby at lists.open-bio.org > *Cc:* Raoul Bonnal [mailto:bonnalraoul at ingm.it] > *Sent:* Wed, 06 Apr 2011 20:48:32 +0200 > *Subject:* Re: [BioRuby] GSoC - project "Represent bio-objects and related > information with images" > > > Hi, Micha?: > > You timeline is much better now! > > I put some comments/question into your text (see below). > > > > > Week 1: > > Goal: choose one representative type of BioRuby object and develop class > > that would convert its data to proposed format. That should come along > with > > unit tests. > > > This is a good idea -- to deliver a proof of concept first! > > Did you think about how exactly the image(s) will be produced? > > Which library (if any) do you plan to use? > > > Also do you plan to produce (interactive) graphics on the fly and/or create > > (static) image files (such as .png) to be viewed with other software? > > > > > > Week 2: > > Goal: develop graphical module that would create image files based on > > data in unified format and provide user interface, write unit tests. > > > > On this point it should be possible to fully visualize chosen BioRuby > > object. > > > > Weeks 3 to 8: > > Goal: basing on first weeks work, prepare similar classes for all of the > > remaining BioRuby objects. Each class should have unit tests. > > > > Week 9: > > Goal: develop mechanism of browsing images in shell. It should include > > simple search and a way of opening images. > > > > Week 10: > > Goal: write integration tests. > > > > Weeks 11 and 12: > > Goal: write documentation. > > > > I would like to be more specific about what should be done from weeks 3 > to > > 8, though. It would be nice to plan some time for every object that needs > > visualization, but I don't know which that would be exactly. Could you > give > > me a hand with this? > > I think Raoul can answer this better. > > > I guess a good candidate would be sequence objects with features, such as > intron/exon, mutations, etc. > > > > > What about anticipated problems? Can you propose alternatives for things > which > might not work as planned? > > Christian > > From francesco.strozzi at gmail.com Thu Apr 7 18:07:30 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Thu, 7 Apr 2011 20:07:30 +0200 Subject: [BioRuby] BioRuby Wrapper for Command line application (GSOC 2011) In-Reply-To: References: <4B02CC0A-20DE-4A60-93C3-E7EDACC9BA64@ingm.org> Message-ID: Excellent! To me the timeline looks good and the working plan is fine. Anyone else have some comment on this? Cheers Francesco On Thu, Apr 7, 2011 at 18:24, ????? wrote: > Sorry for this dellay. I just wanted to polish timeline and better > understand for myself how will I undertake this project. > > ** Timeline > > * getting in (4 weeks) 27 apr - 24 may > > - getting familiar with BioRuby project (2-3 weeks) > - getting into bioinformatics basics (at least 1 week) > - getting into project goals and project usage (1 week) > - reading articles about BioRuby > - reading usage documentation > - checking out usage examples > - getting into source codebase (1 week) > - reading source code documentation (4 days) > - looking through source code (2 days) > - defining coding guidelines (1 evening) > - getting into comunity (in parallel with above) > - reading mailing list archive (2-3 days) > - hanging up on IRC (all the time) > > - getting familiar with problem (1-2 weeks) > - finding examples of applications that will be used with this wrapper > - getting familiar with EMBOSS and ACD configuration files > - exploring ways to define wrapper configuration > > * coding-1 (7 weeks) 25 may - 11 july > - writing specs (4 weeks) > - defining complete API/DSL for end-users (1 week) > - defining interface for adding new CLI tools and EMBOSS suites. (1 > week) > - defining additional specs (1 week) > - writing code (3 weeks) > - writing code for API generation (1 week) > - writing code for interprocess communication and data passing (1-2 > week) > 0-1 additional week to have for finishing all this stuff. > > * mid-term evaluation (5 days) 11 july - 15 july > At this moment we have complete API/DSL specs and code wich allows > us wrapping CLI applications. > > * coding 2 (4 weeks) 17 july - 16 aug > - writing ACD file parser (1-2 weeks) > - writing automatic wrapper generation based on ACD files (2-3 weeks) > > * documentation and refactoring (1 week) 16 aug - 21 aug > > * final evaluation > > > On Thu, Apr 7, 2011 at 5:33 PM, Francesco Strozzi > wrote: > > Hi Ales, > > did you had the chance to update your proposal on BioRuby Wrapper for the > > GSoC ? Deadline is tomorrow for student application and we think with > this > > proposal we could be able to get some interesting results. But for your > > application to have a better chance to be considered and evaluated you > > should provide an updated timeline (even a draft but a bit more detailed) > > with the activities and tasks broken down into weeks. > > If you need some help or advise please write here on the Maling List and > we > > will provide our contributions. > > Cheers > > Francesco > > > > On Wed, Apr 6, 2011 at 11:48, Raoul Bonnal wrote: > >> > >> Hello Ales, > >> thank you for submitting your proposal, > >> like Michal: > >> I quote here the discussion with Chris and Christian, if you could write > a > >> better time line in form of days/weeks with tasks/objectives I think it > >> would be better: > >> > >> this is the quote from Christian and Chris > >> > >> Hi, Michal: > >> > >> I think your project plan needs to be much more detailed. > >> > >> It might be best in a format similar to the template/example below: > >> > >> Prior to coding ("community bonding period"): > >> -Familiarize myself with BioRuby code base > >> -Learn about graphics within/from Ruby > >> -Discuss ... with mentors/BioRuby community > >> -... > >> -Learn about git, set up my repository > >> > >> > >> > >> Week 1: > >> Goal: Develop necessary utility classes for ... > >> Anticipated problems: None > >> > >> Weeks 2 and 3: > >> Goal: Develop class to visualize intron/exon structures... > >> Anticipated problems: Such and such might not ... > >> Alternatives: If XYZ turns out not feasible, I plan to ... instead > >> > >> Week X: > >> Goal: Unit tests for ... > >> > >> > >> > >> Week Y: > >> Documentation ... > >> > >> Hope this helps, > >> > >> Christian Zmasek > >> ---- > >> Micha?, > >> > >> In general, the proposal should answer the questions below, but should > >> also have a rough timeline on how you would go about coding the project, > >> creating deliverables for the community for testing, etc. This should > come > >> with the input of your possible mentor for the project or from others in > the > >> bioruby community. > >> > >> The timeline is a little problematic, but the OBF mentors can further > >> discuss that. One thing that will cause a problem is that there is a > >> significant amount of time (about one month) for community bonding, so > any > >> coding on a significant project in that period will be tricky. > >> > >> chris > >> > >> > >> > >> ----- Original Message ---- > >> > From: Micha? Koziarski > >> > To: bioruby at lists.open-bio.org > >> > Sent: Tue, April 5, 2011 10:24:22 AM > >> > Subject: [BioRuby] GSoC - project "Represent bio-objects and related > >> > information with images" > >> > > >> > I've completed my application. Chris Fields suggested that I should > >> > write it > >> > up, he hasn't specified what parts exactly though. If you have any > >> > advice > >> > about it, please let me know. > >> > > >> > I use some of my answers to questions asked here in the application, > I > >> > hope > >> > that's not a problem: I didn't see much point in rewriting it, since > >> > the > >> > meaning would be the same. > >> > > >> > I don't include the first point, about the address, since it's a > public > >> > ML > >> > and I don't think it's important here. > >> > > >> > I am basing the application on the OBF's template, which I enclose > too. > >> > > >> > > >> > 1. Why you are interested in the project you are proposing and are > >> > well-suited to undertake it. > >> > 2. A summary of your programming experience and skills. > >> > 3. Programs or projects you have previously authored or contributed > >> > to, > >> > in particular those available as open-source, including, if > >> > applicable, > >> any > >> > past Summer of Code involvement. > >> > 4. A project plan for the project you are proposing, even if your > >> > proposed project is directly based on one of the proposed project > >> > ideas > >> for > >> > member projects. > >> > 5. Any obligations, vacations, or plans for the summer that may > >> > require > >> > scheduling during the GSoC work period. > >> > > >> > > >> > > >> > 1. I find the problem of representing computer data in format > >> > readable by humans interesting, partially because it's so > >> > significant: we > >> > could have the best algorithms, the fastest computers, but the > output > >> would > >> > be useless if we wouldn't be able to read it. Additionally, I love > >> > the > >> idea > >> > of writing code for organisation such as OBF: it makes me think > that > >> > I do > >> > have, even slightest, impact on science. I must also admit that > >> > working > >> > with > >> > Ruby is very tempting, I really enjoy writing Ruby code. > >> > 2. I have fairly strong Ruby knowledge, I have been using it > for > >> > about a year and a half. There were no really big projects there > >> > though, > >> > the > >> > biggest I've got was probably small LAN IM. Nevertheless, I use > Ruby > >> > on > >> > daily basis and I am familiar with most of its, even complex, > >> > features. > >> > Also, from the beginning of this year I work as a RoR > >> > developer. > >> > I've worked on a bigger, team project and now I am developing one > >> > solo. > >> > I've > >> > learned a lot here: working with version control systems, > developing > >> > in > >> > team, operating on other people's code, testing... not to mention > >> > further > >> > developing my Ruby knowledge. > >> > Other than that, I know C++ pretty well: it was my first > >> > language > >> > and I still use it whenever I see fit. I also have some basic > Python > >> > and > >> C# > >> > knowledge. > >> > 3. I can't say much more than what I've written in previous > >> > paragraph. > >> > 4. 