From clements at nescent.org Tue Feb 1 00:57:52 2011 From: clements at nescent.org (Dave Clements) Date: Mon, 31 Jan 2011 21:57:52 -0800 Subject: [Open-bio-l] March 2011 GMOD Meeting Registration is now open In-Reply-To: References: Message-ID: Hello all, Registration is now open for the March 2011 GMOD Meeting ( http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting). This meeting will be held March 5-6, as part of GMOD Americas 2011, which also includes a day of Satellite Meetings, a GMOD Course (already full), and for the first time, an "Introduction to GMOD" session the night before the meeting for GMOD newcomers. GMOD Americas 2011 events are being held at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United States. As with previous GMOD meetings, this meeting will have a mixture of project talks, component talks, and user talks. Our guest speaker is Dr. Eric Stone of North Carolina State University. Dr. Stone will talk about his experience on the "Drosophila Genome Reference Panel," a project that is sequencing 192 lines. See http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting#Agenda for more. The agenda is driven by attendee suggestions, and you are encouraged to add your suggestions now ( http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting#Agenda_Proposals). For examples of what happens at a GMOD meeting, see the writeup of the September 2010 GMOD Meeting (http://gmod.oicr.on.ca/wiki/September_2010_GMOD_Meeting), or any previous meeting. GMOD meetings are an excellent way to meet GMOD developers and users and to learn (and affect) what's coming in the project. Registration for the March 2011 GMOD Meeting is $80 on or before February 18 <<<<======= $95 after February 18 Please register early, both to save money, and ensure a spot. You are also strongly encouraged to sign up for (or propose) a Satellite Meeting (more details to come). Details on transportation, suggested lodging, and other logistics are on the GMOD Americas 2011 page. This meeting, and all GMOD Americas 2011 events, are jointly sponsored by NESCent and the Galaxy Project. Dave Clements Galaxy Project -- http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://nescent.org http://usegalaxy.org/ From clements at nescent.org Wed Feb 2 01:25:39 2011 From: clements at nescent.org (Dave Clements) Date: Tue, 1 Feb 2011 22:25:39 -0800 Subject: [Open-bio-l] GMOD Satellite Meetings, March 7, NESCent, Durham, NC In-Reply-To: References: Message-ID: Hello all, Yesterday, we opened registration for the March 2011 GMOD Meeting (see http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting). *That meeting is part of a larger event, GMOD Americas 2011, that also includes several Satellite Meetings on March 7*, the day after the meeting ends. Satellite meetings are smaller groups of people meeting to discuss a common interest, or work on a common problem (think special interest groups / birds-of-a-feather). Unlike the GMOD Meeting, there is *no registration fee * for the Satellites, and you don't even need to go to any other GMOD Americas events to participate in the Satellites. *If you are in the area, or attending other GMOD Americas events, or are just very interested in the topic, we strongly encourage you to attend.* The current list of Satellites (see http://gmod.oicr.on.ca/wiki/Satellite_Meetings_-_GMOD_Americas_2011) includes: - *GMOD Evo Hackathon Followup*, organized by Duke Leto . A followup to the GMOD Evo Hackathonheld at NESCent in November 2011. You didn't to participate in the original event to participate in this followup. Also, if there is interest, this satellite can extend for more than one day. - *Customizing and Extending JBrowse *, organized by Mitch Skinner . JBrowse has a few different extension points, but they're not (yet) well-documented or widely used. The GMOD meeting would be a good time to review those APIs, relate them to the things that people want to do with them, discuss any potential changes or new APIs to support specific use cases, and potentially start to implement an extension. - *GMOD Web services toolkit* , organized by Josh Goodman . Come to work on or discuss the GMOD Web services API and the toolkit . - *GMOD in the Sequencing Center*, organized by Chris Hemmerich , Dave Clements . Sequencing centers have tremendous bioinformatics needs that GMOD can help address. Attend this satellite to find out what other sequencing centers are doing with GMOD, and how GMOD can help you help your researchers. If you are interested in participating in these, please contact the organizers, and/or add your name to the satellite's participants list on the wiki. Satellites can be organized by anyone. If you have a topic you would like to cover, please add it to the list and announce it the appropriate mailing lists. Several previous satellites are written up on the GMOD wiki, if you want an idea of what happens at a satellite. Finally, please let me and Scott know if you have any questions. Thanks, and hope to see you in March! Dave C. -- http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://usegalaxy.org/ From clementsgalaxy at gmail.com Thu Feb 3 20:01:01 2011 From: clementsgalaxy at gmail.com (Dave Clements) Date: Thu, 3 Feb 2011 17:01:01 -0800 Subject: [Open-bio-l] Galaxy Community Conference, May 25-26, Lunteren, The Netherlands Message-ID: We are pleased to announce the *2011 Galaxy Community Conference*, being held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your own and your community's research. See http://galaxy.psu.edu/gcc2011/* for complete details. * *About Galaxy: *Galaxy is an open, web-based platform for *accessible, reproducible, and transparent* computational biomedical research. - *Accessibility:* Galaxy enables users without programming experience to easily specify parameters and run tools and workflows. - *Reproducibility:* Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis. - *Transparency:* Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis. Galaxy is open source for all organizations. The public Galaxy service ( http://usegalaxy.org) makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist that has access to the Internet. Local Galaxy servers can be set up by downloading the Galaxy application and customizing it to meet particular needs. *Conference Overview: * This event aims to engage a broader community of developers, data producers, tool creators, and core facility and other research hub staff to become an active part of the Galaxy community. We'll cover defining resources in the Galaxy framework, increasing their visibility and making them easier to use and integrate with other resources, how to extend Galaxy to use custom data sources and custom tools, and best practices for using Galaxy in your organization. Additional topics include, but are not limited to: * Talks submitted by the Galaxy community * Integration of tools (including NGS analysis tools) and distributed job management * Deployment of Galaxy instances on local resources and on the Cloud * Management of large datasets with the Galaxy Library System * Using the Galaxy LIMS functionality at NGS sequencing facilities * Visualizing Data without leaving Galaxy * Performing reproducible research * Performing and sharing complex analyses with Workflows * An "Introduction to Galaxy" session, offered on May 24, for Galaxy newcomers. *Registration: * The conference fee is ?100 on or before April 24, and ?120 after that. The meeting is being held at the Conference Centre De Werelt in Lunteren, The Netherlands, which is also the conference hotel. You are encouraged to register early, as space at the hotel (and at the "Intro to Galaxy" session) is limited and is likely to fill up before the conference itself does. See http://galaxy.psu.edu/gcc2011/Register.html * Abstract Submission: * Abstracts are now being accepted for short oral presentations. Proposals on any topic of interest to the Galaxy community are welcome and encouraged. The abstract submission deadline is the end of February 28. See http://galaxy.psu.edu/gcc2011/Abstracts.html * * *Sponsors * The 2011 Galaxy Community Conference is co-sponsored by the US National Science Foundation (NSF, http://www.nsf.gov/), and the Netherlands Bioinformatics Centre (NBIC, http://www.nbic.nl/). NBIC is a collaborative institute of the bioinformatics groups in the Netherlands. Together, these groups perform cutting-edge research, develop novel tools and support platforms, create an e-science infrastructure and educate the next generations of bioinformaticians. We are looking forward to a great conference and hope to see you in the Netherlands! The Galaxy and NBIC Teams -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ From bonnalraoul at ingm.it Wed Feb 9 06:58:50 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 9 Feb 2011 12:58:50 +0100 Subject: [Open-bio-l] [BioRuby] Workflows and Parallelization In-Reply-To: <4D509731.4050209@be.to> References: <2D62D256-4CBD-4793-97F1-37A908C734F6@ingm.it> <4D10B9AE.2010206@be.to> <5EB99E14-47EF-4267-99F5-216C16A93426@ingm.it> <20110207171655.GA25517@thebird.nl> <4D509731.4050209@be.to> Message-ID: <97CFB702-337B-4608-8AF5-CADAB7B1702A@ingm.it> Hello folks, tweeting around I found these videos http://www.youtube.com/watch?v=1ntxT-47VPA http://www.youtube.com/watch?v=OpaiGYxkSuQ&feature=related http://www.youtube.com/watch?v=P40akGWJ_gY&feature=related Project home page: http://www.gnu.org/software/parallel/ Very useful in many contexts. @BioRuby: I think that we can explore how to use it in workflows. On 08/feb/2011, at 02.06, MISHIMA, Hiroyuki wrote: > Hi, > > I added Pjotr's information on the BioRuby wiki > ( http://bioruby.open-bio.org/wiki/Workflows ). > > I also updated a subsection about GridEngine. Univa took over GridEngine > development from Oracle. > > Sincerely yours, > Hiro. > > Pjotr Prins wrote (2011/02/08 2:16): >> rq - which can parallelize calculations with zero-administration >> (all that is needed is a shared dir). > > -- > 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 -- Ra From clements at nescent.org Mon Feb 14 14:43:22 2011 From: clements at nescent.org (Dave Clements) Date: Mon, 14 Feb 2011 11:43:22 -0800 Subject: [Open-bio-l] March 2011 GMOD Meeting early registration closes this Friday In-Reply-To: References: Message-ID: Hello all, *Register for the March 2011 GMOD Meeting ( http://gmod.org/wiki/March_2011_GMOD_Meeting) by this Friday, Feb 18, and save over 15%.* The March meeting is part of GMOD Americas 2011 ( http://gmod.org/wiki/GMOD_Americas_2011), an event that includes Satellite Meetings, a GMOD Course (already full), and for the first time, an "Introduction to GMOD" session the night before the meeting for GMOD newcomers. GMOD Americas 2011 events are being held at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United States. Also, if you have a topic you want to discuss at the meeting, please send it to Scott Cain ASAP so he can get you on the program. *About GMOD:* GMOD is the Generic Model Organism Database project, a collection of interoperable open-source software components for annotating, visualizing, managing and analyzing biological data. GMOD is also an active community of software developers and biologists addressing common challenges with their data. The GMOD suite includes widely used tools such as GBrowse and JBrowse (and WebGBrowse) for genome browsing, Apollo and MAKER for genome annotation, GBrowse_syn and CMap for comparative genomics visualization, Chado, BioMart and InterMine for data integration, management, and querying, and Galaxy and Ergatis (and ISGA) for data analysis. *Meeting Overview: *As with previous GMOD meetings, this meeting will have a mixture of project talks, component talks, and user talks. Our guest speaker is Dr. Eric Stone of North Carolina State University. Dr. Stone will talk about his experience on the "Drosophila Genome Reference Panel," a project that is sequencing and annotating almost 200 inbred lines. The agenda is driven by attendee suggestions, and you are encouraged to add your suggestions now. For an idea of what happens at a GMOD meeting, see the writeup of the September 2010 GMOD Meeting. GMOD meetings are an excellent way to meet GMOD developers and users and to learn (and affect) what's coming in the project. *Registration: *Registration for the March 2011 GMOD Meeting is $80 on or before February 18 $95 after February 18 Please register early, both to save money, and ensure a spot. You are also strongly encouraged to submit a talk and/or sign up for (or propose) a Satellite Meeting. Details on transportation, suggested lodging, and other logistics are on the GMOD Americas 2011 page. This meeting, and all GMOD Americas 2011 events, are jointly sponsored by NESCent and the Galaxy Project. Hope to see you in North Carolina! Dave Clements Galaxy Project -- http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://usegalaxy.org/ http://getgalaxy.org/ From clementsgalaxy at gmail.com Tue Feb 22 12:16:12 2011 From: clementsgalaxy at gmail.com (Dave Clements) Date: Tue, 22 Feb 2011 09:16:12 -0800 Subject: [Open-bio-l] Galaxy Community Conference, May 25-26, Lunteren, The Netherlands In-Reply-To: References: Message-ID: Hello all, Just a reminder that the abstract submission deadline for the Galaxy Community Conference is next Monday, February 28. See http://galaxy.psu.edu/gcc2011/Abstracts.html for details. Cheers, Dave C. On Thu, Feb 3, 2011 at 5:01 PM, Dave Clements wrote: > We are pleased to announce the *2011 Galaxy Community Conference*, being > held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature > two full days of presentations and discussion on extending Galaxy to use new > tools and data sources, deploying Galaxy at your organization, and best > practices for using Galaxy to further your own and your community's > research. See http://galaxy.psu.edu/gcc2011/* for complete details. > * > *About Galaxy: > *Galaxy is an open, web-based platform for *accessible, reproducible, and > transparent* computational biomedical research. > > - *Accessibility:* Galaxy enables users without programming experience > to easily specify parameters and run tools and workflows. > - *Reproducibility:* Galaxy captures all information necessary so that > any user can repeat and understand a complete computational analysis. > - *Transparency:* Galaxy enables users to share and publish analyses > via the web and create Pages--interactive, web-based documents that describe > a complete analysis. > > Galaxy is open source for all organizations. The public Galaxy service ( > http://usegalaxy.org) makes analysis tools, genomic data, > tutorial demonstrations, persistent workspaces, and publication services > available to any scientist that has access to the Internet. Local > Galaxy servers can be set up by downloading the Galaxy application and > customizing it to meet particular needs. > > *Conference Overview: > * > This event aims to engage a broader community of developers, data > producers, tool creators, and core facility and other research hub staff to > become an active part of the Galaxy community. We'll cover defining > resources in the Galaxy framework, increasing their visibility and making > them easier to use and integrate with other resources, how to extend Galaxy > to use custom data sources and custom tools, and best practices for using > Galaxy in your organization. > > Additional topics include, but are not limited to: > * Talks submitted by the Galaxy community > * Integration of tools (including NGS analysis tools) and distributed job > management > * Deployment of Galaxy instances on local resources and on the Cloud > * Management of large datasets with the Galaxy Library System > * Using the Galaxy LIMS functionality at NGS sequencing facilities > * Visualizing Data without leaving Galaxy > * Performing reproducible research > * Performing and sharing complex analyses with Workflows > * An "Introduction to Galaxy" session, offered on May 24, for Galaxy > newcomers. > > *Registration: > * > The conference fee is ?100 on or before April 24, and ?120 after that. The > meeting is being held at the Conference Centre De Werelt in Lunteren, The > Netherlands, which is also the conference hotel. You are encouraged to > register early, as space at the hotel (and at the "Intro to Galaxy" session) > is limited and is