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[[Image:GSoC2012_300x200.png|right|frame|link=http://code.google.com/soc]]  
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[[Image:GSoC15-logo-small.jpg|right|frame|link=http://code.google.com/soc]]  
  
== GSoC 2013 ==
+
Google Summer of Code (GSoC) is a student internship program for open-source projects. The program offers eligible student developers stipends to write code for open source projects over a period of 3 summer months ("flip bits, not burgers"). See the '''[http://code.google.com/soc Google Summer of Code Main Site]''' for general information about the Google Summer of Code program, how to apply, frequently asked general questions, and more.
  
The Google Summer of Code 2013 is ON! OBF is going to apply for mentoring this year. Interested mentors and students should subscribe to the OBF/GSoC [http://lists.open-bio.org/mailman/listinfo/gsoc mailing list].
 
  
Important dates for 2013:
+
== GSoC 2016 ==
  
* March 22nd: Finalise project ideas
+
The Google Summer of Code 2016 is ON! OBF is once again applying as a GSoC mentoring organization this year. Interested mentors and students should subscribe to the OBF/GSoC [http://lists.open-bio.org/mailman/listinfo/gsoc mailing list]. Please announce yourself, so we know who you are!
* March 29th: Deadline OBF mentoring organisation submission to Google
+
The details of each of our project ideas are listed below, including potential mentors.
  
;Organization administrator: [[User:PjotrPrins|Pjotr Prins]] ([mailto:pjotr.public15@thebird.nl pjotr.public15@thebird.nl])
+
See http://obf.github.io/GSoC/ for more information about the GSoC program and additional ways to get in touch with us.
;Backup administrators: [[User:Lapp|Hilmar Lapp]], Robert Buels, Chris Fields
 
  
== GSoC 2012 ==
+
<!--Our GSoC ideas from each project are collected here: '''[[Google Summer of Code 2015 Ideas |OBF Project Ideas for GSoC 2015]]''' -->
 +
=== Facts & Links ===
  
The Open Bioinformatics Foundation has been accepted as a mentoring organization for Google Summer of Code 2012, with 5 student projects funded!
+
; Time Line :
 +
:* [https://developers.google.com/open-source/gsoc/timeline GSoC time line]
  
== 2012 Student Projects ==
+
; GSoC 2016 FAQ :
 +
:* For questions of eligibility, see the [https://developers.google.com/open-source/gsoc/faq GSoC 2016 FAQ].
  
;Wibowo Arindrarto
+
; Info from Google :
:mentored by Peter Cock
+
:* There is also a [http://groups.google.com/group/google-summer-of-code-discuss Google group for posting GSoC questions] (and receiving answers; note that you will need to sign up for the group) that relate to the program itself (and are not specific to our organization).
:[http://bow.web.id/blog/tag/gsoc/ SearchIO Implementation in Biopython]
+
:* Students receive a stipend from Google if accepted. See the  [https://developers.google.com/open-source/gsoc/faq GSoC 2016 FAQ] for full documentation.
 +
:* Development is done entirely remotely and on-line; there is no requirement or expectation for either students or mentors to travel.
  
;Lenna Peterson
+
=== Why apply? ===
:mentored by Brad Chapman
 
:[http://arklenna.tumblr.com/tagged/gsoc2012 Diff My DNA: Development of a Genomic Variant Toolkit for BioPython]
 
  
;Marjan Povolni
+
One of the most important features of the program is that students are paired with mentors, who are typically experienced developers from the project to which the student is contributing.  The mentor guides the student to work productively within the community, and helps the student avoid obstacles and pitfalls. The program is global - students and mentors may be located anywhere where they have an internet connection (except for countries affected by US trade restrictions), and no travel is required. Thus, aside from the stipend and mentorship aspects, the student's experience in the internship closely mirrors normal work on distributed development projects.  Effective work habits for distributed development are typically not taught as part of computer science curricula, yet are highly desired in the increasingly global and distributed software, IT, and biotechnology industries.
:mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal
 
:[http://blog.mpthecoder.com/tagged/gsoc The world's fastest parallelized GFF3/GTF parser in D, and an interfacing biogem plugin for Ruby]
 
  
;Artem Tarasov
+
From the viewpoint of each open-source project, the program not only offers to pay students for contributing, but more importantly, offers an opportunity to recruit new developers who will hopefully go on to become regular, sustaining contributors.
:mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal
 
:[http://lomereiter.wordpress.com/tag/gsoc Robust and fast parallel BAM parser in D for binding against dynamic languages]
 
  
;Clayton Wheeler
+
==Project Ideas==
:mentored by Francesco Strozzi and Raoul Bonnal
 
:[http://csw.github.com/bioruby-maf/ Multiple Alignment Format parser for BioRuby]
 
