From chapmanb at 50mail.com Sat Mar 27 08:36:53 2010 From: chapmanb at 50mail.com (Brad Chapman) Date: Sat, 27 Mar 2010 08:36:53 -0400 Subject: [GSoC] [Biopython] Introduction In-Reply-To: <201003270606.59717.chintal@iitk.ac.in> References: <201003270606.59717.chintal@iitk.ac.in> Message-ID: <20100327123653.GA1959@kunkel> Chintalagiri; Thanks for the e-mail and introduction. It's great to have you interested in Biopython and GSoC. The path you took to Biopython definitely echos the experience of lots of us; first you try building everything yourself and then realize: there must be some code frameworks out there that make this easier. > I'm interested in working on BioPython/PyCogent interop, because I see a lot > of potential in tying the two toolkits together and doing so before more > wheels are reinvented. The ability to look at evolutionary effects and > structural effects simultaneously could be quite interesting. [...] > I also have a couple of ideas in mind for BioPython projects, which really > aren't well fleshed out yet. I'll think about them, specifically, their need > and feasibility, and send the details to the list in a few days. Great, it sounds like you've already given this a bit of thought. You're welcome to either build off of the Biopython/PyCogent project or develop one of your own ideas into a proposal. Either way, the first step is to start putting together your project proposal and sharing it with us (Google Docs is a good option) so we can offer specific feedback on the programming and science part of things. We can work on the proposals up until Friday, April 9th. If you haven't already it's worth taking a look at the GSoC timeline for all the major dates: http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2010/timeline Generally, the proposal should contain: - A high level overview of what you hope to accomplish during the summer. - A week by week action plan for work to be done, including specific deliverables. This should be the bulk of the proposal. - A short section with relevant background and experience. We can work on this iteratively until the cutoff, and will be able to offer more specific feedback as we get an idea of your interests and directions. It would also be really useful to provide pointers to any open source code we could look at. If you don't have anything online now, uploading some relevant scripts to a GitHub or Bitbucket repository is a good start. Demonstrating bug fixing ability, as you mentioned, is also a helpful way to show off your programming skills to mentors. Thanks again. Looking forward to working on the proposal with you, Brad From diana.irina.lungu at gmail.com Mon Mar 29 18:18:55 2010 From: diana.irina.lungu at gmail.com (Diana Lungu) Date: Tue, 30 Mar 2010 01:18:55 +0300 Subject: [GSoC] [gsoc]All-Java Multiple Sequence Alignment (MSA) Message-ID: <4BB1274F.1070006@gmail.com> Hello to everyone! My name is Diana Lungu and I am an undergraduate at University Alexandru Ioan Cuza, Faculty of Computer Science Iasi, Romania. I am interested in Gsoc 2010 project "All-Java Multiple Sequence Alignment (MSA)". I have worked on several projects in Java in the last two years and I really enjoy Java programming. I have spent a nice amount of time developing with java the last two years but this will be my first open source project. Currently I am attending a course in Bioinformatics at my Faculty of Computer Science that is why I think this project suits me. There are several algorithms that offer an aligment from multiple sequences: Carrillo-Lipman, Feng and Doolittle, Barton-Stenberg etc. Is there a preference for one of these algorithms? What is more important: speed or the best optimum? Have a lovely day :) From andreas at sdsc.edu Mon Mar 29 18:50:47 2010 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 29 Mar 2010 15:50:47 -0700 Subject: [GSoC] [gsoc]All-Java Multiple Sequence Alignment (MSA) In-Reply-To: <4BB1274F.1070006@gmail.com> References: <4BB1274F.1070006@gmail.com> Message-ID: <59a41c431003291550o789299ebx75db945a5e04b99d@mail.gmail.com> Hi Diana, thanks for your email. I have already been contacted by several students who are interested in this project. As such it is not going to be easy to apply for this project and a very well written proposal will be needed in order to get a good ranking and to have a chance of getting selected by Google. We are also suggesting a 2nd project for BioJava: Identification and Classification of Posttranslational Modification of Proteins http://biojava.org/wiki/Google_Summer_of_Code . Besides this, Google also invites students to propose their own ideas... Talking about MSA, I would like to see an approach that is using modern parallelization techniques available through Java. I don't think the goal should be to re-implement an already existing approach but to come up with a combination of new and already established things. There is no