likely to fill up before the conference itself does. See > http://galaxy.psu.edu/gcc2011/Register.html > * > Abstract Submission: > * > Abstracts are now being accepted for short oral presentations. Proposals > on any topic of interest to the Galaxy community are welcome and > encouraged. The abstract submission deadline is the end of February 28. > See http://galaxy.psu.edu/gcc2011/Abstracts.html > * * > *Sponsors > * > The 2011 Galaxy Community Conference is co-sponsored by the US National > Science Foundation (NSF, http://www.nsf.gov/), and the Netherlands > Bioinformatics Centre (NBIC, http://www.nbic.nl/). NBIC is a > collaborative institute of the bioinformatics groups in the Netherlands. > Together, these groups perform cutting-edge research, develop novel tools > and support platforms, create an e-science infrastructure and educate the > next generations of bioinformaticians. > > We are looking forward to a great conference and hope to see you in the > Netherlands! > > The Galaxy and NBIC Teams > > -- > http://galaxy.psu.edu/gcc2011/ > http://getgalaxy.org > http://usegalaxy.org/ > -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ From p.j.a.cock at googlemail.com Wed Feb 23 04:24:21 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 23 Feb 2011 09:24:21 +0000 Subject: [Open-bio-l] [Biopython] Biopython library for muliple sequence alignment In-Reply-To: <001501cbd324$c70a8570$551f9050$@jp> References: <001501cbd324$c70a8570$551f9050$@jp> Message-ID: On Wed, Feb 23, 2011 at 6:42 AM, Rojan Shrestha wrote: > Hello: > > I want to do multiple sequence alignment using CLUSTW. Instead of > standalone, I would like to use in my own program through biopython. I would > like to know that whether biopython has clustw function or not. It would be > very good if somebody ?gives information about this. > > Regards, > > Rojan Hello Rojan, Biopython (and BioPerl too I believe) doesn't have any multiple sequence alignment code itself. Biopython does has pairwise sequence alignment code (with a fast implementation in C). Instead (again, like BioPerl) Biopython has a wrapper and parser for calling the ClustalW command line tool from within your script and loading its output. Similarly for other alignment tools like Muscle. If you really want to be able modify the multiple sequence alignment code itself, some of these command line tools are open source. Also, I *think* that BioJava has some code for this. I don't know what BioRuby does. Peter P.S. You only really need to ask this on the Biopython Discussion List. Since you included the OBF cross project list I have tried to comment on how the other projects handle this as well. From chapmanb at 50mail.com Thu Feb 24 13:24:56 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu, 24 Feb 2011 13:24:56 -0500 Subject: [Open-bio-l] BOSC 2011 topic organizers and Codefest Message-ID: <20110224182456.GI20125@sobchak.mgh.harvard.edu> Hi all; This year the Bioinformatics Open Source Conference (BOSC) will be taking place in Vienna, Austria on July 15-16th. This is a yearly opportunity for open source bioinformatics developers to get together in person and discuss on-going projects. Nomi Harris, Peter Rice and the other organizing committee members are already hard at work planning for the conference: http://www.open-bio.org/wiki/BOSC_2011 The call for abstracts opens next Monday, and extends through April 18th, and we've been brainstorming potential session topics. This year we've tried to focus each of the sessions around a particular biological problem or computational approach. We hope this will draw some interesting parallels between work being done in different groups, and encourage even more collaboration. We are actively looking for community members who are interested in heading up the organization of a topic. The general idea is to build a cohesive set of talks within a session. How you'd like to do this is completely flexible but some of the ideas we've been discussing are: - Having a short introductory talk to provide an overview of an area, framing the different talks within this context. - Forgoing individual question/answer and instead combining this time into a longer panel-style discussion with all of the speakers. This would help stimulate back and forth between the different projects and the audience. If you are interested in a particular topic and would like to help with the organization, please send an e-mail to the BOSC mailing list: bosc at lists.open-bio.org. We're also open to new topic suggestions, and will look to add one or two more topics to our current list. Finally, there will be a two day coding session prior to BOSC as a follow up to last year's fun and productive Codefest: http://www.open-bio.org/wiki/Codefest_2011 The Metalab, a unique hacker space in Vienna, has kindly agreed to host us for the two days. If you are at all interested, please add your name to the attendees list on the wiki. Since the Metalab organizers don't know us personally, we'd like to demonstrate there is interest and that we'll really show up with a bunch of bioinformatics hackers. More details will be in the works as the summer draws closer. Looking forward to the sound of music, Brad From bonnalraoul at ingm.it Fri Feb 25 03:52:59 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Fri, 25 Feb 2011 09:52:59 +0100 Subject: [Open-bio-l] BioRuby+BioGem@Ruby Social Club in Milan Message-ID: Dear All, yesterday I talked about BioRuby and BioGem projects during a Ruby Meeting in Milan. Sorry the presentation is in Italian, I'll translate it in english asap if you are interested. It was a small meeting with few people but they were very interested about our projects. I think because we are facing problems that are not so common, basically the business is more "standard" than expected :-). Many of them believe that bioinformatics is just crunching data. Others known our friends BioPerl and BioPython and nothing about BioRuby. Why ? One or two guys that know BioPython were exited about BioRuby; the answer is simple, at university they learned perl or python, ruby is just relegated to business work aka Rails. What that means for me ? Perl is an institution :-) ,Python's guys did a great job in spreading their project. How can we change the world :-) ? Talking! and in June ( I can't remember the date, around 12) there will be the Ruby Day -Italy- at University of Milano Bicocca and I'm going to help as much as possible in this event. Actually I hope to take part in the organization, everything needs to be planned, talks, tutorials.... etc I'm very surprised for a so strong and vivid interest. The meeting schedule: - Giordano Scalzo. MongoMapper , a wrapper for MongoDB - Raoul Bonnal. BioRuby and BioGem, how to create gems that can be reused from script and rails application aka engines BioGem - Andrea Reginato. Testing ed RSpec best practices. NOTE: please contribute to the document is free and open !!! -Elia Schito:TimeTap helps you track the time you spend coding on each project while in TextMate https://github.com/elia/timetap Just few link that can be of interest for Bio* projetcs, I know that Peter and Chris are reading: >>> CeBIT di Hannover nell'ambito dell'"Open >>> Source Park" >>> >>> http://www.cebit.de/exhibitor/vemar?directLink=Y854924 >>> http://www.open-source-park.com/ > www.nosqlday.it sold out (just for note) MongoUK - 21 March http://www.10gen.com/conferences/mongouk2011 Mongo France - 23 March http://lacantine.org/events/mongo-france-2011 http://www.10gen.com/conferences/mongofr2011 Mongo Berlin - 25 March http://www.10gen.com/conferences/mongoberlin2011 It would be very useful to have a shared calendar where putting this kind of events. Do we agree to use google calendar or do you have a better solution ? Ciao! -- Ra From bonnalraoul at ingm.it Fri Feb 25 06:01:08 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Fri, 25 Feb 2011 12:01:08 +0100 Subject: [Open-bio-l] BOSC 2011 topic organizers and Codefest In-Reply-To: <20110224182456.GI20125@sobchak.mgh.harvard.edu> References: <20110224182456.GI20125@sobchak.mgh.harvard.edu> Message-ID: <0CEE804C-937A-416C-9537-E00EDC6B6CCB@ingm.it> Dear Brad, do we plan to have