1. Getting familiarized with BioRuby objects, mainly with the > way > >> > they > >> > hold data. > >> > 2. Deciding with features should be visualized. > >> > 3. In case of presence data with different format but same way of > >> > visualization, implementing a mechanism converting data to unified > >> format. > >> > 4. Writing a module responsible for creating graphical > representation > >> > of > >> > data. > >> > 5. Final testing. > >> > 6. Writing a documentation. > >> > 5. Possibly short vacation (less than one week) around > beginning > >> > of > >> > July. > >> > Also, I am from Poland, which means that my summer vacations > >> > starts > >> > from July. Because of that I won't be able to focus only on the > >> > project > >> > until than. What I can do, however, is to start coding earlier. I > >> > would > >> > like > >> > to familiarize myself with documentation before bonding period > starts > >> (I've > >> > already began to do it), and when it does start coding right away. > >> > Thanks > >> > to > >> > that I should have just as much time as if I started in May. > >> > Other than that I am all about the project. > >> > > >> > > >> > Also, since as I've told I would probably have to start coding a > little > >> > earlier, I am trying to slowly browse the documentation. It's a big > >> > project > >> > though, and I don't know what's important. Do you have any > suggestions > >> > about > >> > that? Are there parts that would be especially relevant to the > project? > >> > Or > >> > maybe even better, are there any easier tasks to complete? I learn > best > >> > by > >> > exercise, so that would be great. I've looked up at github's issues > >> > page, > >> > but haven't found anything like what I am talking about. Maybe I just > >> > didn't > >> > know on what I was looking? > >> > _______________________________________________ > >> > BioRuby Project - http://www.bioruby.org/ > >> > BioRuby mailing list > >> > BioRuby at lists.open-bio.org > >> > http://lists.open-bio.org/mailman/listinfo/bioruby > >> > > >> > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > >> On 06/apr/2011, at 11.27, ????? wrote: > >> > >> > Hello. My name is Ales and I'd like to implement BioRuby wrapper for > >> > command line applications as my Google Summer of Code 2011 project. > >> > > >> > > >> > 1. Your complete contact information, including full name, physical > >> > address, preferred email address, and telephone number, plus other > >> > pertinent contact information such as IRC handles, etc. > >> > > >> > Ales Guzik > >> > 4th year student at Belarusian State University of Informatics and > >> > Radioelectronics. > >> > Belarus, Minsk, P.Brovki st. 3-1 46 > >> > ales.guzik at gmail.com > >> > +375 25 902 8190 (Belarus) > >> > +1 650 336 5853 (Google Voice) > >> > skype: ales-guzik > >> > IRC, twitter, facebook, github etc.: nekotwi > >> > > >> > 2. Why you are interested in the project you are proposing and are > >> > well-suited to undertake it. > >> > > >> > This project is interesting for me because it requires metaprogramming > >> > - thing I most like in ruby and > >> > because it's BioRuby - project I wanted to get familiar with long time > >> > ago. > >> > I use Ruby more than 2 years for most of my university tasks and daily > >> > linux scripting. 2 month ago I > >> > started working as Ruby on Rails developer. I have pretty good > >> > experience in ruby metaprogramming which > >> > is needed for this project. > >> > > >> > 3. A summary of your programming experience and skills. > >> > > >> > I have well experience in C, know but not heavily used C++ and Qt, > >> > long time ago learned some Erlang, > >> > have coded some C# at university but dislike it, played a bit with > >> > Android/Java programming. > >> > Know and sometimes use Scheme(Racket), now learning some Perl 5. > >> > Started learning Ruby somewhere in the beginning of 2nd university > >> > year and liked it very much. > >> > > >> > 4. Programs or projects you have previously authored or contributed > >> > to, in particular those available as open-source, including, if > >> > applicable, any past Summer of Code involvement. > >> > > >> > I haven't yet contributed to opensource projects (except for some tiny > >> > projects by myself) but really want to. > >> > > >> > 5. A project plan for the project you are proposing, even if your > >> > proposed project is directly based on one of the proposed project > >> > ideas for member projects. > >> > > >> > 1) Get familiar with source code, use cases and documentation of > >> > BioRuby and BioRuby-ngs > >> > 2) Define specs and write rspec tests for this CLI application > wrapper > >> > 3) Code to make all tests pass > >> > 4) Optimize code for processing BIG ammounts of information > >> > 5) Refactor > >> > 6) Document undocumented parts > >> > > >> > 6. Any obligations, vacations, or plans for the summer that may > >> > require scheduling during the GSoC work period. > >> > > >> > I work as rails programmer 30 hours a week. It's like 8:00 - 14:00 > >> > GMT+2 DST monday - friday, so I can code for > >> > my project 14:30 - 22:00 or even more. It will be like this in june > and > >> > august. > >> > In july I'll be at military training. I'll have time and internet > >> > access but can't tell my schedule for now. > >> > > >> > -- > >> > Regards, > >> > Ales Guzik > >> > ------------------------------------------------------------ > >> > e-mail: ales.guzik at gmail.com > >> > skype: ales-guzik > >> > tel: +375 25 9028190 > >> > _______________________________________________ > >> > BioRuby Project - http://www.bioruby.org/ > >> > BioRuby mailing list > >> > BioRuby at lists.open-bio.org > >> > http://lists.open-bio.org/mailman/listinfo/bioruby > >> > >> -- > >> Ra > >> > >> linkedin: http://it.linkedin.com/in/raoulbonnal > >> twitter: http://twitter.com/ilpuccio > >> skype: ilpuccio > >> irc.freenode.net: Helius > >> github: https://github.com/helios > >> > >> > >> > >> > >> > >> > >> > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > > > -- > > > > Francesco > > > > > > > > -- > Regards, > Ales Guzik > ------------------------------------------------------------ > e-mail: ales.guzik at gmail.com > skype: ales-guzik > tel: +375 25 9028190 > -- Francesco From bonnal at ingm.org Thu Apr 7 18:36:29 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 7 Apr 2011 20:36:29 +0200 Subject: [BioRuby] BioRuby Wrapper for Command line application (GSOC 2011) In-Reply-To: References: <4B02CC0A-20DE-4A60-93C3-E7EDACC9BA64@ingm.org> Message-ID: <06B3D501-BB88-4848-B8B2-28C7A05EAB31@ingm.org> it's a detailed time line for sure. Emboss is an example with a structured configuration file for parameters, but we are not bound only to that suite. On 07/apr/2011, at 20.07, Francesco Strozzi wrote: > Excellent! To me the timeline looks good and the working plan is fine. > > Anyone else have some comment on this? > > Cheers > Francesco > > On Thu, Apr 7, 2011 at 18:24, ????? wrote: > Sorry for this dellay. I just wanted to polish timeline and better > understand for myself how will I undertake this project. > > ** Timeline > > * getting in (4 weeks) 27 apr - 24 may > > - getting familiar with BioRuby project (2-3 weeks) > - getting into bioinformatics basics (at least 1 week) > - getting into project goals and project usage (1 week) > - reading articles about BioRuby > - reading usage documentation > - checking out usage examples > - getting into source codebase (1 week) > - reading source code documentation (4 days) > - looking through source code (2 days) > - defining coding guidelines (1 evening) > - getting into comunity (in parallel with above) > - reading mailing list