  
== About Google Summer of Code ==
 
  
For those not familiar with the program, Google Summer of Code (GSoC) is a student internship program for open-source projects. The program offers eligible student developers stipends to write code for open source projects over a period of 3 summer months ("flip bits, not burgers").  Aside from the stipend, one of the most important features of the program is that students are paired with mentors, who are typically experienced developers from the project to which the student is contributing.  The mentor guides the student to work productively within the community, and helps the student avoid obstacles and pitfalls.  The program is global - students and mentors may be located anywhere where they have an internet connection (except for countries affected by US trade restrictions), and no travel is required. Thus, aside from the stipend and mentorship aspects, the student's experience in the internship closely mirrors normal work on distributed development projects.  Effective work habits for distributed development are typically not taught as part of computer science curricula, yet are highly desired in the increasingly global and distributed software, IT, and biotechnology industries.
+
Our GSoC ideas from each project are collected here: http://obf.github.io/GSoC/
 
 
From the viewpoint of each open-source project, the program not only offers to pay students for contributing, but more importantly offers an opportunity to recruit new developers who will hopefully go on to become regular, sustaining contributors.
 
 
 
See the [http://code.google.com/soc Main GSoC Site] for general information about the Google Summer of Code program, how to apply, frequently asked general questions, and more.
 
 
 
== 2012 Mentor Volunteers and Project Ideas ==
 
 
 
Mentor names and project ideas are hosted on each member project's wiki on a dedicated Google Summer of Code page.  See each of the member projects, linked below, for more details about any project:
 
 
 
;BioPerl:
 
:* [http://bioperl.org/wiki/Google_Summer_of_Code#Lightweight.2FLazy_BioPerl_Classes Lightweight Sequence objects and Lazy Parsing]
 
:* [http://bioperl.org/wiki/Google_Summer_of_Code#Perl_Run_Wrappers_for_External_Programs_in_a_Flash  Perl Generic Wrappers for External Programs]
 
:* [http://bioperl.org/wiki/Google_Summer_of_Code#BioPerl_2.0_.28and_beyond.29  BioPerl 2.0: Modern::Perl, Perl6, and BioPerl]
 
:* [http://bioperl.org/wiki/Google_Summer_of_Code#Bio::Assembly Bio::Assembly updates]
 
:* [http://bioperl.org/wiki/Google_Summer_of_Code#Semantic_Web_Support  Semantic web support]
 
 
 
;BioPython:
 
:* [http://biopython.org/wiki/Google_Summer_of_Code SearchIO]
 
:* [http://biopython.org/wiki/Google_Summer_of_Code Variant representation, parser, generator, and coordinate converter]
 
 
 
;BioJava:
 
:* [http://biojava.org/wiki/Google_Summer_of_Code_2012#Take_BioJava_into_the_Cloud Take BioJava into the Cloud]
 
:* [http://biojava.org/wiki/Google_Summer_of_Code_2012#New_File_Parsers_for_BioJava New File Parsers]
 
:* [http://biojava.org/wiki/Google_Summer_of_Code_2012#Port_an_Algorithm_to_Java Port an algorithm to BioJava]
 
 
 
;BioRuby:
 
:* [http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Write_the_world.27s_fastest_parallelized_GFF3.2FGTF_parser_in_D.2C_for_Ruby_FFI Write the world's fastest parallelized GFF3/GTF parser in D, for Ruby FFI]
 
:* [http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Testing_framework_for_biogem_plugins Testing framework for biogem plugins]
 
:* [http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Extend_bio-alignment_plug-in_with_Multiple_Alignment_Format_-MAF-_parser_.28FFI.3F.29 Extend bio-alignment plug-in with Multiple Alignment Format -MAF- parser (FFI?)]
 
:* [http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Adding_social_networking_functionality_to_BioRuby.org Adding social networking functionality to BioRuby.org]
 
:* [http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Update_bio-images_a_plugin_to_represent_bio-object_with_cool_images Update bio-images a plugin to represent bio-object with cool images]
 
:* [http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Update_to_the_Ruby_Ensembl_API Update to the Ruby Ensembl API]
 
 
 
;BioLib:
 
:* [http://biolib.open-bio.org/wiki/GSoC2012  Mapping EMBOSS to Perl, Ruby or Python using BioLib+SWIG+EMBOSS]
 
:* [http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Write_the_world.27s_fastest_parallelized_GFF3.2FGTF_parser_in_D.2C_for_Ruby_FFI Write the world's fastest parallelized GFF3/GTF parser in D, for Ruby FFI] (together with the BioRuby project)
 
 
 
''Note to students: project ideas on the wikis of member projects are only selected projects, albeit well thought-out ones. You are encouraged to propose your own project, just make sure it is still a contribution to one the OBF member projects (see list below)! If we like your proposal, we will try to find a mentor to help you with the project.  Regardless of what you decide to do, make sure you read and follow the guidelines for students below.''
 
 
 
== Contact ==
 
 
 
=== IRC - Internet Relay Chat ===
 
 
 
IRC is the preferred method of real-time communication between GSoC participants.  OBF IRC channels are maintained on [http://freenode.net freenode], connect your IRC client to <code>chat.freenode.net</code>.
 