talks about Bio* projetcs updates ? -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Heluis github: https://github.com/helios From cjfields at illinois.edu Fri Feb 25 09:43:28 2011 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 25 Feb 2011 08:43:28 -0600 Subject: [Open-bio-l] BOSC 2011 topic organizers and Codefest In-Reply-To: <0CEE804C-937A-416C-9537-E00EDC6B6CCB@ingm.it> References: <20110224182456.GI20125@sobchak.mgh.harvard.edu> <0CEE804C-937A-416C-9537-E00EDC6B6CCB@ingm.it> Message-ID: <4BDC4A37-6041-414A-AA38-7EF2A7D970E8@illinois.edu> Raoul, Yes, that is generally a yearly thing. I very likely can't make it this year, as I'll be moving around that period of time, but I'm hoping we can get someone there for an update on the BioPerl end (some interesting things in the pipeline :) chris On Feb 25, 2011, at 5:01 AM, Raoul Bonnal wrote: > Dear Brad, > do we plan to have talks about Bio* projetcs updates ? > > > -- > Ra > > linkedin: http://it.linkedin.com/in/raoulbonnal > twitter: http://twitter.com/ilpuccio > skype: ilpuccio > irc.freenode.net: Heluis > github: https://github.com/helios > > > > > > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l From bonnalraoul at ingm.it Fri Feb 25 11:09:49 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Fri, 25 Feb 2011 17:09:49 +0100 Subject: [Open-bio-l] BOSC 2011 topic organizers and Codefest In-Reply-To: <4BDC4A37-6041-414A-AA38-7EF2A7D970E8@illinois.edu> References: <20110224182456.GI20125@sobchak.mgh.harvard.edu> <0CEE804C-937A-416C-9537-E00EDC6B6CCB@ingm.it> <4BDC4A37-6041-414A-AA38-7EF2A7D970E8@illinois.edu> Message-ID: <1B9EEF72-88A2-445A-AD29-5A9763304DEA@ingm.it> Dear Chirs, On 25/feb/2011, at 15.43, Chris Fields wrote: > Yes, that is generally a yearly thing. I very likely can't make it this year, as I'll be moving around that period of time, but I'm hoping we can get someone there for an update on the BioPerl end (some interesting things in the pipeline :) OK :-) I think I'll do it. For sure we'd like to discuss with all of you guys about our approaches on ngs pipelines etc, during Codefest and BOSC I like the new approach +1but this implies presentations with more opportunities for talking so it's our responsibility to make this happen. About short introduction talks I suggest this model: http://en.wikipedia.org/wiki/Ignite_(event) http://www.youtube.com/watch?v=rRa1IPkBFbg&feature=player_embedded -- 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 chapmanb at 50mail.com Fri Feb 25 12:05:39 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 25 Feb 2011 12:05:39 -0500 Subject: [Open-bio-l] BOSC 2011 topic organizers and Codefest In-Reply-To: <1B9EEF72-88A2-445A-AD29-5A9763304DEA@ingm.it> References: <20110224182456.GI20125@sobchak.mgh.harvard.edu> <0CEE804C-937A-416C-9537-E00EDC6B6CCB@ingm.it> <4BDC4A37-6041-414A-AA38-7EF2A7D970E8@illinois.edu> <1B9EEF72-88A2-445A-AD29-5A9763304DEA@ingm.it> Message-ID: <20110225170539.GE5954@sobchak.mgh.harvard.edu> Chris and Raoul; > do we plan to have talks about Bio* projetcs updates ? We definitely want to have talks from all of the Bio* projects. What we'd like to do this year is make them more focused on particular area of work, rather than just a general update. So instead of a dedicated section, we can put these talks wherever they fit within the other scientific topics. > For sure we'd like to discuss with all of you guys about our > approaches on ngs pipelines etc, during Codefest and BOSC This is exactly what we were thinking of -- it would be great to have a talk focused around BioRuby's work in next-gen pipeline development. Then ideally we could put that together with other similar talks and compare/contrast/learn during the session. > I like the new approach +1but this implies presentations with more > opportunities for talking so it's our responsibility to make this > happen. Absolutely, it should be a fun challenge. This will also help us be a bit different in terms of focus and interaction in comparison with other special interest groups. The big advantage of talking about open source work is that we can focus on very practical concerns for day to day bioinformatics and share real code that you can take away and use immediately. Brad From hlapp at gmx.net Sat Feb 5 18:44:42 2011 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 05 Feb 2011 23:44:42 -0000 Subject: [Open-bio-l] NESCent Seeks Hackathon Whitepapers In-Reply-To: <0D7D89E4-C0D4-4347-A94C-21800E927746@ad.unc.edu> References: <0D7D89E4-C0D4-4347-A94C-21800E927746@ad.unc.edu> Message-ID: The National Evolutionary Synthesis Center (NESCent), in keeping with its objective to promote collaborative development of open-source, reusable, and standards-supporting informatics resources, sponsors highly collaborative, face-to-face software development events, called "hackathons" (see [1]). To ensure that this program continues to be responsive to user needs and to tap into the expertise and creativity of the evolutionary biology community, NESCent is soliciting short whitepapers (2-6 pages) [2] on potential target areas for future hackathons. To further encourage submissions, we have now distilled specific guidelines for proposing hackathon events, based on the experiences gained from events we have sponsored in the past: http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines The Center's Call for Informatics Whitepapers [3] includes not only hackathons, but also a large spectrum of other initiatives to be undertaken by the Center, including training, software development, collaborative ontology development, and coordination of data standards. Whitepapers are accepted at any time and reviewed on an on- going basis. URLs: [1] Collaborative cyberinfrastructure events and programs organized by NESCent: http://informatics.nescent.org/wiki/Main_Page [2] NESCent Call for Informatics Whitepapers http://www.nescent.org/informatics/whitepapers.php [3] Hackathon Whitepaper Guidelines: http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines [4] Past NESCent-sponsored hackathons: http://informatics.nescent.org/wiki/Main_Page#Hackathons From rojan at riken.jp Wed Feb 23 01:42:02 2011 From: rojan at riken.jp (Rojan Shrestha) Date: Wed, 23 Feb 2011 15:42:02 +0900 Subject: [Open-bio-l] Biopython library for muliple sequence alignment Message-ID: <001501cbd324$c70a8570$551f9050$@jp> Hello: I want to do multiple sequence alignment using CLUSTW. Instead of standalone, I would like to use in my own program through biopython. I would like to know that whether biopython has clustw function or not. It would be very good if somebody gives information about this. Regards, Rojan From ss2489 at cornell.edu Mon Feb 28 10:17:25 2011 From: ss2489 at cornell.edu (Surya Saha) Date: Mon, 28 Feb 2011 10:17:25 -0500 Subject: [Open-bio-l] Call for abstracts and travel fellowships for 7th ISCB Student Council Symposium 2011 (Vienna, Austria) Message-ID: Submit your abstract today to participate in the 7th Symposium of the International Society for Computational Biology Student Council on July 15th 2011 in Vienna! The Student Council Symposium aims at bringing together young computational biologists from all areas of research and parts of the world. As the central part of our symposium 12 student presentations will be selected from the submitted abstracts. This is your chance to present your work! We accept abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. Travel Fellowships are available (see website) and awards will be given to best poster and best presentation. *Submission website: http://bit.ly/iscbsc-scs7-sub Travel Fellowship information: http://bit.ly/iscbsc-scs7-tsub General information: http://bit.ly/iscbsc-scs7 * *Important dates:* January 31: Abstract and Travel Fellowship submission opens February 15: Travel Fellowships submission opens April 29: Abstract submission closes May 6: Travel Fellowships submission closes May 23: Travel Fellowship winners and Abstract acceptance notification We look forward to receiving your abstract, Noura Chelbat Chair, 7th ISCB Student Council Symposium 2011 Lorena Pantnao Co-Chair, 7th ISCB Student Council Symposium 2011 From clements at nescent.org Tue Feb 