archive (2-3 days) > - hanging up on IRC (all the time) > > - getting familiar with problem (1-2 weeks) > - finding examples of applications that will be used with this wrapper > - getting familiar with EMBOSS and ACD configuration files > - exploring ways to define wrapper configuration > > * coding-1 (7 weeks) 25 may - 11 july > - writing specs (4 weeks) > - defining complete API/DSL for end-users (1 week) > - defining interface for adding new CLI tools and EMBOSS suites. (1 week) > - defining additional specs (1 week) > - writing code (3 weeks) > - writing code for API generation (1 week) > - writing code for interprocess communication and data passing (1-2 week) > 0-1 additional week to have for finishing all this stuff. > > * mid-term evaluation (5 days) 11 july - 15 july > At this moment we have complete API/DSL specs and code wich allows > us wrapping CLI applications. > > * coding 2 (4 weeks) 17 july - 16 aug > - writing ACD file parser (1-2 weeks) > - writing automatic wrapper generation based on ACD files (2-3 weeks) > > * documentation and refactoring (1 week) 16 aug - 21 aug > > * final evaluation > > > On Thu, Apr 7, 2011 at 5:33 PM, Francesco Strozzi > wrote: > > Hi Ales, > > did you had the chance to update your proposal on BioRuby Wrapper for the > > GSoC ? Deadline is tomorrow for student application and we think with this > > proposal we could be able to get some interesting results. But for your > > application to have a better chance to be considered and evaluated you > > should provide an updated timeline (even a draft but a bit more detailed) > > with the activities and tasks broken down into weeks. > > If you need some help or advise please write here on the Maling List and we > > will provide our contributions. > > Cheers > > Francesco > > > > On Wed, Apr 6, 2011 at 11:48, Raoul Bonnal wrote: > >> > >> Hello Ales, > >> thank you for submitting your proposal, > >> like Michal: > >> I quote here the discussion with Chris and Christian, if you could write a > >> better time line in form of days/weeks with tasks/objectives I think it > >> would be better: > >> > >> this is the quote from Christian and Chris > >> > >> Hi, Michal: > >> > >> I think your project plan needs to be much more detailed. > >> > >> It might be best in a format similar to the template/example below: > >> > >> Prior to coding ("community bonding period"): > >> -Familiarize myself with BioRuby code base > >> -Learn about graphics within/from Ruby > >> -Discuss ... with mentors/BioRuby community > >> -... > >> -Learn about git, set up my repository > >> > >> > >> > >> Week 1: > >> Goal: Develop necessary utility classes for ... > >> Anticipated problems: None > >> > >> Weeks 2 and 3: > >> Goal: Develop class to visualize intron/exon structures... > >> Anticipated problems: Such and such might not ... > >> Alternatives: If XYZ turns out not feasible, I plan to ... instead > >> > >> Week X: > >> Goal: Unit tests for ... > >> > >> > >> > >> Week Y: > >> Documentation ... > >> > >> Hope this helps, > >> > >> Christian Zmasek > >> ---- > >> Micha?, > >> > >> In general, the proposal should answer the questions below, but should > >> also have a rough timeline on how you would go about coding the project, > >> creating deliverables for the community for testing, etc. This should come > >> with the input of your possible mentor for the project or from others in the > >> bioruby community. > >> > >> The timeline is a little problematic, but the OBF mentors can further > >> discuss that. One thing that will cause a problem is that there is a > >> significant amount of time (about one month) for community bonding, so any > >> coding on a significant project in that period will be tricky. > >> > >> chris > >> > >> > >> > >> ----- Original Message ---- > >> > From: Micha? Koziarski > >> > To: bioruby at lists.open-bio.org > >> > Sent: Tue, April 5, 2011 10:24:22 AM > >> > Subject: [BioRuby] GSoC - project "Represent bio-objects and related > >> > information with images" > >> > > >> > I've completed my application. Chris Fields suggested that I should > >> > write it > >> > up, he hasn't specified what parts exactly though. If you have any > >> > advice > >> > about it, please let me know. > >> > > >> > I use some of my answers to questions asked here in the application, I > >> > hope > >> > that's not a problem: I didn't see much point in rewriting it, since > >> > the > >> > meaning would be the same. > >> > > >> > I don't include the first point, about the address, since it's a public > >> > ML > >> > and I don't think it's important here. > >> > > >> > I am basing the application on the OBF's template, which I enclose too. > >> > > >> > > >> > 1. Why you are interested in the project you are proposing and are > >> > well-suited to undertake it. > >> > 2. A summary of your programming experience and skills. > >> > 3. Programs or projects you have previously authored or contributed > >> > to, > >> > in particular those available as open-source, including, if > >> > applicable, > >> any > >> > past Summer of Code involvement. > >> > 4. A project plan for the project you are proposing, even if your > >> > proposed project is directly based on one of the proposed project > >> > ideas > >> for > >> > member projects. > >> > 5. Any obligations, vacations, or plans for the summer that may > >> > require > >> > scheduling during the GSoC work period. > >> > > >> > > >> > > >> > 1. I find the problem of representing computer data in format > >> > readable by humans interesting, partially because it's so > >> > significant: we > >> > could have the best algorithms, the fastest computers, but the output > >> would > >> > be useless if we wouldn't be able to read it. Additionally, I love > >> > the > >> idea > >> > of writing code for organisation such as OBF: it makes me think that > >> > I do > >> > have, even slightest, impact on science. I must also admit that > >> > working > >> > with > >> > Ruby is very tempting, I really enjoy writing Ruby code. > >> > 2. I have fairly strong Ruby knowledge, I have been using it for > >> > about a year and a half. There were no really big projects there > >> > though, > >> > the > >> > biggest I've got was probably small LAN IM. Nevertheless, I use Ruby > >> > on > >> > daily basis and I am familiar with most of its, even complex, > >> > features. > >> > Also, from the beginning of this year I work as a RoR > >> > developer. > >> > I've worked on a bigger, team project and now I am developing one > >> > solo. > >> > I've > >> > learned a lot here: working with version control systems, developing > >> > in > >> > team, operating on other people's code, testing... not to mention > >> > further > >> > developing my Ruby knowledge. > >> > Other than that, I know C++ pretty well: it was my first > >> > language > >> > and I still use it whenever I see fit. I also have some basic Python > >> > and > >> C# > >> > knowledge. > >> > 3. I can't say much more than what I've written in previous > >> > paragraph. > >> > 4. 1. Getting familiarized with BioRuby objects, mainly with the way > >> > they > >> > hold data. > >> > 2. Deciding with features should be visualized. > >> > 3. In case of presence data with different format but same way of > >> > visualization, implementing a mechanism converting data to unified > >> format. > >> > 4. Writing a module responsible for creating graphical representation > >> > of > >> > data. > >> > 5. Final testing. > >> > 6. Writing a documentation. > >> > 5. Possibly short vacation (less than one week) around beginning > >> > of > >> > July. > >> > Also, I am from Poland, which means that my summer vacations > >> > starts > >> > from July. Because of that I won't be able to focus only on the > >> > project > >> > until than. What I can do, however, is to start coding earlier. I > >> > would > >> > like > >> > to familiarize myself with documentation before bonding period starts > >> (I've > >> > already began to do it), and when it does start coding right away. > >> > Thanks > >> > to > >> > that I should have just as much time as if I started in May. > >> > Other than that I am all about the project. > >> > > >> > > >> > Also, since as I've told I would probably have to start coding a little > >> > earlier, I am trying to slowly browse the documentation. It's a big > >> > project > >> > though, and I don't know what's important. Do you have any suggestions > >> > about > >> > that? Are there parts that would be especially relevant to the project? > >> > Or > >> > maybe even better, are there any easier tasks to complete? I learn best > >> > by > >> > exercise, so that would be great. I've looked up at github's issues > >> > page, > >> > but haven't found anything like what I am talking about. Maybe I just > >> > didn't > >> > know on what I was looking? > >> > _______________________________________________ > >> > BioRuby Project - http://www.bioruby.org/ > >> > BioRuby mailing list > >> > BioRuby at lists.open-bio.org > >> > http://lists.open-bio.org/mailman/listinfo/bioruby > >> > > >> > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > >> On 06/apr/2011, at 11.27, ????? wrote: > >> > >> > Hello. My name is Ales and I'd like to implement BioRuby wrapper for > >> > command line applications as my Google Summer of Code 2011 project. > >> > > >> > > >> > 1. Your complete contact information, including full name, physical > >> > address, preferred email address, and telephone number, plus other > >> > pertinent contact information such as IRC handles, etc. > >> > > >> > Ales Guzik > >> > 4th year student at Belarusian State University of Informatics and > >> > Radioelectronics. > >> > Belarus, Minsk, P.Brovki st. 3-1 46 > >> > ales.guzik at gmail.com > >> > +375 25 902 8190 (Belarus) > >> > +1 650 336 5853 (Google Voice) > >> > skype: ales-guzik > >> > IRC, twitter, facebook, github etc.: nekotwi > >> > > >> > 2. Why you are interested in the project you are proposing and are > >> > well-suited to undertake it. > >> > > >> > This project is interesting for me because it requires metaprogramming > >> > - thing I most like in ruby and > >> > because it's BioRuby - project I wanted to get familiar with long time > >> > ago. > >> > I use Ruby more than 2 years for most of my university tasks and daily > >> > linux scripting. 