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We need to copy content here from the main [[Google Summer of Code]] page.
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== GSoC 2012 ==
 +
 
 +
The Open Bioinformatics Foundation has been accepted as a mentoring organization for Google Summer of Code 2012, with 5 student projects funded!
 +
 
 +
== 2012 Student Projects ==
 +
 
 +
=== Wibowo Arindrarto ===
 +
 
 +
:[http://bow.web.id/blog/tag/gsoc/ SearchIO Implementation in Biopython]
 +
:mentored by Peter Cock
 +
 
 +
Bow continues to develop and maintain the SearchIO module, the product of his GSoC work, and contributes to other areas of Biopython as well.
 +
 
 +
=== Lenna Peterson ===
 +
 
 +
:[http://arklenna.tumblr.com/tagged/gsoc2012 Diff My DNA: Development of a Genomic Variant Toolkit for BioPython]
 +
:mentored by Brad Chapman
 +
 
 +
Lenna continues to actively contribute to several parts of Biopython.
 +
 
 +
=== Marjan Povolni ===
 +
 
 +
:[http://blog.mpthecoder.com/tagged/gsoc The world's fastest parallelized GFF3/GTF parser in D, and an interfacing biogem plugin for Ruby]
 +
:mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal
 +
 
 +
Marjan is still actively developing in FOSS, and also contributes to [http://www.biogems.info/ biogems.info].
 +
 
 +
''An interview with Marjan''
 +
 
 +
'''You participated in OBF/GSoC, what did it bring you in your current pursuits?'''
 +
 
 +
It connected me to experienced people who helped me to into science.
 +
 
 +
'''What projects did you work on and are they still in use?'''
 +
 
 +
My project was about parsing the GFF3 textual format used in bioinformatics, but at the same time increasing the speed and reducing the memory footprint of the parser manyfold. I don't believe the project is used by many people right now. However, I do think it has potential to be integrated into data processing pipelines. Since GSoC 2012 ended I didn't have the time to keep working on it, but I'm still positive it will change very soon and I'll continue working on it.
 +
 
 +
'''Are you still involved with these projects or elsewhere in FOSS?'''
 +
 
 +
My schedule currently doesn't allow it, but I'm positive that will change very soon, I would like to continue working on the project and related themes.
 +
 
 +
'''Did you enjoy OBF/GSoC and do you have any special memories?'''
 +
 
 +
I did, working from home is great and challenges suit me well. I also had the fortune to meet some of the people behind OBF at a codefest that was organized nearby. Releasing the first development version of the code was a feeling that cannot be described in words, and the feedback I received made me feel I had accomplished something, even though I had work experience before.
 +
 
 +
'''Was the OBF/GSoC organisation good for you? What stood out?'''
 +
 
 +
Yes, it was very good. What I liked most were the weekly hangouts with the other accepted students and mentors. I was working on the project myself, but never felt alone.
 +
 
 +
'''Would you recommend OBF/GSoC to other students and do you have any hints for
 +
them?'''
 +
 
 +
Definitely. Bioinformatics is a great place to be right now, there is already so much that has been discovered, but that's only the tip of the iceberg. And going forward the field of biology can advance only with the help from bioinformatics.
 +
 
 +
 
 +
=== Artem Tarasov ===
 +
 
 +
:[http://lomereiter.wordpress.com/tag/gsoc Robust and fast parallel BAM parser in D for binding against dynamic languages]
 +
:mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal
 +
 
 +
''An interview with Artem''
 +
 
 +
'''You participated in OBF/GSoC, what did it bring you in your pursuits?'''
 +
 
 +
GSoC gave me experience of collaborative open-source development, and OBF introduced me to the bioinformatics field.
 +
 
 +
'''What projects did you work on and are they still in use?'''
 +
 
 +
I worked on a new library for working with SAM/BAM files; it is now used by a few people but we aim to attract more by publishing a paper soon.
 +
 
 +
'''Are you still involved with these projects or elsewhere in FOSS?'''
 +
 
 +
Yes, the development has been continuing after GSoC, and quite a lot of new
 +
functionality has been added.
 +
 
 +
'''Did you enjoy OBF/GSoC and do you have any special memories?'''
 +
 
 +
I enjoyed GSoC a lot. It was wonderful to realise how geographically diverse the OBF community is.
 +
 