1 05:57:52 2011 From: clements at nescent.org (Dave Clements) Date: Mon, 31 Jan 2011 21:57:52 -0800 Subject: [Open-bio-l] March 2011 GMOD Meeting Registration is now open In-Reply-To: References: Message-ID: Hello all, Registration is now open for the March 2011 GMOD Meeting ( http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting). This meeting will be held March 5-6, as part of GMOD Americas 2011, which also includes a day of Satellite Meetings, a GMOD Course (already full), and for the first time, an "Introduction to GMOD" session the night before the meeting for GMOD newcomers. GMOD Americas 2011 events are being held at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United States. As with previous GMOD meetings, this meeting will have a mixture of project talks, component talks, and user talks. Our guest speaker is Dr. Eric Stone of North Carolina State University. Dr. Stone will talk about his experience on the "Drosophila Genome Reference Panel," a project that is sequencing 192 lines. See http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting#Agenda for more. The agenda is driven by attendee suggestions, and you are encouraged to add your suggestions now ( http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting#Agenda_Proposals). For examples of what happens at a GMOD meeting, see the writeup of the September 2010 GMOD Meeting (http://gmod.oicr.on.ca/wiki/September_2010_GMOD_Meeting), or any previous meeting. GMOD meetings are an excellent way to meet GMOD developers and users and to learn (and affect) what's coming in the project. Registration for the March 2011 GMOD Meeting is $80 on or before February 18 <<<<======= $95 after February 18 Please register early, both to save money, and ensure a spot. You are also strongly encouraged to sign up for (or propose) a Satellite Meeting (more details to come). Details on transportation, suggested lodging, and other logistics are on the GMOD Americas 2011 page. This meeting, and all GMOD Americas 2011 events, are jointly sponsored by NESCent and the Galaxy Project. Dave Clements Galaxy Project -- http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://nescent.org http://usegalaxy.org/ From clements at nescent.org Wed Feb 2 06:25:39 2011 From: clements at nescent.org (Dave Clements) Date: Tue, 1 Feb 2011 22:25:39 -0800 Subject: [Open-bio-l] GMOD Satellite Meetings, March 7, NESCent, Durham, NC In-Reply-To: References: Message-ID: Hello all, Yesterday, we opened registration for the March 2011 GMOD Meeting (see http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting). *That meeting is part of a larger event, GMOD Americas 2011, that also includes several Satellite Meetings on March 7*, the day after the meeting ends. Satellite meetings are smaller groups of people meeting to discuss a common interest, or work on a common problem (think special interest groups / birds-of-a-feather). Unlike the GMOD Meeting, there is *no registration fee * for the Satellites, and you don't even need to go to any other GMOD Americas events to participate in the Satellites. *If you are in the area, or attending other GMOD Americas events, or are just very interested in the topic, we strongly encourage you to attend.* The current list of Satellites (see http://gmod.oicr.on.ca/wiki/Satellite_Meetings_-_GMOD_Americas_2011) includes: - *GMOD Evo Hackathon Followup*, organized by Duke Leto . A followup to the GMOD Evo Hackathonheld at NESCent in November 2011. You didn't to participate in the original event to participate in this followup. Also, if there is interest, this satellite can extend for more than one day. - *Customizing and Extending JBrowse *, organized by Mitch Skinner . JBrowse has a few different extension points, but they're not (yet) well-documented or widely used. The GMOD meeting would be a good time to review those APIs, relate them to the things that people want to do with them, discuss any potential changes or new APIs to support specific use cases, and potentially start to implement an extension. - *GMOD Web services toolkit* , organized by Josh Goodman . Come to work on or discuss the GMOD Web services API and the toolkit . - *GMOD in the Sequencing Center*, organized by Chris Hemmerich , Dave Clements . Sequencing centers have tremendous bioinformatics needs that GMOD can help address. Attend this satellite to find out what other sequencing centers are doing with GMOD, and how GMOD can help you help your researchers. If you are interested in participating in these, please contact the organizers, and/or add your name to the satellite's participants list on the wiki. Satellites can be organized by anyone. If you have a topic you would like to cover, please add it to the list and announce it the appropriate mailing lists. Several previous satellites are written up on the GMOD wiki, if you want an idea of what happens at a satellite. Finally, please let me and Scott know if you have any questions. Thanks, and hope to see you in March! Dave C. -- http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://usegalaxy.org/ From clementsgalaxy at gmail.com Fri Feb 4 01:01:01 2011 From: clementsgalaxy at gmail.com (Dave Clements) Date: Thu, 3 Feb 2011 17:01:01 -0800 Subject: [Open-bio-l] Galaxy Community Conference, May 25-26, Lunteren, The Netherlands Message-ID: We are pleased to announce the *2011 Galaxy Community Conference*, being held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your own and your community's research. See http://galaxy.psu.edu/gcc2011/* for complete details. * *About Galaxy: *Galaxy is an open, web-based platform for *accessible, reproducible, and transparent* computational biomedical research. - *Accessibility:* Galaxy enables users without programming experience to easily specify parameters and run tools and workflows. - *Reproducibility:* Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis. - *Transparency:* Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis. Galaxy is open source for all organizations. The public Galaxy service ( http://usegalaxy.org) makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist that has access to the Internet. Local Galaxy servers can be set up by downloading the Galaxy application and customizing it to meet particular needs. *Conference Overview: * This event aims to engage a broader community of developers, data producers, tool creators, and core facility and other research hub staff to become an active part of the Galaxy community. We'll cover defining resources in the Galaxy framework, increasing their visibility and making them easier to use and integrate with other resources, how to extend Galaxy to use custom data sources and custom tools, and best practices for using Galaxy in your organization. Additional topics include, but are not limited to: * Talks submitted by the Galaxy community * Integration of tools (including NGS analysis tools) and distributed job management * Deployment of Galaxy instances on local resources and on the Cloud * Management of large datasets with the Galaxy Library System * Using the Galaxy LIMS functionality at NGS sequencing facilities * Visualizing Data without leaving Galaxy * Performing reproducible research * Performing and sharing complex analyses with Workflows * An "Introduction to Galaxy" session, offered on May 24, for Galaxy newcomers. *Registration: * The conference fee is ?100 on or before April 24, and ?120 after that. The meeting is being held at the Conference Centre De Werelt in Lunteren, The Netherlands, which is also the conference hotel. You are encouraged to register early, as space at the hotel (and at the "Intro to Galaxy" session) is limited and is likely to fill up before the conference itself does. See http://galaxy.psu.edu/gcc2011/Register.html * Abstract Submission: * Abstracts are now being accepted for short oral presentations. Proposals on any topic of interest to the Galaxy community are welcome and encouraged. The abstract submission deadline is the end of February 28. See http://galaxy.psu.edu/gcc2011/Abstracts.html * * *Sponsors * The 2011 Galaxy Community Conference is co-sponsored by the US National Science Foundation (NSF, http://www.nsf.gov/), and the