simple answer to speed vs best optimum, both are important ... Andreas On Mon, Mar 29, 2010 at 3:18 PM, Diana Lungu wrote: > Hello to everyone! > > My name is Diana Lungu and I am an undergraduate at University Alexandru > Ioan Cuza, Faculty of Computer Science Iasi, Romania. > > I am interested in Gsoc 2010 project "All-Java Multiple Sequence Alignment > (MSA)". I have worked on several projects in Java in the last two years and > I really enjoy Java programming. I have spent a nice amount of time > developing with java the last two years but this will be my first open > source project. Currently I am attending a course in Bioinformatics at my > Faculty of Computer Science that is why I think this project suits me. There > are several algorithms that offer an aligment from multiple sequences: > Carrillo-Lipman, Feng and Doolittle, Barton-Stenberg etc. Is there a > preference for one of these algorithms? What is more important: speed or the > best optimum? > > Have a lovely day :) > > _______________________________________________ > GSoC mailing list > GSoC at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/gsoc > From rmb32 at cornell.edu Sun May 23 14:45:00 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Sun, 23 May 2010 11:45:00 -0700 Subject: [GSoC] coding period starting, set up project status blogs/pages Message-ID: <4BF977AC.5010506@cornell.edu> Hi all, As you are no doubt aware, the GSoC coding period begins tomorrow, May 24th. Students should begin work on their projects tomorrow. After some discussion on the OBF mentors mailing list, we've decided to make it a requirement that all GSoC students maintain a public log of progress updates for their project. Requirements for these are listed at the end of this email. I will be monitoring these pages to make sure students are on track. Students, please have these set up, with at least one status update, by next Sunday (May 29th). Here's to a great summer of code. This is OBF's first summer participating, let's make it count! Rob Buels 2010 OBF GSoC Administrator ====================================== Requirements for Student Progress Pages ====================================== 1.) The page must be linked from both the OBF subproject's GSoC page (for example, http://biojava.org/wiki/Google_Summer_of_Code), and from the main OBF GSoC page (http://open-bio.org/wiki/Google_Summer_of_Code) under the heading for your project that is already present there. 2.) The page can take any form, but must be either a new page on the project's wiki, or be hosted on a free blogging service. Example of externally-hosted project blog: http://gsoc-biolib-libsequence.blogspot.com/ 3.) Suggested frequency for posting new status updates is weekly, but the hard minimum is one (very significant) update every two weeks. Note: The OBF GSoC administrator will be monitoring these pages to make sure that students projects are progressing adequately. From rmb32 at cornell.edu Mon Jul 12 12:48:43 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Mon, 12 Jul 2010 09:48:43 -0700 Subject: [GSoC] gsoc midterm evaluations due Friday Message-ID: <4C3B476B.3030003@cornell.edu> Hi students and mentors, Please note that GSoC midterm evaluations are due this Friday, the 16th at 19:00 UTC. Mentors: The link for submitting evaluations is supposed to become available to mentors about 2.25 hours from now in the GSoC web application (http://socghop.appspot.com). Students: Good luck on your evaluations! Make sure your mentor(s) have everything they need to submit an accurate one! Thanks! Rob =========== GSoC web app: http://socghop.appspot.com GSoC Timeline: http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2010/timeline From rmb32 at cornell.edu Fri Jul 16 12:44:39 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 16 Jul 2010 09:44:39 -0700 Subject: [GSoC] midterm evaluations all in Message-ID: <4C408C77.5080207@cornell.edu> Hi all, I'm pleased to report that everybody has gotten their evaluation in before the deadline. Thanks! Rob From rmb32 at cornell.edu Thu Aug 12 18:01:09 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Thu, 12 Aug 2010 15:01:09 -0700 Subject: [GSoC] program ending soon Message-ID: <4C646F25.8040807@cornell.edu> Hi all, As you probably know from the GSoC timeline (http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2010/timeline), Monday was the suggested 'pencils down' date, and final evaluations are due from mentors on the 16th, which is Monday. If you aren't doing this already, mentors and students should be cooperating to tie up loose ends on the project, and prepare it for conclusion. Please note, in general it is more important to leave things in a cleaned-up, working state than it is to accomplish every objective of the project. You are working on an open-source project, other people are going to have to maintain the things you have done, and it's much easier for them to