2 month ago I > >> > started working as Ruby on Rails developer. I have pretty good > >> > experience in ruby metaprogramming which > >> > is needed for this project. > >> > > >> > 3. A summary of your programming experience and skills. > >> > > >> > I have well experience in C, know but not heavily used C++ and Qt, > >> > long time ago learned some Erlang, > >> > have coded some C# at university but dislike it, played a bit with > >> > Android/Java programming. > >> > Know and sometimes use Scheme(Racket), now learning some Perl 5. > >> > Started learning Ruby somewhere in the beginning of 2nd university > >> > year and liked it very much. > >> > > >> > 4. Programs or projects you have previously authored or contributed > >> > to, in particular those available as open-source, including, if > >> > applicable, any past Summer of Code involvement. > >> > > >> > I haven't yet contributed to opensource projects (except for some tiny > >> > projects by myself) but really want to. > >> > > >> > 5. A project plan for the project you are proposing, even if your > >> > proposed project is directly based on one of the proposed project > >> > ideas for member projects. > >> > > >> > 1) Get familiar with source code, use cases and documentation of > >> > BioRuby and BioRuby-ngs > >> > 2) Define specs and write rspec tests for this CLI application wrapper > >> > 3) Code to make all tests pass > >> > 4) Optimize code for processing BIG ammounts of information > >> > 5) Refactor > >> > 6) Document undocumented parts > >> > > >> > 6. Any obligations, vacations, or plans for the summer that may > >> > require scheduling during the GSoC work period. > >> > > >> > I work as rails programmer 30 hours a week. It's like 8:00 - 14:00 > >> > GMT+2 DST monday - friday, so I can code for > >> > my project 14:30 - 22:00 or even more. It will be like this in june and > >> > august. > >> > In july I'll be at military training. I'll have time and internet > >> > access but can't tell my schedule for now. > >> > > >> > -- > >> > Regards, > >> > Ales Guzik > >> > ------------------------------------------------------------ > >> > e-mail: ales.guzik at gmail.com > >> > skype: ales-guzik > >> > tel: +375 25 9028190 > >> > _______________________________________________ > >> > BioRuby Project - http://www.bioruby.org/ > >> > BioRuby mailing list > >> > BioRuby at lists.open-bio.org > >> > http://lists.open-bio.org/mailman/listinfo/bioruby > >> > >> -- > >> Ra > >> > >> linkedin: http://it.linkedin.com/in/raoulbonnal > >> twitter: http://twitter.com/ilpuccio > >> skype: ilpuccio > >> irc.freenode.net: Helius > >> github: https://github.com/helios > >> > >> > >> > >> > >> > >> > >> > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > > > -- > > > > Francesco > > > > > > > > -- > Regards, > Ales Guzik > ------------------------------------------------------------ > e-mail: ales.guzik at gmail.com > skype: ales-guzik > tel: +375 25 9028190 > > > > -- > > Francesco > -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Helius github: https://github.com/helios From bonnal at ingm.org Thu Apr 7 19:21:43 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 7 Apr 2011 21:21:43 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <313339.26768.qm@web38403.mail.mud.yahoo.com> <20110406201636.3f58bcc0@mail.ingm.it> Message-ID: <84B3BBBA-3E8C-4202-B50F-68948811350D@ingm.org> On 07/apr/2011, at 19.39, Micha? Koziarski wrote: > 2011/4/6 Raoul Bonnal > Hi Michal, > the time line is more detailed now. > As Francesco suggested and also reported on our page we suggest RubyVis library, Claudio the coder of the binding offers his help and this is a very good news for us. > > Week 9: what do you mean for browsing images in shell ? I can't grasp the benefit now, but we can discuss. The main problem is how to control the application which displays the image; for web browsers there are techniques but are not so easy. > I'm just thinking to an add-on for this week: if we have different types of data that we can display quite easily on the web(done in the previous weeks) , why not spending this time to enrich the images with controls (bars, check boxes, interaction in general). This part requires a skill in javascript. http://vis.stanford.edu/protovis/ex/cartogram-full.html > Or another interesting feature would be: adding layers of information to the standard image. > Note: perhaps these ideas are a bit complicate for 1 week but it would be interesting to evaluate the feasibility. > > I thought about whether to implement that shell browser or work on images enrichment, and I am quite confused. Generally, I would agree that your idea seems to be better, but right now I can't come up with specific ways of enriching them. I guess it should be more obvious once images itself are created, but then there may be not enough time to implement everything. Those were just ideas and were not mandatory. I think, as you wrote, when the images will be ready and you'll be more familiar with bioinformatics problems, the enrichment will be more clear. What about the possibility to evaluate how to "fuse"/enrich and image with data coming from slightly different objects ? Like tagging data sets etc... (today american football training, I hope to find inspiration ^_^ ) > > I forgot to mention, in some case I think that if there are web services which produce images that services could be used. Consider the possibility to display Venn diagrams Google has one service http://code.google.com/intl/it-IT/apis/chart/docs/gallery/venn_charts.html or another one is http://bioinfogp.cnb.csic.es/tools/venny/index.html. > Sets are a kind of data type that in my daily work I have to display with a high frequency, specially when the boss needs to make reports :-) > > So we arrived to the which bioruby objects we want to display. This is a quite complex question because some are there and other are not. > This library as been always sequence/feature centric (please correct me if I'm wrong), because we were used to demand to R tasks more statistics. > Main areas are > * NGS: display create coverage alignemnt for a region with the possible annotation that are accessible from bioruby > * Matrix: display heatmaps, scatter plots, bars ( I wrote a very alpha lib for handling real time PCR and gene expression datasets -not images-) > > Is that lib public now? And if so, could you provide me with repo url? Did you mean R? http://www.bioconductor.org/developers/package-guidelines/ this library is voted to bioinformatics + statistic note that Claudio Bustos (RubyVis) has coded another great library for R http://ruby-statsample.rubyforge.org/rserve-client/ and this is for statistics http://ruby-statsample.rubyforge.org/ > > * Sets: a seq could be generated from any kind of analysis, enrichment, annotation, reports > ** reports could be meta-objects for instance the results of an allignment or mapping or gene quantification when you need to compare multiple populations or technical replicates > * Phylo (i'm not an expert) > > That seems to be the most complicated one of those to visualize (or am I wrong?), it would be great to hear some specifics. If you mean phylo, I think Christian is an expert . > > Out of those, I think that Matrix would be a good place to start. They could be generated only with Rubyvis, and as I believe are used quite often. Would you agree? Yeah at low level I think that most of the problems could be reduced to matrices. Another great tool for visualizing data and I love it, coded in perl, is http://mkweb.bcgsc.ca/circos/ we could you is to find inspirations. and http://vizbi.org/2011/Posters/List/?poster=D10 Ciao. > > > with the idea to produce high quality