 
 
;Main OBF GSoC Channel: <code>#obf-soc</code>
 
;BioPerl: <code>#bioperl</code>
 
;BioRuby: <code>#bioruby</code>
 
 
 
=== Email ===
 
 
 
For prospective students, the first point of contact should be the mailing list of the OBF project you are interested in working with:
 
 
 
;BioPerl: [mailto:bioperl-l@lists.open-bio.org bioperl-l@lists.open-bio.org]
 
;BioPython: [mailto:biopython@lists.open-bio.org biopython@lists.open-bio.org]
 
;BioJava: [mailto:biojava-l@lists.open-bio.org biojava-l@lists.open-bio.org]
 
;BioRuby: [mailto:bioruby@lists.open-bio.org bioruby@lists.open-bio.org]
 
;BioSQL: [mailto:biosql-l@lists.open-bio.org biosql-l@lists.open-bio.org]
 
;BioLib: [mailto:biolib-dev@lists.open-bio.org biolib-dev@lists.open-bio.org]
 
 
 
Also, it would be a good idea to CC the organization administrator, so he can make sure that you are properly taken care of:
 
 
 
;Organization administrator: [[User:RobertBuels|Robert Buels]] ([mailto:rmb32@cornell.edu rmb32@cornell.edu])
 
;Backup administrator: [[User:Lapp|Hilmar Lapp]] ([mailto:hlapp%40gmx%2enet hlapp&#64;gmx&#46;net])
 
 
 
If you are not quite sure which project you would like to contribute to, you can email to the organization administrator for help.  However, do not worry overly much about picking the right OBF project at the outset.  If you are unsure, simply make your best guess, and other members of the email list will help you to find the best organization to suit your idea.
 
 
 
Before applying, please read our [[#What_should_prospective_students_know.3F|documentation on information that students should know and guidelines we expect you to follow]]. We also require that you include certain information, listed below, under "[[#When you apply|When you apply]]."
 
 
 
Some mentors and developers can regularly be found on IRC, see the list of OBF projects below for information on which projects have a channel and the name of the channel. And/or join <code>#obf-soc</code> on [http://freenode.net Freenode.] ''(If you do not have an IRC client installed, you might find the [http://en.wikipedia.org/wiki/List_of_IRC_clients comparison on Wikipedia], the [http://directory.google.com/Top/Computers/Software/Internet/Clients/Chat/IRC/ Google directory], or the [http://www.ircreviews.org/clients/ IRC Reviews] helpful. For Macs, [http://en.wikipedia.org/wiki/X-Chat X-Chat Aqua] works pretty well. If you have never used IRC, try the [http://irchelp.org/irchelp/ircprimer.html IRC Primer] at [http://irchelp.org/ IRC Help], which also has links to lots of other material.)''
 
  
 
== OBF Projects Accepting Applicants ==
 
== OBF Projects Accepting Applicants ==
Line 158: Line 81:
 
:* No IRC channel at present
 
:* No IRC channel at present
  
[[Image:BioLib_logo_tiny.png|right|link=http://biolib.open-bio.org]]
+
; [http://biohaskell.org/ BioHaskell] :
; [http://biolib.open-bio.org BioLib] :
+
:* [http://biohaskell.org/ Project website]]
:* [http://biolib.open-bio.org Project website]
+
:* [http://hackage.haskell.org/packages/#cat:Bioinformatics Bioinformatics section on HackageDB]
:* [http://lists.open-bio.org/mailman/listinfo/biolib-dev developers mailing list]
+
 
:* [http://github.com/pjotrp/biolib/tree/master source code]
+
; [http://biocaml.org Biocaml] :
:* No IRC channel at present
+
:* [http://biocaml.org Project website]
 +
:* [https://groups.google.com/d/forum/biocaml Mailing list]
 +
:* [http://www.open-bio.org/wiki/Google_Summer_of_Code_2015_Ideas#Biocaml Project ideas]
  
 
== Guide for prospective GSoC students ==
 
== Guide for prospective GSoC students ==
Line 197: Line 122:
 
== Student Progress Reports ==
 
== Student Progress Reports ==
  
To encourage community bonding and awareness of what the GSoC students are doing, from 2012 the OBF is being much clearer about our progress report expectations.
+
In addition to writing code, accepted students send weekly updates to the OBF community on their project's progress. These updates allow us to keep aware of how GSoC students are doing, give students a forum to ask any questions, and promote overall community bonding.
  