pick up where you left off if things are in a clean state. It should be obvious or at least documented what things are not done yet, which tests are passing and which are not, and why. I hope you all had a fun and productive summer! Rob OBF GSoC 2010 Admin From rmb32 at cornell.edu Thu Aug 12 18:04:22 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Thu, 12 Aug 2010 15:04:22 -0700 Subject: [GSoC] Fwd: GSoC 2010: Mentor + Org Admin Evaluation Questions In-Reply-To: References: Message-ID: <4C646FE6.8060109@cornell.edu> Hi all, In case this got lost in your mailbox, here are the questions for the final evaluations. I'm going ahead and sending this to students also since they might be interested in some of the things they are evaluated on. Rob ---------- Forwarded message ---------- From: Carol Smith Date: Mon, Aug 9, 2010 at 1:12 PM Subject: GSoC 2010: Mentor + Org Admin Evaluation Questions To: Google Summer of Code Mentors List Hi everyone, As promised, here are the questions for the final evaluations next week. Final evaluations are due 20 August at 19:00 UTC. Also, please note that there are two sets of questions here: the mentor evaluation questions and question for the org admins. Mentor evaluations, as always, are required for all mentors with assigned students participating in the program. Org admin evaluations are optional and are simply for us to continue improving the program. Please let me know if you have any further questions. Cheers, Carol ----- Mentor Evaluation Questions How would you rate the student?s performance on his/her project since the midterm evaluations? It?s improved since the midterm It?s stayed the same since the midterm It?s gotten worse since the midterm Considering your student?s original project proposal, how closely does the project produced reflect the project proposed? It?s almost exactly the same - there have been few changes to the project at all It?s similar - there have been changes over the course of the summer It?s significantly different - we changed the goals or scope of the project How much time have you spent on Google Summer of Code since the midterm evaluations (again, take into consideration both time mentoring the student and working on the program as a whole)? Less than 5 hours a week 5-10 hours a week 10-20 hours a week 20-30 hours a week 30-40 hours per week 40+ hours per week How does this amount of time compare to before the midterms? It?s less then before the midterms Its about the same It?s more than before the midterms How would you rate your student?s performance overall? Excellent - amongst the best people I?ve ever worked with Strong, solid performance OK Poor How would you rate your experience with the program overall? Excellent - one of the best programs I?ve ever participated in Very good OK Poor Did you have a co-mentor in the program this year? If so, would you consider this a help or a hindrance? Why? What one thing would you tell mentors for your organization to do in the future to help the students? experience with the program? What was the most rewarding or difficult part of the program for you this year? Anything else you?d like to tell us? Org Admin (Optional) Evaluation Questions How many years have you been involved in the Google Summer of Code program? This is my first year 2-3 years More than 3 years How many years has your organization been involved in the Google Summer of Code program (these don?t have to consecutive)? This is our first year 2-3 years 3+ years Please list one or two things you looked for when choosing mentors for the program this year. How would you say these things helped or hurt your organization?s experience with the program this year? What was the most rewarding or challenging part of participating in Google Summer of Code for you this year? Do you have any other feedback you?d like to offer us on how to improve the program? From andreas at sdsc.edu Wed Aug 18 14:26:23 2010 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 18 Aug 2010 11:26:23 -0700 Subject: [GSoC] Last week of Google Summer of Code Message-ID: Hi, This is the last week of this year's Google Summer of Code project and I am happy to announce that our two students Mark Chapman and Jianjiong Gao did an amazing job on their two projects "All Java Multiple Sequence Alignment" (MSA) and "Identification and Classification of Posttranslational Modification of Proteins" (PTM). For Multiple Sequence Alignments we?now have a flexible and multi-threaded MSA implementation that works in linear space and that, as an option, allows the users to define anchors that are used in the build up of the multiple alignment. The code is available as part of the new biojava3-alignment module. The Posttranslational Modification module (biojava3-protmod) can detect three different types of protein modifications in protein structures. It comes with an XML file & Java data structures to store information