images ready to be published. > > > These are a bunch of ideas and words. > About tomorrow IRC meeting, @work they scheduled a meeting for (my) afternoon, I'll do my best to be on IRC. Feel free to contact who is around. > > Regards. > > From: Christian Zmasek [mailto:cmzmasek at yahoo.com] > To: Micha? Koziarski [mailto:michalkoziarski at gmail.com], Chris Fields [mailto:cjfields at illinois.edu], bioruby at lists.open-bio.org > Cc: Raoul Bonnal [mailto:bonnalraoul at ingm.it] > Sent: Wed, 06 Apr 2011 20:48:32 +0200 > Subject: Re: [BioRuby] GSoC - project "Represent bio-objects and related information with images" > > > Hi, Micha?: > > You timeline is much better now! > > I put some comments/question into your text (see below). > > > > > Week 1: > > Goal: choose one representative type of BioRuby object and develop class > > that would convert its data to proposed format. That should come along with > > unit tests. > > > This is a good idea -- to deliver a proof of concept first! > > Did you think about how exactly the image(s) will be produced? > > Which library (if any) do you plan to use? > > > Also do you plan to produce (interactive) graphics on the fly and/or create > (static) image files (such as .png) to be viewed with other software? > > > > > > Week 2: > > Goal: develop graphical module that would create image files based on > > data in unified format and provide user interface, write unit tests. > > > > On this point it should be possible to fully visualize chosen BioRuby > > object. > > > > Weeks 3 to 8: > > Goal: basing on first weeks work, prepare similar classes for all of the > > remaining BioRuby objects. Each class should have unit tests. > > > > Week 9: > > Goal: develop mechanism of browsing images in shell. It should include > > simple search and a way of opening images. > > > > Week 10: > > Goal: write integration tests. > > > > Weeks 11 and 12: > > Goal: write documentation. > > > > I would like to be more specific about what should be done from weeks 3 to > > 8, though. It would be nice to plan some time for every object that needs > > visualization, but I don't know which that would be exactly. Could you give > > me a hand with this? > > I think Raoul can answer this better. > > > I guess a good candidate would be sequence objects with features, such as > intron/exon, mutations, etc. > > > > > What about anticipated problems? Can you propose alternatives for things which > might not work as planned? > > Christian > > -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Helius github: https://github.com/helios From michalkoziarski at gmail.com Thu Apr 7 20:27:44 2011 From: michalkoziarski at gmail.com (=?ISO-8859-2?Q?Micha=B3_Koziarski?=) Date: Thu, 7 Apr 2011 22:27:44 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: <84B3BBBA-3E8C-4202-B50F-68948811350D@ingm.org> References: <313339.26768.qm@web38403.mail.mud.yahoo.com> <20110406201636.3f58bcc0@mail.ingm.it> <84B3BBBA-3E8C-4202-B50F-68948811350D@ingm.org> Message-ID: 2011/4/7 Raoul Bonnal > > On 07/apr/2011, at 19.39, Micha? Koziarski wrote: > > 2011/4/6 Raoul Bonnal > >> Hi Michal, >> the time line is more detailed now. >> As Francesco suggested and also reported on our page we suggest RubyVis >> library, Claudio the coder of the binding offers his help and this is a very >> good news for us. >> >> Week 9: what do you mean for browsing images in shell ? I can't grasp the >> benefit now, but we can discuss. The main problem is how to control the >> application which displays the image; for web browsers there are techniques >> but are not so easy. >> > I'm just thinking to an add-on for this week: if we have different types of >> data that we can display quite easily on the web(done in the previous weeks) >> , why not spending this time to enrich the images with controls (bars, check >> boxes, interaction in general). This part requires a skill in javascript. >> http://vis.stanford.edu/protovis/ex/cartogram-full.html >> Or another interesting feature would be: adding layers of information to >> the standard image. >> Note: perhaps these ideas are a bit complicate for 1 week but it would be >> interesting to evaluate the feasibility. >> > > I thought about whether to implement that shell browser or work on images > enrichment, and I am quite confused. Generally, I would agree that your idea > seems to be better, but right now I can't come up with specific ways of > enriching them. I guess it should be more obvious once images itself are > created, but then there may be not enough time to implement everything. > > Those were just ideas and were not mandatory. I think, as you wrote, when > the images will be ready and you'll be more familiar with bioinformatics > problems, the enrichment will be more clear. What about the possibility to > evaluate how to "fuse"/enrich and image with data coming from slightly > different objects ? Like tagging data sets etc... (today american football > training, I hope to find inspiration ^_^ ) > Yeah, I realize that they were not mandatory, I just would like to make the best of this time. Anyway, I guess I will just stick to the file browsing idea for now, and later on reevaulate which one will be better at the time. > > >> I forgot to mention, in some case I think that if there are web services >> which produce images that services could be used. Consider the possibility >> to display Venn diagrams Google has one service >> http://code.google.com/intl/it-IT/apis/chart/docs/gallery/venn_charts.htmlor another one is >> http://bioinfogp.cnb.csic.es/tools/venny/index.html. >> Sets are a kind of data type that in my daily work I have to display with >> a high frequency, specially when the boss needs to make reports :-) >> >> So we arrived to the which bioruby objects we want to display. This is a >> quite complex question because some are there and other are not. >> This library as been always sequence/feature centric (please correct me if >> I'm wrong), because we were used to demand to R tasks more statistics. >> Main areas are >> * NGS: display create coverage alignemnt for a region with the possible >> annotation that are accessible from bioruby >> * Matrix: display heatmaps, scatter plots, bars ( I wrote a very alpha lib >> for handling real time PCR and gene expression datasets -not images-) >> > > Is that lib public now? And if so, could you provide me with repo url? > > Did you mean R? > http://www.bioconductor.org/developers/package-guidelines/ > this library is voted to bioinformatics + statistic > note that Claudio Bustos (RubyVis) has coded another great library for R > http://ruby-statsample.rubyforge.org/rserve-client/ > and this is for statistics http://ruby-statsample.rubyforge.org/ > > Sorry, I wasn't very specific. I ment your lib for handling real time PCR. > > >> * Sets: a seq could be generated from any kind of analysis, enrichment, >> annotation, reports >> ** reports could be meta-objects for instance the results of an >> allignment or mapping or gene quantification when you need to compare >> multiple populations or technical replicates >> * Phylo (i'm not an expert) >> > > That seems to be the most complicated one of those to visualize (or am I > wrong?), it would be great to hear some specifics. > > If you mean phylo, I think Christian is an expert . > Yes, I ment Phylo. > > > Out of those, I think that Matrix would be a good place to start. They > could be generated only with Rubyvis, and as I believe are used quite often. > Would you agree? > > Yeah at low level I think that most of the problems could be reduced to > matrices. > Another great tool for visualizing data and I love it, coded in perl, is > http://mkweb.bcgsc.ca/circos/ we could you is to find inspirations. > and http://vizbi.org/2011/Posters/List/?poster=D10 > Indeed, Circos looks really great. Have you used it? How about the readibility? > > > Ciao. > > > >> with the idea to produce high quality images ready to be published. >> >> >> These are a bunch of ideas and words. >> About tomorrow IRC meeting, @work they scheduled a meeting for (my) >> afternoon, I'll do my best to be on IRC. Feel free to contact who is around. >> >> Regards. >> >> ------------------------------ >> *From:* Christian Zmasek [mailto:cmzmasek at yahoo.com] >> *To:* Micha? Koziarski [mailto:michalkoziarski at gmail.com], Chris Fields >> [mailto:cjfields at illinois.edu], bioruby at lists.open-bio.org >> *Cc:* Raoul Bonnal [mailto:bonnalraoul at ingm.it] >> *Sent:* Wed, 06 Apr 2011 20:48:32 +0200 >> *Subject:* Re: [BioRuby] GSoC - project "Represent bio-objects and >> related information with images" >> >> >> Hi, Micha?: >> >> You timeline is much better now! >> >> I put some comments/question into your text (see below). >> >> >> >> > Week 1: >> > Goal: choose one representative type of BioRuby object and develop class >> > that would convert its data to proposed format. That should come along >> with >> > unit tests. >> >> >> This is a good idea -- to deliver a proof of concept first! >> >> Did you