We would like every student to setup a blog for the GSoC project (or a category/tag on your existing blog) which you will use to summarize your progress every week, as well as longer posts at the half way evaluation, and at the end of the summer.
+
At the beginning of the summer, we ask that you set up a blog for the GSoC project (or a category/tag on your existing blog) which you will use to summarize your progress every week, as well as longer posts about your work if you'd like. (See [http://zruanweb.com/tag/gsoc.html these] [http://www.yeyanbo.com/tag/gsoc.html examples] from 2013.)
 +
 
 +
Then, at the start of each week:
 +
 
 +
# Post an update on your blog: What did you do last week? What do you plan to do this week? Do you have any unanswered questions, any unsolved problems from the last week, interesting observations or anything else you'd like to mention?
 +
# Email the URL and text of the post (or a short summary) to the host project's mailing list (your mentors will confirm which one to use) ''and'' the main OBF GSoC mailing list (gsoc@lists.open-bio.org).
 +
 
 +
You will be writing under your own name, but with a clear association with your mentors, the OBF and its projects, so please take this seriously and be professional. Remember that your blog will be one of the first things found by anyone interested in the project you're working on, and can be a valuable resource to them &mdash; as well as a significant part of your online presence.
 +
 
 +
== Contact ==
 +
 
 +
Before applying, please read our [[#What_should_prospective_students_know.3F|documentation on information that students should know and guidelines we expect you to follow]]. We also require that you include certain information, listed below, under "[[#When you apply|When you apply]]."
 +
 
 +
=== Staff and org Admins ===
 +
;Organization administrator: Eric Talevich ([mailto:eric&#46;talevich&#64;gmail&#46;com eric&#46;talevich&#64;gmail&#46;com])
 +
;Backup administrator: Raoul Bonnal ([mailto:ilpuccio&#46;febo&#64;gmail&#46;com email]) (IRC: helius | channels: #obf-soc, #bioruby, #gsoc ) (Skype: ilpuccio)
 +
<!--
 +
Other organisations relevant for bioinformatics students are: [http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2013 Nescent], [https://github.com/SciRuby/sciruby/wiki/Google-Summer-of-Code-2013-Ideas SciRuby], [http://gmod.org/wiki/GSoC GMOD], who took on some of our projects and mentors.
 +
 
 +
;2013 Organization administrator: [[User:PjotrPrins|Pjotr Prins]] ([mailto:pjotr.gsoc2013@thebird.nl pjotr.gsoc2013@thebird.nl])
 +
;Backup administrators: Chris Fields, [[User:Lapp|Hilmar Lapp]], Robert Buels
 +
-->
 +
 
 +
=== Google Plus ===
 +
 
 +
[https://plus.google.com/communities/103096212020630764091 OBF Summer of Code] on G+
 +
 
 +
=== Email ===
 +
 
 +
For prospective students, the first point of contact should be the mailing list of the OBF project you are interested in working with:
 +
 
 +
;BioPerl: [mailto:bioperl-l@lists.open-bio.org bioperl-l@lists.open-bio.org]
 +
;BioPython: [mailto:biopython@lists.open-bio.org biopython@lists.open-bio.org]
 +
;BioJava: [mailto:biojava-l@lists.open-bio.org biojava-l@lists.open-bio.org]
 +
;BioRuby: [mailto:bioruby@lists.open-bio.org bioruby@lists.open-bio.org]
 +
;BioSQL: [mailto:biosql-l@lists.open-bio.org biosql-l@lists.open-bio.org]
 +
;BioLib: [mailto:biolib-dev@lists.open-bio.org biolib-dev@lists.open-bio.org]
 +
 
 +
Also, it would be a good idea to CC the organization administrator ([[User:EricTalevich|Eric Talevich]], [mailto:eric&#46;talevich&#64;gmail&#46;com eric&#46;talevich&#64;gmail&#46;com]), so he can make sure that you are properly taken care of!
 +
 
 +
If you are not quite sure which project you would like to contribute to, you can email to the organization administrator for help.  However, do not worry overly much about picking the right OBF project at the outset.  If you are unsure, simply make your best guess, and other members of the email list will help you to find the best organization to suit your idea.
 +
 
 +
=== IRC - Internet Relay Chat ===
 +
 
 +
OBF IRC channels are maintained on [http://freenode.net freenode], connect your IRC client to <code>chat.freenode.net</code>.
 +
 
 +
;Main OBF GSoC Channel: <code>#obf-soc</code>
 +
;BioPerl: <code>#bioperl</code>
 +
;BioRuby: <code>#bioruby</code>
 +
 
 +
Some mentors and developers can regularly be found on IRC, see the list of OBF projects below for information on which projects have a channel and the name of the channel. And/or join <code>#obf-soc</code> on [http://freenode.net Freenode.] ''(If you do not have an IRC client installed, you might find the [http://en.wikipedia.org/wiki/List_of_IRC_clients comparison on Wikipedia], the [http://directory.google.com/Top/Computers/Software/Internet/Clients/Chat/IRC/ Google directory], or the [http://www.ircreviews.org/clients/ IRC Reviews] helpful. For Macs, [http://en.wikipedia.org/wiki/X-Chat X-Chat Aqua] works pretty well. If you have never used IRC, try the [http://irchelp.org/irchelp/ircprimer.html IRC Primer] at [http://irchelp.org/ IRC Help], which also has links to lots of other material.)''
  
In addition, after publishing each blog post, we expect you to email the URL and the text of the blog (or if important images or formatting would be lost, at least a short summary) to the host project's mailing list(s) (check with your mentors if the project has more than one) AND the gsoc@open-bio.org mailing list.
 