about different types of protein modifications, and contains entries from RESID, PDBCC and PSI-MOD. There is also a visualisation component to display cross linked PTM on a sequence viewer. Both Mark and Jianjiong have expressed their interest in maintaining and further developing their modules and I am looking forward to interacting more with them in the future. I want to thank the Mentors and Co-Mentors Peter Rose, Kyle Ellrott and Scooter Willis for their help and guidance for the projects, without them this would not have been possible. Thanks also to Robert Buels and the ?Open Bioinformatics Foundation for organizing our applications for GSoC and last, but not least, Google for sponsoring this Summer of Code. Happy BioJava-ing, Andreas From rmb32 at cornell.edu Wed Aug 18 21:46:40 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Wed, 18 Aug 2010 18:46:40 -0700 Subject: [GSoC] mentor final evaluations due Friday Message-ID: <4C6C8D00.4040207@cornell.edu> Hi all, A reminder: mentor final evaluations are due this Friday, August 20, at 19:00 UTC. At this time, students should be very close to having their projects wrapped up neatly, in preparation for submitting code samples to Google at the end of the month. I hope the program met everybody's expectations. Students and mentors, I'd be very interested in hearing any comments (confidential or otherwise) you might have about the program and how the summer went. Students, thanks for all your hard work! I hope you found your summer fun and rewarding! Even more thanks to the mentors for volunteering, mentoring a student can be really hard! Hopefully, you found it worthwhile. Thanks for a great summer all, let's hope we can do it again next year! Rob From czmasek at sanfordburnham.org Thu Aug 19 16:20:24 2010 From: czmasek at sanfordburnham.org (Christian M Zmasek) Date: Thu, 19 Aug 2010 13:20:24 -0700 Subject: [GSoC] mentor final evaluations due Friday In-Reply-To: <4C6C8D00.4040207@cornell.edu> References: <4C6C8D00.4040207@cornell.edu> Message-ID: <4C6D9208.3090607@sanfordburnham.org> Done! Robert Buels wrote: > Hi all, > > A reminder: mentor final evaluations are due this Friday, August 20, at > 19:00 UTC. > > At this time, students should be very close to having their projects > wrapped up neatly, in preparation for submitting code samples to Google > at the end of the month. > > I hope the program met everybody's expectations. Students and mentors, > I'd be very interested in hearing any comments (confidential or > otherwise) you might have about the program and how the summer went. > > Students, thanks for all your hard work! I hope you found your summer > fun and rewarding! Even more thanks to the mentors for volunteering, > mentoring a student can be really hard! Hopefully, you found it worthwhile. > > Thanks for a great summer all, let's hope we can do it again next year! > > Rob > _______________________________________________ > GSoC mailing list > GSoC at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/gsoc From cjfields at illinois.edu Thu Aug 19 16:45:54 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 19 Aug 2010 15:45:54 -0500 Subject: [GSoC] mentor final evaluations due Friday In-Reply-To: <4C6D9208.3090607@sanfordburnham.org> References: <4C6C8D00.4040207@cornell.edu> <4C6D9208.3090607@sanfordburnham.org> Message-ID: <4E306C1F-15CB-4EFD-BCD1-9A7868B46E21@illinois.edu> Thanks Christian! chris On Aug 19, 2010, at 3:20 PM, Christian M Zmasek wrote: > Done! > > > Robert Buels wrote: >> Hi all, >> A reminder: mentor final evaluations are due this Friday, August 20, at 19:00 UTC. >> At this time, students should be very close to having their projects wrapped up neatly, in preparation for submitting code samples to Google at the end of the month. >> I hope the program met everybody's expectations. Students and mentors, I'd be very interested in hearing any comments (confidential or otherwise) you might have about the program and how the summer went. >> Students, thanks for all your hard work! I hope you found your summer fun and rewarding! Even more thanks to the mentors for volunteering, mentoring a student can be really hard! Hopefully, you found it worthwhile. >> Thanks for a great summer all, let's hope we can do it again next year! >> Rob >> _______________________________________________ >> GSoC mailing list >> GSoC at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/gsoc > > _______________________________________________ > GSoC mailing list > GSoC at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/gsoc From rmb32 at cornell.edu Fri Aug 20 16:55:17 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 20 Aug 2010 13:55:17 -0700 Subject: [GSoC] all mentor evaluations completed Message-ID: <4C6EEBB5.7090807@cornell.edu> I'm pleased to report that all of our mentor evaluations and remaining student evaluations have been completed on time. Good job everyone! Rob