 +
'''Was the OBF/GSoC organisation good for you? What stood out?'''
 +
 
 +
The community was very helpful and friendly. With respect to programming, they encouraged students to do thorough testing and write proper documentation. Plus, we had a few rounds of code reviews.
 +
 
 +
'''Would you recommend OBF/GSoC to other students and do you have any hints for them?'''
 +
 
 +
Yes, definitely! It is a good opportunity to learn a bit about bioinformatics and to practice some agile software development approaches.
 +
 
 +
 
 +
=== Clayton Wheeler ===
 +
 
 +
:[http://csw.github.com/bioruby-maf/ Multiple Alignment Format parser for BioRuby]
 +
:mentored by Francesco Strozzi and Raoul Bonnal
 +
 
 +
== 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.''

Latest revision as of 07:32, 12 February 2014

GSoC 2012

The Open Bioinformatics Foundation has been accepted as a mentoring organization for Google Summer of Code 2012, with 5 student projects funded!

2012 Student Projects

Wibowo Arindrarto

SearchIO Implementation in Biopython
mentored by Peter Cock

Bow continues to develop and maintain the SearchIO module, the product of his GSoC work, and contributes to other areas of Biopython as well.

Lenna Peterson

Diff My DNA: Development of a Genomic Variant Toolkit for BioPython
mentored by Brad Chapman

Lenna continues to actively contribute to several parts of Biopython.

Marjan Povolni

The world's fastest parallelized GFF3/GTF parser in D, and an interfacing biogem plugin for Ruby
mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal

Marjan is still actively developing in FOSS, and also contributes to biogems.info.

An interview with Marjan

You participated in OBF/GSoC, what did it bring you in your current pursuits?

It connected me to experienced people who helped me to into science.

What projects did you work on and are they still in use?

My project was about parsing the GFF3 textual format used in bioinformatics, but at the same time increasing the speed and reducing the memory footprint of the parser manyfold. I don't believe the project is used by many people right now. However, I do think it has potential to be integrated into data processing pipelines. Since GSoC 2012 ended I didn't have the time to keep working on it, but I'm still positive it will change very soon and I'll continue working on it.

Are you still involved with these projects or elsewhere in FOSS?

My schedule currently doesn't allow it, but I'm positive that will change very soon, I would like to continue working on the project and related themes.

Did you enjoy OBF/GSoC and do you have any special memories?

I did, working from home is great and challenges suit me well. I also had the fortune to meet some of the people behind OBF at a codefest that was organized nearby. Releasing the first development version of the code was a feeling that cannot be described in words, and the feedback I received made me feel I had accomplished something, even though I had work experience before.

Was the OBF/GSoC organisation good for you? What stood out?

Yes, it was very good. What I liked most were the weekly hangouts with the other accepted students and mentors. I was working on the project myself, but never felt alone.

Would you recommend OBF/GSoC to other students and do you have any hints for them?

Definitely. Bioinformatics is a great place to be right now, there is already so much that has been discovered, but that's only the tip of the iceberg. And going forward the field of biology can advance only with the help from bioinformatics.


Artem Tarasov

Robust and fast parallel BAM parser in D for binding against dynamic languages
mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal

An interview with Artem

You participated in OBF/GSoC, what did it bring you in your pursuits?

GSoC gave me experience of collaborative open-source development, and OBF introduced me to the bioinformatics field.

What projects did you work on and are they still in use?

I worked on a new library for working with SAM/BAM files; it is now used by a few people but we aim to attract more by publishing a paper soon.

Are you still involved with these projects or elsewhere in FOSS?

Yes, the development has been continuing after GSoC, and quite a lot of new functionality has been added.

Did you enjoy OBF/GSoC and do you have any special memories?

I enjoyed GSoC a lot. It was wonderful to realise how geographically diverse the OBF community is.

Was the OBF/GSoC organisation good for you? What stood out?

The community was very helpful and friendly. With respect to programming, they encouraged students to do thorough testing and write proper documentation. Plus, we had a few rounds of code reviews.

Would you recommend OBF/GSoC to other students and do you have any hints for them?

Yes, definitely! It is a good opportunity to learn a bit about bioinformatics and to practice some agile software development approaches.


Clayton Wheeler

Multiple Alignment Format parser for BioRuby
mentored by Francesco Strozzi and Raoul Bonnal

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
BioPython
BioJava
BioRuby
BioLib

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.

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