  
You will be writing under your own name, but with a clear association with your mentors, the OBF and its projects, so please take this seriously and be professional. Remember this will become part of your online presence, and potentially looked at by future employers and colleagues.
 
  
 
== Mentor Resources ==
 
== Mentor Resources ==
Line 209: Line 182:
 
* [http://en.flossmanuals.net/GSoCMentoring/ GSoC Mentoring Guide]
 
* [http://en.flossmanuals.net/GSoCMentoring/ GSoC Mentoring Guide]
 
* [[Google_Summer_of_Code_Application_Evaluation|OBF Application Evaluation Guidelines]]
 
* [[Google_Summer_of_Code_Application_Evaluation|OBF Application Evaluation Guidelines]]
 +
 +
== Scientific Achievements ==
 +
In this section we want to report all the scientific achievements of our community, scientific papers or grant funded project that used the tools developed during the Google Summer of Code over the years.
 +
* [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btv098 Sambamba: fast processing of NGS alignment formats.] Bioinformatics (2015) doi: 10.1093/bioinformatics/btv098
 +
* [http://csw.github.io/bioruby-maf/ bio-maf]: The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4. Ranzani V et al. Nat Immunol. 2015 Mar;16(3):318-25. doi: 10.1038/ni.3093. Epub 2015 Jan 26.
 +
* [http://www.biomedcentral.com/1471-2105/13/209 Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython.] BMC Bioinformatics 2012, 13:209  doi:10.1186/1471-2105-13-209
 +
* [http://www.open-bio.org/wiki/Google_Summer_of_Code_2014#Loris_Cro vcf-mongo ]: Gene2Farm and WHEALBI European Research projects
 +
* [http://news.open-bio.org/news/2015/02/obf-gsoc-2014-wrapup/ OBF-GSoC-2014-WrapUp] is rich of science activities and results.
 +
* [http://www.rcsb.org RCSB PDB] is the north american access point to the world wide protein data bank, and uses BioJava extensively
 +
* Publications using BioJava:
 +
** Prlić, Andreas, et al. "BioJava: an open-source framework for bioinformatics in 2012." Bioinformatics 28.20 (2012): 2693-2695.
 +
** Holland, Richard CG, et al. "BioJava: an open-source framework for bioinformatics." Bioinformatics 24.18 (2008): 2096-2097.
 +
** Pocock, Matthew, Thomas Down, and Tim Hubbard. "BioJava: open source components for bioinformatics." ACM Sigbio Newsletter 20.2 (2000): 10-12.
 +
*** 181 citations on Google Scholar
 +
** Myers-Turnbull, Douglas, et al. "Systematic Detection of Internal Symmetry in Proteins Using CE-Symm." Journal of Molecular Biology, (2014) 426:11 pp. 2255–2268.
 +
** Prlić, Andreas, et al. (2010) “Precalculated Protein Structure Alignments at the RCSB PDB website.” Bioinformatics 26(23), 2983-2985
 +
** Bliven, Spencer, et al. (2015) "Detection of circular permutations within protein structures using CE-CP Bioinformatics." Bioinformatics. In press.
 +
** Aerts, Stein, et al. "Toucan: deciphering the cis‐regulatory logic of coregulated genes." Nucleic acids research 31.6 (2003): 1753-1764.
 +
** Vaida, Mircea-Florin, Radu Terec, and Lenuta Alboaie. "Alternative DNA Security Using BioJava." Digital Information and Communication Technology and Its Applications. Springer Berlin Heidelberg, 2011. 455-469.
 +
** Ross, Christian, and Qingxi J. Shen. "Computational prediction and experimental verification of HVA1-like abscisic acid responsive promoters in rice (Oryza sativa)." Plant molecular biology 62.1-2 (2006): 233-246.
 +
** Finak, G., et al. "BIAS: bioinformatics integrated application software." Bioinformatics 21.8 (2005): 1745-1746.
 +
** Aerts, Stein, et al. "A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes." Bioinformatics 20.12 (2004): 1974-1976.
 +
** Hanganu, A. N. D. R. E. I., et al. "SLIDE: An interactive threading refinement tool for homology modeling." Rom J Biochem 1009.46: 123-127.
 +
** Kaladhar, DSVGK. "BioJava: A Programming Guide." (2012). LAP Lambert Academic Publishing , Germany. ISBN:3659167509 9783659167508
 +
** Prins, J. C. P. "BioLib: Sharing high performance code between BioPerl, BioPython, BioRuby, R/Bioconductor and BioJAVA." 17th Annual International Conference on Intelligent Systems for Molecular Biology, Stockhol, Sweden, June 27-July 2, 2009. 2009.
 +
** Tang, Si-Xin, Yi-Bing Li, and Hong-Bo He. "Designing a BioJava-based Software for RNA Sequence Analysis." Journal of Luoyang Institute of Technology 6 (2005): 016.
 +
** Mangalam, Harry. "The Bio* toolkits—a brief overview." Briefings in bioinformatics 3.3 (2002): 296-302.
 +
** Ryu, Taewan. "Benchmarking of BioPerl, Perl, BioJava, Java, BioPython, and Python for primitive bioinformatics tasks and choosing a suitable language." International Journal of Contents 5.2 (2009): 6-15.
 +
** McGuffee, James W. "Programming languages and the biological sciences." Journal of Computing Sciences in Colleges 22.4 (2007): 178-183.
  