From chapmanb at 50mail.com Sat Mar 27 12:36:53 2010 From: chapmanb at 50mail.com (Brad Chapman) Date: Sat, 27 Mar 2010 08:36:53 -0400 Subject: [GSoC] [Biopython] Introduction In-Reply-To: <201003270606.59717.chintal@iitk.ac.in> References: <201003270606.59717.chintal@iitk.ac.in> Message-ID: <20100327123653.GA1959@kunkel> Chintalagiri; Thanks for the e-mail and introduction. It's great to have you interested in Biopython and GSoC. The path you took to Biopython definitely echos the experience of lots of us; first you try building everything yourself and then realize: there must be some code frameworks out there that make this easier. > I'm interested in working on BioPython/PyCogent interop, because I see a lot > of potential in tying the two toolkits together and doing so before more > wheels are reinvented. The ability to look at evolutionary effects and > structural effects simultaneously could be quite interesting. [...] > I also have a couple of ideas in mind for BioPython projects, which really > aren't well fleshed out yet. I'll think about them, specifically, their need > and feasibility, and send the details to the list in a few days. Great, it sounds like you've already given this a bit of thought. You're welcome to either build off of the Biopython/PyCogent project or develop one of your own ideas into a proposal. Either way, the first step is to start putting together your project proposal and sharing it with us (Google Docs is a good option) so we can offer specific feedback on the programming and science part of things. We can work on the proposals up until Friday, April 9th. If you haven't already it's worth taking a look at the GSoC timeline for all the major dates: http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2010/timeline Generally, the proposal should contain: - A high level overview of what you hope to accomplish during the summer. - A week by week action plan for work to be done, including specific deliverables. This should be the bulk of the proposal. - A short section with relevant background and experience. We can work on this iteratively until the cutoff, and will be able to offer more specific feedback as we get an idea of your interests and directions. It would also be really useful to provide pointers to any open source code we could look at. If you don't have anything online now, uploading some relevant scripts to a GitHub or Bitbucket repository is a good start. Demonstrating bug fixing ability, as you mentioned, is also a helpful way to show off your programming skills to mentors. Thanks again. Looking forward to working on the proposal with you, Brad From diana.irina.lungu at gmail.com Mon Mar 29 22:18:55 2010 From: diana.irina.lungu at gmail.com (Diana Lungu) Date: Tue, 30 Mar 2010 01:18:55 +0300 Subject: [GSoC] [gsoc]All-Java Multiple Sequence Alignment (MSA) Message-ID: <4BB1274F.1070006@gmail.com> Hello to everyone! My name is Diana Lungu and I am an undergraduate at University Alexandru Ioan Cuza, Faculty of Computer Science Iasi, Romania. I am interested in Gsoc 2010 project "All-Java Multiple Sequence Alignment (MSA)". I have worked on several projects in Java in the last two years and I really enjoy Java programming. I have spent a nice amount of time developing with java the last two years but this will be my first open source project. Currently I am attending a course in Bioinformatics at my Faculty of Computer Science that is why I think this project suits me. There are several algorithms that offer an aligment from multiple sequences: Carrillo-Lipman, Feng and Doolittle, Barton-Stenberg etc. Is there a preference for one of these algorithms? What is more important: speed or the best optimum? Have a lovely day :) From andreas at sdsc.edu Mon Mar 29 22:50:47 2010 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 29 Mar 2010 15:50:47 -0700 Subject: [GSoC] [gsoc]All-Java Multiple Sequence Alignment (MSA) In-Reply-To: <4BB1274F.1070006@gmail.com> References: <4BB1274F.1070006@gmail.com> Message-ID: <59a41c431003291550o789299ebx75db945a5e04b99d@mail.gmail.com> Hi Diana, thanks for your email. I have already been contacted by several students who are interested in this project. As such it is not going to be easy to apply for this project and a very well written proposal will be needed in order to get a good ranking and to have a chance of getting selected by Google. We are also suggesting a 2nd project for BioJava: Identification and Classification of Posttranslational Modification of Proteins http://biojava.org/wiki/Google_Summer_of_Code . Besides this, Google also invites students to propose their own ideas... Talking about MSA, I would like to see an approach that is using modern parallelization techniques available through Java. I don't think the goal should be to re-implement an already existing approach but to come up with a combination of new and already established things. There is no