Netherlands Bioinformatics Centre (NBIC, http://www.nbic.nl/). NBIC is a collaborative institute of the bioinformatics groups in the Netherlands. Together, these groups perform cutting-edge research, develop novel tools and support platforms, create an e-science infrastructure and educate the next generations of bioinformaticians. We are looking forward to a great conference and hope to see you in the Netherlands! The Galaxy and NBIC Teams -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ From bonnalraoul at ingm.it Wed Feb 9 11:58:50 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 9 Feb 2011 12:58:50 +0100 Subject: [Open-bio-l] [BioRuby] Workflows and Parallelization In-Reply-To: <4D509731.4050209@be.to> References: <2D62D256-4CBD-4793-97F1-37A908C734F6@ingm.it> <4D10B9AE.2010206@be.to> <5EB99E14-47EF-4267-99F5-216C16A93426@ingm.it> <20110207171655.GA25517@thebird.nl> <4D509731.4050209@be.to> Message-ID: <97CFB702-337B-4608-8AF5-CADAB7B1702A@ingm.it> Hello folks, tweeting around I found these videos http://www.youtube.com/watch?v=1ntxT-47VPA http://www.youtube.com/watch?v=OpaiGYxkSuQ&feature=related http://www.youtube.com/watch?v=P40akGWJ_gY&feature=related Project home page: http://www.gnu.org/software/parallel/ Very useful in many contexts. @BioRuby: I think that we can explore how to use it in workflows. On 08/feb/2011, at 02.06, MISHIMA, Hiroyuki wrote: > Hi, > > I added Pjotr's information on the BioRuby wiki > ( http://bioruby.open-bio.org/wiki/Workflows ). > > I also updated a subsection about GridEngine. Univa took over GridEngine > development from Oracle. > > Sincerely yours, > Hiro. > > Pjotr Prins wrote (2011/02/08 2:16): >> rq - which can parallelize calculations with zero-administration >> (all that is needed is a shared dir). > > -- > 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 -- Ra From clements at nescent.org Mon Feb 14 19:43:22 2011 From: clements at nescent.org (Dave Clements) Date: Mon, 14 Feb 2011 11:43:22 -0800 Subject: [Open-bio-l] March 2011 GMOD Meeting early registration closes this Friday In-Reply-To: References: Message-ID: Hello all, *Register for the March 2011 GMOD Meeting ( http://gmod.org/wiki/March_2011_GMOD_Meeting) by this Friday, Feb 18, and save over 15%.* The March meeting is part of GMOD Americas 2011 ( http://gmod.org/wiki/GMOD_Americas_2011), an event that includes Satellite Meetings, a GMOD Course (already full), and for the first time, an "Introduction to GMOD" session the night before the meeting for GMOD newcomers. GMOD Americas 2011 events are being held at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United States. Also, if you have a topic you want to discuss at the meeting, please send it to Scott Cain ASAP so he can get you on the program. *About GMOD:* GMOD is the Generic Model Organism Database project, a collection of interoperable open-source software components for annotating, visualizing, managing and analyzing biological data. GMOD is also an active community of software developers and biologists addressing common challenges with their data. The GMOD suite includes widely used tools such as GBrowse and JBrowse (and WebGBrowse) for genome browsing, Apollo and MAKER for genome annotation, GBrowse_syn and CMap for comparative genomics visualization, Chado, BioMart and InterMine for data integration, management, and querying, and Galaxy and Ergatis (and ISGA) for data analysis. *Meeting Overview: *As with previous GMOD meetings, this meeting will have a mixture of project talks, component talks, and user talks. Our guest speaker is Dr. Eric Stone of North Carolina State University. Dr. Stone will talk about his experience on the "Drosophila Genome Reference Panel," a project that is sequencing and annotating almost 200 inbred lines. The agenda is driven by attendee suggestions, and you are encouraged to add your suggestions now. For an idea of what happens at a GMOD meeting, see the writeup of the September 2010 GMOD Meeting. GMOD meetings are an excellent way to meet GMOD developers and users and to learn (and affect) what's coming in the project. *Registration: *Registration for the March 2011 GMOD Meeting is $80 on or before February 18 $95 after February 18 Please register early, both to save money, and ensure a spot. You are also strongly encouraged to submit a talk and/or sign up for (or propose) a Satellite Meeting. Details on transportation, suggested lodging, and other logistics are on the GMOD Americas 2011 page. This meeting, and all GMOD Americas 2011 events, are jointly sponsored by NESCent and the Galaxy Project. Hope to see you in North Carolina! Dave Clements Galaxy Project -- http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://usegalaxy.org/ http://getgalaxy.org/ From clementsgalaxy at gmail.com Tue Feb 22 17:16:12 2011 From: clementsgalaxy at gmail.com (Dave Clements) Date: Tue, 22 Feb 2011 09:16:12 -0800 Subject: [Open-bio-l] Galaxy Community Conference, May 25-26, Lunteren, The Netherlands In-Reply-To: References: Message-ID: Hello all, Just a reminder that the abstract submission deadline for the Galaxy Community Conference is next Monday, February 28. See http://galaxy.psu.edu/gcc2011/Abstracts.html for details. Cheers, Dave C. On Thu, Feb 3, 2011 at 5:01 PM, Dave Clements wrote: > We are pleased to announce the *2011 Galaxy Community Conference*, being > held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature > two full days of presentations and discussion on extending Galaxy to use new > tools and data sources, deploying Galaxy at your organization, and best > practices for using Galaxy to further your own and your community's > research. See http://galaxy.psu.edu/gcc2011/* for complete details. > * > *About Galaxy: > *Galaxy is an open, web-based platform for *accessible, reproducible, and > transparent* computational biomedical research. > > - *Accessibility:* Galaxy enables users without programming experience > to easily specify parameters and run tools and workflows. > - *Reproducibility:* Galaxy captures all information necessary so that > any user can repeat and understand a complete computational analysis. > - *Transparency:* Galaxy enables users to share and publish analyses > via the web and create Pages--interactive, web-based documents that describe > a complete analysis. > > Galaxy is open source for all organizations. The public Galaxy service ( > http://usegalaxy.org) makes analysis tools, genomic data, > tutorial demonstrations, persistent workspaces, and publication services > available to any scientist that has access to the Internet. Local > Galaxy servers can be set up by downloading the Galaxy application and > customizing it to meet particular needs. > > *Conference Overview: > * > This event aims to engage a broader community of developers, data > producers, tool creators, and core facility and other research hub staff to > become an active part of the Galaxy community. We'll cover defining > resources in the Galaxy framework, increasing their visibility and making > them easier to use and integrate with other resources, how to extend Galaxy > to use custom data sources and custom tools, and best practices for using > Galaxy in your organization. > > Additional topics include, but are not limited to: > * Talks submitted by the Galaxy community > * Integration of tools (including NGS analysis tools) and distributed job > management > * Deployment of Galaxy instances on local resources and on the Cloud > * Management of large datasets with the Galaxy Library System > * Using the Galaxy LIMS functionality at NGS sequencing facilities > * Visualizing Data without leaving Galaxy > * Performing reproducible research > * Performing and sharing complex analyses with Workflows > * An "Introduction to Galaxy" session, offered on May 24, for Galaxy > newcomers. > > *Registration: > * > The conference fee is ?100 on or before April 24, and ?120 after that. The > meeting is being held at the Conference Centre De Werelt in Lunteren, The > Netherlands, which is also the conference hotel. You are encouraged to > register early, as space at the hotel (and at the "Intro to Galaxy" session) > is limited and is likely to fill up before the conference