 
== Previous Years ==
 
== Previous Years ==
Line 214: Line 216:
 
This section contains links to content related to OBF's participation
 
This section contains links to content related to OBF's participation
 
in GSoC in previous years.
 
in GSoC in previous years.
 
+
* [[Google_Summer_of_Code_2014|2014]] - 6 student projects
 +
* Google Summer of Code 2013 - OBF not accepted, some Bio* projects partnered with other organisations
 +
* [[Google_Summer_of_Code_2012|2012]] - 5 student projects
 
* [[Google_Summer_of_Code_2011|2011]] - 6 student projects
 
* [[Google_Summer_of_Code_2011|2011]] - 6 student projects
 
* [[Google_Summer_of_Code_2010|2010]] - 6 student projects
 
* [[Google_Summer_of_Code_2010|2010]] - 6 student projects
 
== Other Facts & Links ==
 
 
'''[http://code.google.com/soc Google Summer of Code Main Site]'''
 
 
* [http://www.google-melange.com/gsoc/events/google/gsoc2012 GSoC 2012 time line]
 
* Google expects to accept around 150 mentoring organizations.
 
* Development is done entirely remotely and on-line, there is no requirement or expectation for either students or mentors to travel.
 
* Org application documents, with Google's questions and our answers:
 
** [[Google Summer of Code 2010 Org Application | 2010 ]]
 
** [http://docs.google.com/Doc?id=dhs98hzv_7zn8bxqjm 2009]
 
* For questions of eligibility, see the [http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs GSoC 2012 FAQ].
 
* There is also a [http://groups.google.com/group/google-summer-of-code-discuss Google group for posting GSoC questions] (and receiving answers; note that you will need to sign up for the group) that relate to the program itself (and are not specific to our organization).
 
* Students receive a stipend from Google if accepted. See the  [http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs GSoC 2012 FAQ] for full documentation.
 
  
  
 
[[Category:Google Summer of Code]]
 
[[Category:Google Summer of Code]]

Latest revision as of 10:39, 18 February 2016

GSoC15-logo-small.jpg

Google Summer of Code (GSoC) is a student internship program for open-source projects. The program offers eligible student developers stipends to write code for open source projects over a period of 3 summer months ("flip bits, not burgers"). See the Google Summer of Code Main Site for general information about the Google Summer of Code program, how to apply, frequently asked general questions, and more.


GSoC 2016

The Google Summer of Code 2016 is ON! OBF is once again applying as a GSoC mentoring organization this year. Interested mentors and students should subscribe to the OBF/GSoC mailing list. Please announce yourself, so we know who you are! The details of each of our project ideas are listed below, including potential mentors.

See http://obf.github.io/GSoC/ for more information about the GSoC program and additional ways to get in touch with us.

Facts & Links

Time Line 
GSoC 2016 FAQ 
Info from Google 
  • There is also a Google group for posting GSoC questions (and receiving answers; note that you will need to sign up for the group) that relate to the program itself (and are not specific to our organization).
  • Students receive a stipend from Google if accepted. See the GSoC 2016 FAQ for full documentation.
  • Development is done entirely remotely and on-line; there is no requirement or expectation for either students or mentors to travel.

Why apply?

One of the most important features of the program is that students are paired with mentors, who are typically experienced developers from the project to which the student is contributing. The mentor guides the student to work productively within the community, and helps the student avoid obstacles and pitfalls. The program is global - students and mentors may be located anywhere where they have an internet connection (except for countries affected by US trade restrictions), and no travel is required. Thus, aside from the stipend and mentorship aspects, the student's experience in the internship closely mirrors normal work on distributed development projects. Effective work habits for distributed development are typically not taught as part of computer science curricula, yet are highly desired in the increasingly global and distributed software, IT, and biotechnology industries.

From the viewpoint of each open-source project, the program not only offers to pay students for contributing, but more importantly, offers an opportunity to recruit new developers who will hopefully go on to become regular, sustaining contributors.

Project Ideas

Our GSoC ideas from each project are collected here: http://obf.github.io/GSoC/

OBF Projects Accepting Applicants

BioPerl logo tiny.jpg
BioPerl 
Biopython logo tiny.png
BioPython 
Biojava logo tiny.jpg
BioJava 
BioRuby logo tiny.png
BioRuby 
BioSQL logo.png
BioSQL 
BioHaskell 
Biocaml 

Guide for prospective GSoC students

Before you apply

  • Proposals should extend one of affiliated toolkits, not start a new project.
  • If you want to apply with your own idea, it's best to contact the OBF subproject you're interested in well before the application deadline, so we can work with you to find a mentor and solidify your project idea and application.
  • Ask us questions on the subproject mailing lists about the project idea you have in mind.
  • Write a project proposal draft, include a project plan (see below), and send it to a project mailing list for comments before submitting it.