simple answer to speed vs best optimum, both are important ... Andreas On Mon, Mar 29, 2010 at 3:18 PM, Diana Lungu wrote: > Hello to everyone! > > My name is Diana Lungu and I am an undergraduate at University Alexandru > Ioan Cuza, Faculty of Computer Science Iasi, Romania. > > I am interested in Gsoc 2010 project "All-Java Multiple Sequence Alignment > (MSA)". I have worked on several projects in Java in the last two years and > I really enjoy Java programming. I have spent a nice amount of time > developing with java the last two years but this will be my first open > source project. Currently I am attending a course in Bioinformatics at my > Faculty of Computer Science that is why I think this project suits me. There > are several algorithms that offer an aligment from multiple sequences: > Carrillo-Lipman, Feng and Doolittle, Barton-Stenberg etc. Is there a > preference for one of these algorithms? What is more important: speed or the > best optimum? > > Have a lovely day :) > > _______________________________________________ > GSoC mailing list > GSoC at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/gsoc > From rmb32 at cornell.edu Sun May 23 18:45:00 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Sun, 23 May 2010 11:45:00 -0700 Subject: [GSoC] coding period starting, set up project status blogs/pages Message-ID: <4BF977AC.5010506@cornell.edu> Hi all, As you are no doubt aware, the GSoC coding period begins tomorrow, May 24th. Students should begin work on their projects tomorrow. After some discussion on the OBF mentors mailing list, we've decided to make it a requirement that all GSoC students maintain a public log of progress updates for their project. Requirements for these are listed at the end of this email. I will be monitoring these pages to make sure students are on track. Students, please have these set up, with at least one status update, by next Sunday (May 29th). Here's to a great summer of code. This is OBF's first summer participating, let's make it count! Rob Buels 2010 OBF GSoC Administrator ====================================== Requirements for Student Progress Pages ====================================== 1.) The page must be linked from both the OBF subproject's GSoC page (for example, http://biojava.org/wiki/Google_Summer_of_Code), and from the main OBF GSoC page (http://open-bio.org/wiki/Google_Summer_of_Code) under the heading for your project that is already present there. 2.) The page can take any form, but must be either a new page on the project's wiki, or be hosted on a free blogging service. Example of externally-hosted project blog: http://gsoc-biolib-libsequence.blogspot.com/ 3.) Suggested frequency for posting new status updates is weekly, but the hard minimum is one (very significant) update every two weeks. Note: The OBF GSoC administrator will be monitoring these pages to make sure that students projects are progressing adequately. From rmb32 at cornell.edu Mon Jul 12 16:48:43 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Mon, 12 Jul 2010 09:48:43 -0700 Subject: [GSoC] gsoc midterm evaluations due Friday Message-ID: <4C3B476B.3030003@cornell.edu> Hi students and mentors, Please note that GSoC midterm evaluations are due this Friday, the 16th at 19:00 UTC. Mentors: The link for submitting evaluations is supposed to become available to mentors about 2.25 hours from now in the GSoC web application (http://socghop.appspot.com). Students: Good luck on your evaluations! Make sure your mentor(s) have everything they need to submit an accurate one! Thanks! Rob =========== GSoC web app: http://socghop.appspot.com GSoC Timeline: http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2010/timeline From rmb32 at cornell.edu Fri Jul 16 16:44:39 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 16 Jul 2010 09:44:39 -0700 Subject: [GSoC] midterm evaluations all in Message-ID: <4C408C77.5080207@cornell.edu> Hi all, I'm pleased to report that everybody has gotten their evaluation in before the deadline. Thanks! Rob From rmb32 at cornell.edu Thu Aug 12 22:01:09 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Thu, 12 Aug 2010 15:01:09 -0700 Subject: [GSoC] program ending soon Message-ID: <4C646F25.8040807@cornell.edu> Hi all, As you probably know from the GSoC timeline (http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2010/timeline), Monday was the suggested 'pencils down' date, and final evaluations are due from mentors on the 16th, which is Monday. If you aren't doing this already, mentors and students should be cooperating to tie up loose ends on the project, and prepare it for conclusion. Please note, in general it is more important to leave things in a cleaned-up, working state than it is to accomplish every objective of the project. You are working on an open-source project, other people are going to have to maintain the things you have done, and it's much easier for them to