itself does. See > http://galaxy.psu.edu/gcc2011/Register.html > * > Abstract Submission: > * > Abstracts are now being accepted for short oral presentations. Proposals > on any topic of interest to the Galaxy community are welcome and > encouraged. The abstract submission deadline is the end of February 28. > See http://galaxy.psu.edu/gcc2011/Abstracts.html > * * > *Sponsors > * > The 2011 Galaxy Community Conference is co-sponsored by the US National > Science Foundation (NSF, http://www.nsf.gov/), and the Netherlands > Bioinformatics Centre (NBIC, http://www.nbic.nl/). NBIC is a > collaborative institute of the bioinformatics groups in the Netherlands. > Together, these groups perform cutting-edge research, develop novel tools > and support platforms, create an e-science infrastructure and educate the > next generations of bioinformaticians. > > We are looking forward to a great conference and hope to see you in the > Netherlands! > > The Galaxy and NBIC Teams > > -- > http://galaxy.psu.edu/gcc2011/ > http://getgalaxy.org > http://usegalaxy.org/ > -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ From p.j.a.cock at googlemail.com Wed Feb 23 09:24:21 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 23 Feb 2011 09:24:21 +0000 Subject: [Open-bio-l] [Biopython] Biopython library for muliple sequence alignment In-Reply-To: <001501cbd324$c70a8570$551f9050$@jp> References: <001501cbd324$c70a8570$551f9050$@jp> Message-ID: On Wed, Feb 23, 2011 at 6:42 AM, Rojan Shrestha wrote: > Hello: > > I want to do multiple sequence alignment using CLUSTW. Instead of > standalone, I would like to use in my own program through biopython. I would > like to know that whether biopython has clustw function or not. It would be > very good if somebody ?gives information about this. > > Regards, > > Rojan Hello Rojan, Biopython (and BioPerl too I believe) doesn't have any multiple sequence alignment code itself. Biopython does has pairwise sequence alignment code (with a fast implementation in C). Instead (again, like BioPerl) Biopython has a wrapper and parser for calling the ClustalW command line tool from within your script and loading its output. Similarly for other alignment tools like Muscle. If you really want to be able modify the multiple sequence alignment code itself, some of these command line tools are open source. Also, I *think* that BioJava has some code for this. I don't know what BioRuby does. Peter P.S. You only really need to ask this on the Biopython Discussion List. Since you included the OBF cross project list I have tried to comment on how the other projects handle this as well. From chapmanb at 50mail.com Thu Feb 24 18:24:56 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu, 24 Feb 2011 13:24:56 -0500 Subject: [Open-bio-l] BOSC 2011 topic organizers and Codefest Message-ID: <20110224182456.GI20125@sobchak.mgh.harvard.edu> Hi all; This year the Bioinformatics Open Source Conference (BOSC) will be taking place in Vienna, Austria on July 15-16th. This is a yearly opportunity for open source bioinformatics developers to get together in person and discuss on-going projects. Nomi Harris, Peter Rice and the other organizing committee members are already hard at work planning for the conference: http://www.open-bio.org/wiki/BOSC_2011 The call for abstracts opens next Monday, and extends through April 18th, and we've been brainstorming potential session topics. This year we've tried to focus each of the sessions around a particular biological problem or computational approach. We hope this will draw some interesting parallels between work being done in different groups, and encourage even more collaboration. We are actively looking for community members who are interested in heading up the organization of a topic. The general idea is to build a cohesive set of talks within a session. How you'd like to do this is completely flexible but some of the ideas we've been discussing are: - Having a short introductory talk to provide an overview of an area, framing the different talks within this context. - Forgoing individual question/answer and instead combining this time into a longer panel-style discussion with all of the speakers. This would help stimulate back and forth between the different projects and the audience. If you are interested in a particular topic and would like to help with the organization, please send an e-mail to the BOSC mailing list: bosc at lists.open-bio.org. We're also open to new topic suggestions, and will look to add one or two more topics to our current list. Finally, there will be a two day coding session prior to BOSC as a follow up to last year's fun and productive Codefest: http://www.open-bio.org/wiki/Codefest_2011 The Metalab, a unique hacker space in Vienna, has kindly agreed to host us for the two days. If you are at all interested, please add your name to the attendees list on the wiki. Since the Metalab organizers don't know us personally, we'd like to demonstrate there is interest and that we'll really show up with a bunch of bioinformatics hackers. More details will be in the works as the summer draws closer. Looking forward to the sound of music, Brad From bonnalraoul at ingm.it Fri Feb 25 08:52:59 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Fri, 25 Feb 2011 09:52:59 +0100 Subject: [Open-bio-l] BioRuby+BioGem@Ruby Social Club in Milan Message-ID: Dear All, yesterday I talked about BioRuby and BioGem projects during a Ruby Meeting in Milan. Sorry the presentation is in Italian, I'll translate it in english asap if you are interested. It was a small meeting with few people but they were very interested about our projects. I think because we are facing problems that are not so common, basically the business is more "standard" than expected :-). Many of them believe that bioinformatics is just crunching data. Others known our friends BioPerl and BioPython and nothing about BioRuby. Why ? One or two guys that know BioPython were exited about BioRuby; the answer is simple, at university they learned perl or python, ruby is just relegated to business work aka Rails. What that means for me ? Perl is an institution :-) ,Python's guys did a great job in spreading their project. How can we change the world :-) ? Talking! and in June ( I can't remember the date, around 12) there will be the Ruby Day -Italy- at University of Milano Bicocca and I'm going to help as much as possible in this event. Actually I hope to take part in the organization, everything needs to be planned, talks, tutorials.... etc I'm very surprised for a so strong and vivid interest. The meeting schedule: - Giordano Scalzo. MongoMapper , a wrapper for MongoDB - Raoul Bonnal. BioRuby and BioGem, how to create gems that can be reused from script and rails application aka engines BioGem - Andrea Reginato. Testing ed RSpec best practices. NOTE: please contribute to the document is free and open !!! -Elia Schito:TimeTap helps you track the time you spend coding on each project while in TextMate https://github.com/elia/timetap Just few link that can be of interest for Bio* projetcs, I know that Peter and Chris are reading: >>> CeBIT di Hannover nell'ambito dell'"Open >>> Source Park" >>> >>> http://www.cebit.de/exhibitor/vemar?directLink=Y854924 >>> http://www.open-source-park.com/ > www.nosqlday.it sold out (just for note) MongoUK - 21 March http://www.10gen.com/conferences/mongouk2011 Mongo France - 23 March http://lacantine.org/events/mongo-france-2011 http://www.10gen.com/conferences/mongofr2011 Mongo Berlin - 25 March http://www.10gen.com/conferences/mongoberlin2011 It would be very useful to have a shared calendar where putting this kind of events. Do we agree to use google calendar or do you have a better solution ? Ciao! -- Ra From bonnalraoul at ingm.it Fri Feb 25 11:01:08 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Fri, 25 Feb 2011 12:01:08 +0100 Subject: [Open-bio-l] BOSC 2011 topic organizers and Codefest In-Reply-To: <20110224182456.GI20125@sobchak.mgh.harvard.edu> References: <20110224182456.GI20125@sobchak.mgh.harvard.edu> Message-ID: <0CEE804C-937A-416C-9537-E00EDC6B6CCB@ingm.it> Dear Brad, do we plan to have talks about Bio* projetcs updates ? -- Ra linkedin: http://it.linkedin.com/in/raoulbonnal twitter: http://twitter.com/ilpuccio skype: ilpuccio irc.freenode.net: Heluis github: https://github.com/helios From cjfields at illinois.edu Fri Feb 25 14:43:28 2011 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 25 Feb 2011 08:43:28 -0600 Subject: [Open-bio-l] BOSC 2011 topic organizers and Codefest In-Reply-To: <0CEE804C-937A-416C-9537-E00EDC6B6CCB@ingm.it> References: <20110224182456.GI20125@sobchak.mgh.harvard.edu> <0CEE804C-937A-416C-9537-E00EDC6B6CCB@ingm.it> Message-ID: <4BDC4A37-6041-414A-AA38-7EF2A7D970E8@illinois.edu> Raoul, Yes, that is generally a yearly thing. I very likely can't make it this year, as I'll be moving around that period of time, but I'm hoping we can get someone there for an update on the BioPerl end (some interesting things in the pipeline :) chris On Feb 25, 2011, at 5:01 AM, Raoul Bonnal wrote: > Dear Brad, > do we plan to have talks about Bio* projetcs updates ? > > > -- > Ra > > linkedin: http://it.linkedin.com/in/raoulbonnal > twitter: http://twitter.com/ilpuccio > skype: ilpuccio > irc.freenode.net: Heluis > github: https://github.com/helios > > > > > > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l From bonnalraoul at ingm.it Fri Feb 25 16:09:49 2011 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Fri, 25 Feb 2011 17:09:49 +0100 Subject: [Open-bio-l] BOSC 2011 topic organizers and Codefest In-Reply-To: <4BDC4A37-6041-414A-AA38-7EF2A7D970E8@illinois.edu> References: <20110224182456.GI20125@sobchak.mgh.harvard.edu> <0CEE804C-937A-416C-9537-E00EDC6B6CCB@ingm.it> <4BDC4A37-6041-414A-AA38-7EF2A7D970E8@illinois.edu> Message-ID: <1B9EEF72-88A2-445A-AD29-5A9763304DEA@ingm.it> Dear Chirs, On 25/feb/2011, at 15.43, Chris Fields wrote: > Yes, that is generally a yearly thing. I very likely can't make it this year, as I'll be moving around that period of time, but I'm hoping we can get someone there for an update on the BioPerl end (some interesting things in the pipeline :) OK :-) I think I'll do it. For sure we'd like to discuss with all of you guys about our approaches on ngs pipelines etc, during Codefest and BOSC I like the new approach +1but this implies presentations with more opportunities for talking so it's our responsibility to make this happen. About short introduction talks I suggest this model: http://en.wikipedia.org/wiki/Ignite_(event) http://www.youtube.com/watch?v=rRa1IPkBFbg&feature=player_embedded -- 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 chapmanb at 50mail.com Fri Feb 25 17:05:39 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 25 Feb 2011 12:05:39 -0500 Subject: [Open-bio-l] BOSC 2011 topic organizers and Codefest In-Reply-To: <1B9EEF72-88A2-445A-AD29-5A9763304DEA@ingm.it> References: <20110224182456.GI20125@sobchak.mgh.harvard.edu> <0CEE804C-937A-416C-9537-E00EDC6B6CCB@ingm.it> <4BDC4A37-6041-414A-AA38-7EF2A7D970E8@illinois.edu> <1B9EEF72-88A2-445A-AD29-5A9763304DEA@ingm.it> Message-ID: <20110225170539.GE5954@sobchak.mgh.harvard.edu> Chris and Raoul; > do we plan to have talks about Bio* projetcs updates ? We definitely want to have talks from all of the Bio* projects. What we'd like to do this year is make them more focused on particular area of work, rather than just a general update. So instead of a dedicated section, we can put these talks wherever they fit within the other scientific topics. > For sure we'd like to discuss with all of you guys about our > approaches on ngs pipelines etc, during Codefest and BOSC This is exactly what we were thinking of -- it would be great to have a talk focused around BioRuby's work in next-gen pipeline development. Then ideally we could put that together with other similar talks and compare/contrast/learn during the session. > I like the new approach +1but this implies presentations with more > opportunities for talking so it's our responsibility to make this > happen. Absolutely, it should be a fun challenge. This will also help us be a bit different in terms of focus and interaction in comparison with other special interest groups. The big advantage of talking about open source work is that we can focus on very practical concerns for day to day bioinformatics and share real code that you can take away and use immediately. Brad From hlapp at gmx.net Sat Feb 5 23:44:42 2011 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 05 Feb 2011 23:44:42 -0000 Subject: [Open-bio-l] NESCent Seeks Hackathon Whitepapers In-Reply-To: <0D7D89E4-C0D4-4347-A94C-21800E927746@ad.unc.edu> References: <0D7D89E4-C0D4-4347-A94C-21800E927746@ad.unc.edu> Message-ID: The National Evolutionary Synthesis Center (NESCent), in keeping with its objective to promote collaborative development of open-source, reusable, and standards-supporting informatics resources, sponsors highly collaborative, face-to-face software development events, called "hackathons" (see [1]). To ensure that this program continues to be responsive to user needs and to tap into the expertise and creativity of the evolutionary biology community, NESCent is soliciting short whitepapers (2-6 pages) [2] on potential target areas for future hackathons. To further encourage submissions, we have now distilled specific guidelines for proposing hackathon events, based on the experiences gained from events we have sponsored in the past: http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines The Center's Call for Informatics Whitepapers [3] includes not only hackathons, but also a large spectrum of other initiatives to be undertaken by the Center, including training, software development, collaborative ontology development, and coordination of data standards. Whitepapers are accepted at any time and reviewed on an on- going basis. URLs: [1] Collaborative cyberinfrastructure events and programs organized by NESCent: http://informatics.nescent.org/wiki/Main_Page [2] NESCent Call for Informatics Whitepapers http://www.nescent.org/informatics/whitepapers.php [3] Hackathon Whitepaper Guidelines: http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines [4] Past NESCent-sponsored hackathons: http://informatics.nescent.org/wiki/Main_Page#Hackathons From rojan at riken.jp Wed Feb 23 06:42:02 2011 From: rojan at riken.jp (Rojan Shrestha) Date: Wed, 23 Feb 2011 15:42:02 +0900 Subject: [Open-bio-l] Biopython library for muliple sequence alignment Message-ID: <001501cbd324$c70a8570$551f9050$@jp> Hello: I want to do multiple sequence alignment using CLUSTW. Instead of standalone, I would like to use in my own program through biopython. I would like to know that whether biopython has clustw function or not. It would be very good if somebody gives information about this. Regards, Rojan From ss2489 at cornell.edu Mon Feb 28 15:17:25 2011 From: ss2489 at cornell.edu (Surya Saha) Date: Mon, 28 Feb 2011 10:17:25 -0500 Subject: [Open-bio-l] Call for abstracts and travel fellowships for 7th ISCB Student Council Symposium 2011 (Vienna, Austria) Message-ID: Submit your abstract today to participate in the 7th Symposium of the International Society for Computational Biology Student Council on July 15th 2011 in Vienna! The Student Council Symposium aims at bringing together young computational biologists from all areas of research and parts of the world. As the central part of our symposium 12 student presentations will be selected from the submitted abstracts. This is your chance to present your work! We accept abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. Travel Fellowships are available (see website) and awards will be given to best poster and best presentation. *Submission website: http://bit.ly/iscbsc-scs7-sub Travel Fellowship information: http://bit.ly/iscbsc-scs7-tsub General information: http://bit.ly/iscbsc-scs7 * *Important dates:* January 31: Abstract and Travel Fellowship submission opens February 15: Travel Fellowships submission opens April 29: Abstract submission closes May 6: Travel Fellowships submission closes May 23: Travel Fellowship winners and Abstract acceptance notification We look forward to receiving your abstract, Noura Chelbat Chair, 7th ISCB Student Council Symposium 2011 Lorena Pantnao Co-Chair, 7th ISCB Student Council Symposium 2011