Again, students are strongly encouraged to contact us as early as possible. Frequent and early communication is extremely valuable for putting together successful projects.

When you apply

When applying, (aside from the information requested by Google) please provide the following in your application material.

  1. Your complete contact information, including full name, physical address, preferred email address, and telephone number, plus other pertinent contact information such as IRC handles, etc.
  2. Why you are interested in the project you are proposing and are well-suited to undertake it.
  3. A summary of your programming experience and skills.
  4. Programs or projects you have previously authored or contributed to, in particular those available as open-source, including, if applicable, any past Summer of Code involvement.
  5. A project plan for the project you are proposing, even if your proposed project is directly based on one of the proposed project ideas for member projects.
    • A project plan in principle divides up the whole project into a series of manageable milestones and time-lines that, when all accomplished, logically lead to the end goal(s) of the project. Put in another way, a project plan explains what you expect you will need to be doing, and what you expect you need to have accomplished, at which time, so that at the end you reach the goals of the project.
    • Do not take this part lightly. A compelling plan takes a significant amount of work. Empirically, applications with no or a hastily composed project plan have not been competitive, and a more thorough project plan can easily make an applicant out compete another with more advanced skills.
    • A good plan will require you to thoroughly think about the project itself and how one might want to go about the work.
    • We don't expect you to have all the experience, background, and knowledge to come up with the final, real work plan on your own at the time you apply. We do expect your plan to demonstrate, however, that you have made the effort and thoroughly dissected the goals into tasks and successive accomplishments that make sense.
    • We strongly recommend that you bounce your proposed project and your project plan draft off of us, using either the pertinent developers mailing list or the IRC channel(s). Through the project plan exercise you will inevitably discover that you are missing a lot of the pieces - we are there to help you fill those in as best as we can.
  6. Any obligations, vacations, or plans for the summer that may require scheduling during the GSoC work period.
    • We expect the your GSoC project to be your primary focus over the summer. It should not be regarded as a part-time occupation.
    • If you feel that you can manage other work obligations concurrently with your Summer of Code project, make your case and support it with evidence.
    • Be honest and open. If it turns out later that you weren't clear about other obligations, at best (i.e., if your accomplishment record at that point is spotless) our trust in you will be severely degraded. Also, if you are accepted, discuss with your GSoC mentor before taking on additional obligations.
    • One of the most common reasons for students to struggle or fail is being overcommitted. Do not set yourself up for failure! GSoC summers should be fun and rewarding!

Student Progress Reports

In addition to writing code, accepted students send weekly updates to the OBF community on their project's progress. These updates allow us to keep aware of how GSoC students are doing, give students a forum to ask any questions, and promote overall community bonding.

At the beginning of the summer, we ask that you set up a blog for the GSoC project (or a category/tag on your existing blog) which you will use to summarize your progress every week, as well as longer posts about your work if you'd like. (See these examples from 2013.)

Then, at the start of each week:

  1. Post an update on your blog: What did you do last week? What do you plan to do this week? Do you have any unanswered questions, any unsolved problems from the last week, interesting observations or anything else you'd like to mention?
  2. Email the URL and text of the post (or a short summary) to the host project's mailing list (your mentors will confirm which one to use) and the main OBF GSoC mailing list (gsoc@lists.open-bio.org).

You will be writing under your own name, but with a clear association with your mentors, the OBF and its projects, so please take this seriously and be professional. Remember that your blog will be one of the first things found by anyone interested in the project you're working on, and can be a valuable resource to them — as well as a significant part of your online presence.

Contact

Before applying, please read our documentation on information that students should know and guidelines we expect you to follow. We also require that you include certain information, listed below, under "When you apply."

Staff and org Admins

Organization administrator
Eric Talevich (eric.talevich@gmail.com)
Backup administrator
Raoul Bonnal (email) (IRC: helius | channels: #obf-soc, #bioruby, #gsoc ) (Skype: ilpuccio)

Google Plus

OBF Summer of Code on G+

Email

For prospective students, the first point of contact should be the mailing list of the OBF project you are interested in working with:

BioPerl
bioperl-l@lists.open-bio.org
BioPython
biopython@lists.open-bio.org
BioJava
biojava-l@lists.open-bio.org
BioRuby
bioruby@lists.open-bio.org
BioSQL
biosql-l@lists.open-bio.org
BioLib
biolib-dev@lists.open-bio.org

Also, it would be a good idea to CC the organization administrator (Eric Talevich, eric.talevich@gmail.com), so he can make sure that you are properly taken care of!

If you are not quite sure which project you would like to contribute to, you can email to the organization administrator for help. However, do not worry overly much about picking the right OBF project at the outset. If you are unsure, simply make your best guess, and other members of the email list will help you to find the best organization to suit your idea.

IRC - Internet Relay Chat

OBF IRC channels are maintained on freenode, connect your IRC client to chat.freenode.net.