think about how exactly the image(s) will be produced? >> >> Which library (if any) do you plan to use? >> >> >> Also do you plan to produce (interactive) graphics on the fly and/or >> create >> (static) image files (such as .png) to be viewed with other software? >> >> >> >> >> > Week 2: >> > Goal: develop graphical module that would create image files based on >> > data in unified format and provide user interface, write unit tests. >> > >> > On this point it should be possible to fully visualize chosen BioRuby >> > object. >> > >> > Weeks 3 to 8: >> > Goal: basing on first weeks work, prepare similar classes for all of the >> > remaining BioRuby objects. Each class should have unit tests. >> > >> > Week 9: >> > Goal: develop mechanism of browsing images in shell. It should include >> > simple search and a way of opening images. >> > >> > Week 10: >> > Goal: write integration tests. >> > >> > Weeks 11 and 12: >> > Goal: write documentation. >> > >> > I would like to be more specific about what should be done from weeks 3 >> to >> > 8, though. It would be nice to plan some time for every object that >> needs >> > visualization, but I don't know which that would be exactly. Could you >> give >> > me a hand with this? >> >> I think Raoul can answer this better. >> >> >> I guess a good candidate would be sequence objects with features, such as >> intron/exon, mutations, etc. >> >> >> >> >> What about anticipated problems? Can you propose alternatives for things >> which >> might not work as planned? >> >> Christian >> >> > > -- > Ra > > linkedin: http://it.linkedin.com/in/raoulbonnal > twitter: http://twitter.com/ilpuccio > skype: ilpuccio > irc.freenode.net: Helius > github: https://github.com/helios > > > > > > > From bonnal at ingm.org Thu Apr 7 22:26:46 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 8 Apr 2011 00:26:46 +0200 Subject: [BioRuby] GSoC - project "Represent bio-objects and related information with images" In-Reply-To: References: <313339.26768.qm@web38403.mail.mud.yahoo.com> <20110406201636.3f58bcc0@mail.ingm.it> <84B3BBBA-3E8C-4202-B50F-68948811350D@ingm.org> Message-ID: Hi Michal, On 07/apr/2011, at 22.27, Micha? Koziarski wrote: > 2011/4/7 Raoul Bonnal > > On 07/apr/2011, at 19.39, Micha? Koziarski wrote: > >> 2011/4/6 Raoul Bonnal >> Hi Michal, >> the time line is more detailed now. >> As Francesco suggested and also reported on our page we suggest RubyVis library, Claudio the coder of the binding offers his help and this is a very good news for us. >> >> Week 9: what do you mean for browsing images in shell ? I can't grasp the benefit now, but we can discuss. The main problem is how to control the application which displays the image; for web browsers there are techniques but are not so easy. >> I'm just thinking to an add-on for this week: if we have different types of data that we can display quite easily on the web(done in the previous weeks) , why not spending this time to enrich the images with controls (bars, check boxes, interaction in general). This part requires a skill in javascript. http://vis.stanford.edu/protovis/ex/cartogram-full.html >> Or another interesting feature would be: adding layers of information to the standard image. >> Note: perhaps these ideas are a bit complicate for 1 week but it would be interesting to evaluate the feasibility. >> >> I thought about whether to implement that shell browser or work on images enrichment, and I am quite confused. Generally, I would agree that your idea seems to be better, but right now I can't come up with specific ways of enriching them. I guess it should be more obvious once images itself are created, but then there may be not enough time to implement everything. > Those were just ideas and were not mandatory. I think, as you wrote, when the images will be ready and you'll be more familiar with bioinformatics problems, the enrichment will be more clear. What about the possibility to evaluate how to "fuse"/enrich and image with data coming from slightly different objects ? Like tagging data sets etc... (today american football training, I hope to find inspiration ^_^ ) > > Yeah, I realize that they were not mandatory, I just would like to make the best of this time. Anyway, I guess I will just stick to the file browsing idea for now, and later on reevaulate which one will be better at the time. > >> >> I forgot to mention, in some case I think that if there are web services which produce images that services could be used. Consider the possibility to display Venn diagrams Google has one service http://code.google.com/intl/it-IT/apis/chart/docs/gallery/venn_charts.html or another one is http://bioinfogp.cnb.csic.es/tools/venny/index.html. >> Sets are a kind of data type that in my daily work I have to display with a high frequency, specially when the boss needs to make reports :-) >> >> So we arrived to the which bioruby objects we want to display. This is a quite complex question because some are there and other are not. >> This library as been always sequence/feature centric (please correct me if I'm wrong), because we were used to demand to R tasks more statistics. >> Main areas are >> * NGS: display create coverage alignemnt for a region with the possible annotation that are accessible from bioruby >> * Matrix: display heatmaps, scatter plots, bars ( I wrote a very alpha lib for handling real time PCR and gene expression datasets -not images-) >> >> Is that lib public now? And if so, could you provide me with repo url? > Did you mean R? http://www.bioconductor.org/developers/package-guidelines/ > this library is voted to bioinformatics + statistic > note that Claudio Bustos (RubyVis) has coded another great library for R http://ruby-statsample.rubyforge.org/rserve-client/ > and this is for statistics http://ruby-statsample.rubyforge.org/ > > Sorry, I wasn't very specific. I ment your lib for handling real time PCR. It's not yet on github, was/is quite experimental, but is't a good candidate for a new plugins :-D when I'll have time to reopen it, however basically the data are managed like matrices ( in the latest version i was using statsample). >> >> * Sets: a seq could be generated from any kind of analysis, enrichment, annotation, reports >> ** reports could be meta-objects for instance the results of an allignment or mapping or gene quantification when you need to compare multiple populations or technical replicates >> * Phylo (i'm not an expert) >> >> That seems to be the most complicated one of those to visualize (or am I wrong?), it would be great to hear some specifics. > If you mean phylo, I think Christian is an expert . > > Yes, I ment Phylo. Ok wait some hint from Christian. > >> >> Out of those, I think that Matrix would be a good place to start. They could be generated only with Rubyvis, and as I believe are used quite often. Would you agree? > > Yeah at low level I think that most of the problems could be reduced to matrices. > Another great tool for visualizing data and I love it, coded in perl, is http://mkweb.bcgsc.ca/circos/ we could you is to find inspirations. > and http://vizbi.org/2011/Posters/List/?poster=D10 > > Indeed, Circos looks really great. Have you used it? How about the readibility? Yeah for some projects mostly on visualizing feature on circular genome, some time ago I was working on assembling bacterial genome which are circular > > > Ciao. > >> >> >> with the idea to produce high quality images ready to be published. >> >> >> These are a bunch of ideas and words. >> About tomorrow IRC meeting, @work they scheduled a meeting for (my) afternoon, I'll do my best to be on IRC. Feel free to contact who is around. >> >> Regards. >> >> From: Christian Zmasek [mailto:cmzmasek at yahoo.com] >> To: Micha? Koziarski [mailto:michalkoziarski at gmail.com], Chris Fields [mailto:cjfields at illinois.edu], bioruby at lists.open-bio.org >> Cc: Raoul Bonnal [mailto:bonnalraoul at ingm.it] >> Sent: Wed, 06 Apr 2011 20:48:32 +0200 >> Subject: Re: [BioRuby] GSoC - project "Represent bio-objects and related information with images" >> >> >> Hi, Micha?: >> >> You timeline is much better now! >> >> I put some comments/question into your text (see below). >> >> >> >> > Week 1: >> > Goal: choose one representative type of BioRuby object and develop class >> > that would convert its data to proposed format. That should come along with >> > unit tests. >> >> >> This is a good idea -- to deliver a proof of concept first! >> >> Did you think about how exactly the image(s) will be produced? >> >> Which library (if any) do you plan to use? >> >> >> Also do you plan to produce (interactive) graphics on the fly and/or create >> (static) image files (such as .png) to be viewed with other software? >> >> >> >> >> > Week 2: >> > Goal: develop graphical module that would create image files based on >> > data in unified format and provide user interface, write unit tests. >> > >> > On this point it should be possible to fully visualize chosen BioRuby >> > object. >> > >> > Weeks 3 to 8: >> > Goal: basing on first weeks work, prepare similar classes for all of the >> > remaining BioRuby objects. Each class should have unit tests. >> > >> > Week 9: >> > Goal: develop mechanism of browsing images in shell. It should include >> > simple search and a way of opening images. >> > >> > Week 10: >> > Goal: write integration tests. >> > >> > Weeks 11 and 12: >> > Goal: write documentation. >> > >> > I would like to be more specific about what should be done from weeks 3 to >> > 8, though. It would be nice to plan some time for every object that needs >> > visualization, but I don't know which that would be exactly. Could you give >> > me a hand with this? >> >> I think Raoul can answer this better. >> >> >> I guess a good candidate would be sequence objects with features, such as >> intron/exon, mutations, etc. >> >> >> >> >> What about anticipated problems? Can you propose alternatives for things which >> might not work as planned? >> >> Christian >> >> > > > -- > Ra > > linkedin: http://it.linkedin.com/in/raoulbonnal > twitter: http://twitter.com/ilpuccio > skype: ilpuccio > irc.freenode.net: Helius > github: https://github.com/helios > > > > > > > -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Helius github: https://github.com/helios From missy at be.to Fri Apr 22 02:22:49 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Fri, 22 Apr 2011 11:22:49 +0900 Subject: [BioRuby] A new plugin: BioRuby UCSC API Message-ID: <4DB0E679.9080009@be.to> Hi all, I uploaded a new BioRuby plugin 'bio-ucsc-api' to RubyGems.org. RubyGem: https://rubygems.org/gems/bio-ucsc-api GitHub: https://github.com/misshie/bioruby-ucsc-api GitHub-Issues: http://github.com/misshie/bioruby-ucsc-api/issues BioRuby UCSC API is a API for the UCSC genome browser database. The design is based on Ruby-Ensembl-API and Ruby-UCSC-API by Francesco Strozzi and Jan Aerts. Features of Bioruby UCSC API is the followings: * Designed as a BioRuby plugin * Using ActiveRecord as an O/R mapping framework * Using the Bin index system to improve query performance * Automatic conversion of "1-based full-closed intervals" to internal "0-based half-closed intervals" (see also bioruby-genomic-interval) * Supporting non-official MySql hosts (e.g. local servers) * Using Rspec for the testing framework * Trying to support whole hg19 and hg18 databases. Current version is still experimental. I have implemented only tables that I need to use now. Comments, suggestions, and requests are welcome. Sincerely yours, Hiro. -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From pjotr.public14 at thebird.nl Fri Apr 22 06:35:35 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 22 Apr 2011 08:35:35 +0200 Subject: [BioRuby] A new plugin: BioRuby UCSC API In-Reply-To: <4DB0E679.9080009@be.to> References: <4DB0E679.9080009@be.to> Message-ID: <20110422063535.GA32036@thebird.nl> Great stuff :) On Fri, Apr 22, 2011 at 11:22:49AM +0900, MISHIMA, Hiroyuki wrote: > Hi all, > > I uploaded a new BioRuby plugin 'bio-ucsc-api' to RubyGems.org. > > RubyGem: > https://rubygems.org/gems/bio-ucsc-api > > GitHub: > https://github.com/misshie/bioruby-ucsc-api > > GitHub-Issues: > http://github.com/misshie/bioruby-ucsc-api/issues > > BioRuby UCSC API is a API for the UCSC genome browser database. The > design is based on Ruby-Ensembl-API and Ruby-UCSC-API by Francesco > Strozzi and Jan Aerts. > > Features of Bioruby UCSC API is the followings: > * Designed as a BioRuby plugin > * Using ActiveRecord as an O/R mapping framework > * Using the Bin index system to improve query performance > * Automatic conversion of "1-based full-closed intervals" to internal > "0-based half-closed intervals" (see also bioruby-genomic-interval) > * Supporting non-official MySql hosts (e.g. local servers) > * Using Rspec for the testing framework > * Trying to support whole hg19 and hg18 databases. > > Current version is still experimental. I have implemented only tables > that I need to use now. Comments, suggestions, and requests are welcome. > > Sincerely yours, > Hiro. > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From bonnal at ingm.org Fri Apr 22 09:33:17 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 22 Apr 2011 11:33:17 +0200 Subject: [BioRuby] A new plugin: BioRuby UCSC API In-Reply-To: <4DB0E679.9080009@be.to> References: <4DB0E679.9080009@be.to> Message-ID: this is a great plugin. Well done Hiro. We need to update the wiki to make a list of active plugins new etc... On 22/apr/2011, at 04.22, MISHIMA, Hiroyuki wrote: > Hi all, > > I uploaded a new BioRuby plugin 'bio-ucsc-api' to RubyGems.org. > > RubyGem: > https://rubygems.org/gems/bio-ucsc-api > > GitHub: > https://github.com/misshie/bioruby-ucsc-api > > GitHub-Issues: > http://github.com/misshie/bioruby-ucsc-api/issues > > BioRuby UCSC API is a API for the UCSC genome browser database. The > design is based on Ruby-Ensembl-API and Ruby-UCSC-API by Francesco > Strozzi and Jan Aerts. > > Features of Bioruby UCSC API is the followings: > * Designed as a BioRuby plugin > * Using ActiveRecord as an O/R mapping framework > * Using the Bin index system to improve query performance > * Automatic conversion of "1-based full-closed intervals" to internal > "0-based half-closed intervals" (see also bioruby-genomic-interval) > * Supporting non-official MySql hosts (e.g. local servers) > * Using Rspec for the testing framework > * Trying to support whole hg19 and hg18 databases. > > Current version is still experimental. I have implemented only tables > that I need to use now. Comments, suggestions, and requests are welcome. > > Sincerely yours, > Hiro. > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby Raoul Jean Pierre Bonnal __________________________________________________________________ Istituto Nazionale di Genetica Molecolare Via F.Sforza 35 - 20122 - Milano (MI) - Italy Tel Ufficio :+39 02.00660.326 Tel Fax:+39 02.00662.346 E-Mail :bonnal at ingm.org Web site :http://www.ingm.org SOSTIENI LA RICERCA: devolvi il 5 per mille delle imposte alla FONDAZIONE INGM Istituto Nazionale Genetica Molecolare di Milano. 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From jan.aerts at gmail.com Sat Apr 23 09:31:10 2011 From: jan.aerts at gmail.com (Jan Aerts) Date: Sat, 23 Apr 2011 11:31:10 +0200 Subject: [BioRuby] A new plugin: bio-genomic-interval In-Reply-To: <4D9D45A2.9070608@be.to> References: <4D9D45A2.9070608@be.to> Message-ID: Hi Hiro, You might take a look at the Slice class in the ruby-ensembl-api at https://github.com/jandot/ruby-ensembl-api/blob/master/lib/ensembl/core/slice.rb. This has very similar functionality, and might give some additional ideas as well, for example: - Slice#overlaps?(other_slice) => checks whether 2 slices overlap - Slice#within?(other_slice) => checks whether this slices is contained within another slice - Slice#contains?(other_slice) => checks whether this slices contains another slice - Slice#excise(array_of_regions) => takes a slices and removes a certain region, returning an array of smaller slices. For example: # original_slice = Slice.new('chrX',1,10000) # new_slices = original_slice.excise([500..750, 1050..1075]) # new_slices.each do |s| # puts s.display_name # end # # # result: # # chromosome:X:1:499:1 # # chromosome:X:751:1049:1 # # chromosome:X:1076:10000:1 - Slice#sub_slice(start, stop) => creates a truncated version of this slice - Slice#split(length, overlap) => splits a slice into smaller bits (e.g. creates an array of slices of 100bp long), optionally with an overlap between the resultant slices. Just my 2c. (Also: if you have feature requests, ideas or other comments for the ruby-ensembl-api, see rubyensemblapi.userecho.com) jan. On 7 April 2011 07:03, MISHIMA, Hiroyuki wrote: > Hi all, > > I have uploaded a new Bioruby plugin 'bio-genomic-interval'. > > The Bio::GenomicInterval class is designed to handle genomic intervals > such as "chr1:123-456". The class has methods to detect the overlapping > status between two intervals. It may help to avoid messy case branching > and improve readability of codes. > > Developmental tools for BioRuby plugin and documents in the BioRuby wiki > were very helpful. Thank you all the authors. > > Please see also the followings: > GitHub - > https://github.com/misshie/bioruby-genomic-interval > RubyGems.org - > https://rubygems.org/gems/bio-genomic-interval > > Sincerely yours, > Hiro. > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From jan.aerts at gmail.com Sat Apr 23 09:51:15 2011 From: jan.aerts at gmail.com (Jan Aerts) Date: Sat, 23 Apr 2011 11:51:15 +0200 Subject: [BioRuby] help needed to add compara database to ruby-ensembl-api Message-ID: All, Not that long ago we published a Bioinformatics paper describing the Ruby API to the Ensembl database (Bioinformatics 27(7):1013-1014). This API has the same functionality as the Perl API, with some added benefits (e.g. only 1 API for all releases, very little code which makes maintenance a breeze, and a - we believe - more useful implementation