pick up where you left off if things are in a clean state. It should be obvious or at least documented what things are not done yet, which tests are passing and which are not, and why. I hope you all had a fun and productive summer! Rob OBF GSoC 2010 Admin From rmb32 at cornell.edu Thu Aug 12 22:04:22 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Thu, 12 Aug 2010 15:04:22 -0700 Subject: [GSoC] Fwd: GSoC 2010: Mentor + Org Admin Evaluation Questions In-Reply-To: References: Message-ID: <4C646FE6.8060109@cornell.edu> Hi all, In case this got lost in your mailbox, here are the questions for the final evaluations. I'm going ahead and sending this to students also since they might be interested in some of the things they are evaluated on. Rob ---------- Forwarded message ---------- From: Carol Smith Date: Mon, Aug 9, 2010 at 1:12 PM Subject: GSoC 2010: Mentor + Org Admin Evaluation Questions To: Google Summer of Code Mentors List Hi everyone, As promised, here are the questions for the final evaluations next week. Final evaluations are due 20 August at 19:00 UTC. Also, please note that there are two sets of questions here: the mentor evaluation questions and question for the org admins. Mentor evaluations, as always, are required for all mentors with assigned students participating in the program. Org admin evaluations are optional and are simply for us to continue improving the program. Please let me know if you have any further questions. Cheers, Carol ----- Mentor Evaluation Questions How would you rate the student?s performance on his/her project since the midterm evaluations? It?s improved since the midterm It?s stayed the same since the midterm It?s gotten worse since the midterm Considering your student?s original project proposal, how closely does the project produced reflect the project proposed? It?s almost exactly the same - there have been few changes to the project at all It?s similar - there have been changes over the course of the summer It?s significantly different - we changed the goals or scope of the project How much time have you spent on Google Summer of Code since the midterm evaluations (again, take into consideration both time mentoring the student and working on the program as a whole)? Less than 5 hours a week 5-10 hours a week 10-20 hours a week 20-30 hours a week 30-40 hours per week 40+ hours per week How does this amount of time compare to before the midterms? It?s less then before the midterms Its about the same It?s more than before the midterms How would you rate your student?s performance overall? Excellent - amongst the best people I?ve ever worked with Strong, solid performance OK Poor How would you rate your experience with the program overall? Excellent - one of the best programs I?ve ever participated in Very good OK Poor Did you have a co-mentor in the program this year? If so, would you consider this a help or a hindrance? Why? What one thing would you tell mentors for your organization to do in the future to help the students? experience with the program? What was the most rewarding or difficult part of the program for you this year? Anything else you?d like to tell us? Org Admin (Optional) Evaluation Questions How many years have you been involved in the Google Summer of Code program? This is my first year 2-3 years More than 3 years How many years has your organization been involved in the Google Summer of Code program (these don?t have to consecutive)? This is our first year 2-3 years 3+ years Please list one or two things you looked for when choosing mentors for the program this year. How would you say these things helped or hurt your organization?s experience with the program this year? What was the most rewarding or challenging part of participating in Google Summer of Code for you this year? Do you have any other feedback you?d like to offer us on how to improve the program? From andreas at sdsc.edu Wed Aug 18 18:26:23 2010 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 18 Aug 2010 11:26:23 -0700 Subject: [GSoC] Last week of Google Summer of Code Message-ID: Hi, This is the last week of this year's Google Summer of Code project and I am happy to announce that our two students Mark Chapman and Jianjiong Gao did an amazing job on their two projects "All Java Multiple Sequence Alignment" (MSA) and "Identification and Classification of Posttranslational Modification of Proteins" (PTM). For Multiple Sequence Alignments we?now have a flexible and multi-threaded MSA implementation that works in linear space and that, as an option, allows the users to define anchors that are used in the build up of the multiple alignment. The code is available as part of the new biojava3-alignment module. The Posttranslational Modification module (biojava3-protmod) can detect three different types of protein modifications in protein structures. It comes with an XML file & Java data structures to store information