Main OBF GSoC Channel
#obf-soc
BioPerl
#bioperl
BioRuby
#bioruby

Some mentors and developers can regularly be found on IRC, see the list of OBF projects below for information on which projects have a channel and the name of the channel. And/or join #obf-soc on Freenode. (If you do not have an IRC client installed, you might find the comparison on Wikipedia, the Google directory, or the IRC Reviews helpful. For Macs, X-Chat Aqua works pretty well. If you have never used IRC, try the IRC Primer at IRC Help, which also has links to lots of other material.)


Mentor Resources

Scientific Achievements

In this section we want to report all the scientific achievements of our community, scientific papers or grant funded project that used the tools developed during the Google Summer of Code over the years.

  • Sambamba: fast processing of NGS alignment formats. Bioinformatics (2015) doi: 10.1093/bioinformatics/btv098
  • bio-maf: The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4. Ranzani V et al. Nat Immunol. 2015 Mar;16(3):318-25. doi: 10.1038/ni.3093. Epub 2015 Jan 26.
  • Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinformatics 2012, 13:209 doi:10.1186/1471-2105-13-209
  • vcf-mongo : Gene2Farm and WHEALBI European Research projects
  • OBF-GSoC-2014-WrapUp is rich of science activities and results.
  • RCSB PDB is the north american access point to the world wide protein data bank, and uses BioJava extensively
  • Publications using BioJava:
    • Prlić, Andreas, et al. "BioJava: an open-source framework for bioinformatics in 2012." Bioinformatics 28.20 (2012): 2693-2695.
    • Holland, Richard CG, et al. "BioJava: an open-source framework for bioinformatics." Bioinformatics 24.18 (2008): 2096-2097.
    • Pocock, Matthew, Thomas Down, and Tim Hubbard. "BioJava: open source components for bioinformatics." ACM Sigbio Newsletter 20.2 (2000): 10-12.
      • 181 citations on Google Scholar
    • Myers-Turnbull, Douglas, et al. "Systematic Detection of Internal Symmetry in Proteins Using CE-Symm." Journal of Molecular Biology, (2014) 426:11 pp. 2255–2268.
    • Prlić, Andreas, et al. (2010) “Precalculated Protein Structure Alignments at the RCSB PDB website.” Bioinformatics 26(23), 2983-2985
    • Bliven, Spencer, et al. (2015) "Detection of circular permutations within protein structures using CE-CP Bioinformatics." Bioinformatics. In press.
    • Aerts, Stein, et al. "Toucan: deciphering the cis‐regulatory logic of coregulated genes." Nucleic acids research 31.6 (2003): 1753-1764.
    • Vaida, Mircea-Florin, Radu Terec, and Lenuta Alboaie. "Alternative DNA Security Using BioJava." Digital Information and Communication Technology and Its Applications. Springer Berlin Heidelberg, 2011. 455-469.
    • Ross, Christian, and Qingxi J. Shen. "Computational prediction and experimental verification of HVA1-like abscisic acid responsive promoters in rice (Oryza sativa)." Plant molecular biology 62.1-2 (2006): 233-246.
    • Finak, G., et al. "BIAS: bioinformatics integrated application software." Bioinformatics 21.8 (2005): 1745-1746.
    • Aerts, Stein, et al. "A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes." Bioinformatics 20.12 (2004): 1974-1976.
    • Hanganu, A. N. D. R. E. I., et al. "SLIDE: An interactive threading refinement tool for homology modeling." Rom J Biochem 1009.46: 123-127.
    • Kaladhar, DSVGK. "BioJava: A Programming Guide." (2012). LAP Lambert Academic Publishing , Germany. ISBN:3659167509 9783659167508
    • Prins, J. C. P. "BioLib: Sharing high performance code between BioPerl, BioPython, BioRuby, R/Bioconductor and BioJAVA." 17th Annual International Conference on Intelligent Systems for Molecular Biology, Stockhol, Sweden, June 27-July 2, 2009. 2009.
    • Tang, Si-Xin, Yi-Bing Li, and Hong-Bo He. "Designing a BioJava-based Software for RNA Sequence Analysis." Journal of Luoyang Institute of Technology 6 (2005): 016.
    • Mangalam, Harry. "The Bio* toolkits—a brief overview." Briefings in bioinformatics 3.3 (2002): 296-302.
    • Ryu, Taewan. "Benchmarking of BioPerl, Perl, BioJava, Java, BioPython, and Python for primitive bioinformatics tasks and choosing a suitable language." International Journal of Contents 5.2 (2009): 6-15.
    • McGuffee, James W. "Programming languages and the biological sciences." Journal of Computing Sciences in Colleges 22.4 (2007): 178-183.

Previous Years

This section contains links to content related to OBF's participation in GSoC in previous years.

  • 2014 - 6 student projects
  • Google Summer of Code 2013 - OBF not accepted, some Bio* projects partnered with other organisations
  • 2012 - 5 student projects
  • 2011 - 6 student projects
  • 2010 - 6 student projects