of the Slice concept). At the moment, we have however only implemented the core and the variation databases into the codebase. What has to be done: [1] Create full APIs to all tables in the compara database. This will be very straightforward as it only involves a few lines of code due to the ActiveRecord framework. For example: this is the only code needed to create getters and setters for all columns in the exon_transcript table, plus search functionality in that table: class ExonTranscript < DBConnection set_primary_key nil belongs_to :exon belongs_to :transcript end [2] Add additional functionality that cannot be directly derived from the tables themselves. For the core database, this involved for example coordinate transformations and projections; for the variation database, this involved for example consequence prediction for new variations. If you're interested in helping out (even in part), please don't hesitate to contact me at jan.aerts at esat.kuleuven.be. Glory will be bestowed upon you. Project website: http://github.com/jandot/ruby-ensembl-api Feedback (feature requests, questions, bugs, ...): http://rubyensemblapi.userecho.com Thanks, jan. From missy at be.to Sat Apr 23 14:12:11 2011 From: missy at be.to (MISHIMA, Hiroyuki) Date: Sat, 23 Apr 2011 23:12:11 +0900 Subject: [BioRuby] A new plugin: bio-genomic-interval In-Reply-To: References: <4D9D45A2.9070608@be.to> Message-ID: <4DB2DE3B.7030606@be.to> Hi Jan and BioRuby-ML, Thank you your comment on the bio-genomic-interval library. After I have released bio-genomic-interval, I found Jan's ruby-ucsc-api and the Slice class. The Slice class also plays an important role in the Ruby Ensembl API. In conclusion, I think that it is good to merge my bio-genomic-interval into the Slice class and make a BioRuby plugin like "bio-slice" to share among libraries. To do this, we have to separate ensemble/core/slice.rb into common methods to share and the Ensembl API specific methods. The strong points of the Slice class are including the followings: * Using BioRuby objects such as Bio::Sequence::NA. * Slice#excise, #sub_slice, and #split * A short simple class name (Matz says "Name is important") So far, I use bio-genomic-interval in bio-ucsc-api because bio-genomic-interval has methods to convert between the common "1-based full-closed" and UCSC-internal "0-based half-closed" intervals. This conversion is trivial arithmetic but prevents bugs. Other methods only in GenomicInterval are the followings: #parse (parses UCSC style "chr1:1,234-3,456") #comparison (returns :left_adjacent [i.e. distance <20bp], :left_off, :contains, :left_overlapped etc.) #overlap (returns a distance or an overlap-length between two intervals) #expand (returns a minimum interval containing two intervals), #center (returns a center position) Sincerely yours, Hiro. Jan Aerts wrote (2011/04/23 18:31): > Hi Hiro, > > You might take a look at the Slice class in the ruby-ensembl-api at > https://github.com/jandot/ruby-ensembl-api/blob/master/lib/ensembl/core/slice.rb. > This has very similar functionality, and might give some additional > ideas as well, for example: > > - Slice#overlaps?(other_slice) => checks whether 2 slices overlap > - Slice#within?(other_slice) => checks whether this slices is contained > within another slice > - Slice#contains?(other_slice) => checks whether this slices contains > another slice > - Slice#excise(array_of_regions) => takes a slices and removes a certain > region, returning an array of smaller slices. For example: > > # original_slice = Slice.new('chrX',1,10000) > # new_slices = original_slice.excise([500..750, 1050..1075]) > # new_slices.each do |s| > # puts s.display_name > # end > # > # # result: > # # chromosome:X:1:499:1 > # # chromosome:X:751:1049:1 > # # chromosome:X:1076:10000:1 > > - Slice#sub_slice(start, stop) => creates a truncated version of this slice > - Slice#split(length, overlap) => splits a slice into smaller bits (e.g. > creates an array of slices of 100bp long), optionally with an overlap > between the resultant slices. > > Just my 2c. (Also: if you have feature requests, ideas or other comments > for the ruby-ensembl-api, see rubyensemblapi.userecho.com > ) > > jan. -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From pjotr.public14 at thebird.nl Sat Apr 23 17:22:48 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 23 Apr 2011 19:22:48 +0200 Subject: [BioRuby] A new plugin: bio-genomic-interval In-Reply-To: <4DB2DE3B.7030606@be.to> References: <4D9D45A2.9070608@be.to> <4DB2DE3B.7030606@be.to> Message-ID: <20110423172247.GA7846@thebird.nl> Good thinking. And I am glad to see biogem encourage modular design; that is what we set out to achieve. Pj. On Sat, Apr 23, 2011 at 11:12:11PM +0900, MISHIMA, Hiroyuki wrote: > Hi Jan and BioRuby-ML, > > Thank you your comment on the bio-genomic-interval library. > > After I have released bio-genomic-interval, I found Jan's ruby-ucsc-api > and the Slice class. The Slice class also plays an important role in the > Ruby Ensembl API. > > In conclusion, I think that it is good to merge my bio-genomic-interval > into the Slice class and make a BioRuby plugin like "bio-slice" to share > among libraries. To do this, we have to separate ensemble/core/slice.rb > into common methods to share and the Ensembl API specific methods. > > The strong points of the Slice class are including the followings: > * Using BioRuby objects such as Bio::Sequence::NA. > * Slice#excise, #sub_slice, and #split > * A short simple class name (Matz says "Name is important") > > So far, I use bio-genomic-interval in bio-ucsc-api because > bio-genomic-interval has methods to convert between the common "1-based > full-closed" and UCSC-internal "0-based half-closed" intervals. This > conversion is trivial arithmetic but prevents bugs. > > Other methods only in GenomicInterval are the followings: > #parse (parses UCSC style "chr1:1,234-3,456") > #comparison (returns :left_adjacent [i.e. distance <20bp], :left_off, > :contains, :left_overlapped etc.) > #overlap (returns a distance or an overlap-length between two intervals) > #expand (returns a minimum interval containing two intervals), > #center (returns a center position) > > Sincerely yours, > Hiro. > > Jan Aerts wrote (2011/04/23 18:31): >> Hi Hiro, >> >> You might take a look at the Slice class in the ruby-ensembl-api at >> https://github.com/jandot/ruby-ensembl-api/blob/master/lib/ensembl/core/slice.rb. >> This has very similar functionality, and might give some additional >> ideas as well, for example: >> >> - Slice#overlaps?(other_slice) => checks whether 2 slices overlap >> - Slice#within?(other_slice) => checks whether this slices is contained >> within another slice >> - Slice#contains?(other_slice) => checks whether this slices contains >> another slice >> - Slice#excise(array_of_regions) => takes a slices and removes a certain >> region, returning an array of smaller slices. For example: >> >> # original_slice = Slice.new('chrX',1,10000) >> # new_slices = original_slice.excise([500..750, 1050..1075]) >> # new_slices.each do |s| >> # puts s.display_name >> # end >> # >> # # result: >> # # chromosome:X:1:499:1 >> # # chromosome:X:751:1049:1 >> # # chromosome:X:1076:10000:1 >> >> - Slice#sub_slice(start, stop) => creates a truncated version of this slice >> - Slice#split(length, overlap) => splits a slice into smaller bits (e.g. >> creates an array of slices of 100bp long), optionally with an overlap >> between the resultant slices. >> >> Just my 2c. (Also: if you have feature requests, ideas or other comments >> for the ruby-ensembl-api, see rubyensemblapi.userecho.com >> ) >> >> jan. > > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Mon Apr 25 09:33:28 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 25 Apr 2011 11:33:28 +0200 Subject: [BioRuby] A new plugin: BioRuby UCSC API In-Reply-To: References: <4DB0E679.9080009@be.to> Message-ID: <20110425093328.GA15152@thebird.nl> On Fri, Apr 22, 2011 at 11:33:17AM +0200, Raoul Bonnal wrote: > We need to update the wiki to make a list of active plugins new etc... I have created a new page: http://bioruby.open-bio.org/wiki/BioRuby_Plugins which simply lists current, stable, developed, and maintained plugins. Plugin authors are encouraged to keep the information up-to-date, and add their plugin as soon as it is committed to rubygems. Field names still need consolidation, I propose to use: Bio-BlastXMLParser - a fast (low-memory) parser for BLAST XML output * Install: gem install bio-blastxmlparser * Depends: Ruby >1.9, nokogiri * Documentation: https://github.com/pjotrp/blastxmlparser * Source: https://github.com/pjotrp/blastxmlparser * Rubygem: https://rubygems.org/gems/bio-blastxmlparser * Developer(s): Pjotr Prins I know some people favour standardizing plugin names to bio-plugin, which is probably a good idea on rubygems (so you can search for bio-*). Otherwise, I don't think it is so important. It is more important we start 'blessing' plugins from BioRuby itself. Pj.