about different types of protein modifications, and contains entries from RESID, PDBCC and PSI-MOD. There is also a visualisation component to display cross linked PTM on a sequence viewer. Both Mark and Jianjiong have expressed their interest in maintaining and further developing their modules and I am looking forward to interacting more with them in the future. I want to thank the Mentors and Co-Mentors Peter Rose, Kyle Ellrott and Scooter Willis for their help and guidance for the projects, without them this would not have been possible. Thanks also to Robert Buels and the ?Open Bioinformatics Foundation for organizing our applications for GSoC and last, but not least, Google for sponsoring this Summer of Code. Happy BioJava-ing, Andreas From rmb32 at cornell.edu Thu Aug 19 01:46:40 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Wed, 18 Aug 2010 18:46:40 -0700 Subject: [GSoC] mentor final evaluations due Friday Message-ID: <4C6C8D00.4040207@cornell.edu> Hi all, A reminder: mentor final evaluations are due this Friday, August 20, at 19:00 UTC. At this time, students should be very close to having their projects wrapped up neatly, in preparation for submitting code samples to Google at the end of the month. I hope the program met everybody's expectations. Students and mentors, I'd be very interested in hearing any comments (confidential or otherwise) you might have about the program and how the summer went. Students, thanks for all your hard work! I hope you found your summer fun and rewarding! Even more thanks to the mentors for volunteering, mentoring a student can be really hard! Hopefully, you found it worthwhile. Thanks for a great summer all, let's hope we can do it again next year! Rob From czmasek at sanfordburnham.org Thu Aug 19 20:20:24 2010 From: czmasek at sanfordburnham.org (Christian M Zmasek) Date: Thu, 19 Aug 2010 13:20:24 -0700 Subject: [GSoC] mentor final evaluations due Friday In-Reply-To: <4C6C8D00.4040207@cornell.edu> References: <4C6C8D00.4040207@cornell.edu> Message-ID: <4C6D9208.3090607@sanfordburnham.org> Done! Robert Buels wrote: > Hi all, > > A reminder: mentor final evaluations are due this Friday, August 20, at > 19:00 UTC. > > At this time, students should be very close to having their projects > wrapped up neatly, in preparation for submitting code samples to Google > at the end of the month. > > I hope the program met everybody's expectations. Students and mentors, > I'd be very interested in hearing any comments (confidential or > otherwise) you might have about the program and how the summer went. > > Students, thanks for all your hard work! I hope you found your summer > fun and rewarding! Even more thanks to the mentors for volunteering, > mentoring a student can be really hard! Hopefully, you found it worthwhile. > > Thanks for a great summer all, let's hope we can do it again next year! > > Rob > _______________________________________________ > GSoC mailing list > GSoC at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/gsoc From cjfields at illinois.edu Thu Aug 19 20:45:54 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 19 Aug 2010 15:45:54 -0500 Subject: [GSoC] mentor final evaluations due Friday In-Reply-To: <4C6D9208.3090607@sanfordburnham.org> References: <4C6C8D00.4040207@cornell.edu> <4C6D9208.3090607@sanfordburnham.org> Message-ID: <4E306C1F-15CB-4EFD-BCD1-9A7868B46E21@illinois.edu> Thanks Christian! chris On Aug 19, 2010, at 3:20 PM, Christian M Zmasek wrote: > Done! > > > Robert Buels wrote: >> Hi all, >> A reminder: mentor final evaluations are due this Friday, August 20, at 19:00 UTC. >> At this time, students should be very close to having their projects wrapped up neatly, in preparation for submitting code samples to Google at the end of the month. >> I hope the program met everybody's expectations. Students and mentors, I'd be very interested in hearing any comments (confidential or otherwise) you might have about the program and how the summer went. >> Students, thanks for all your hard work! I hope you found your summer fun and rewarding! Even more thanks to the mentors for volunteering, mentoring a student can be really hard! Hopefully, you found it worthwhile. >> Thanks for a great summer all, let's hope we can do it again next year! >> Rob >> _______________________________________________ >> GSoC mailing list >> GSoC at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/gsoc > > _______________________________________________ > GSoC mailing list > GSoC at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/gsoc From rmb32 at cornell.edu Fri Aug 20 20:55:17 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 20 Aug 2010 13:55:17 -0700 Subject: [GSoC] all mentor evaluations completed Message-ID: <4C6EEBB5.7090807@cornell.edu> I'm pleased to report that all of our mentor evaluations and remaining student evaluations have been completed on time. Good job everyone! Rob