[BiO BB] Genome Informatics - Student Recruitment for Google Summer of Code 2011

[Robin Haw]

The Genome Informatics group, encompassing Reactome, Wormbase and GMOD will be participating in Google Summer of Code 2011. This is a great opportunity for students to contribute to the work of one of three bioinformatics projects. More information on project ideas and the program is published at the GMOD website (http://www.gmod.org/wiki/GSoC). If you have any questions or queries, please feel free to send a post to the Genome Informatics Google Groups (http://groups.google.com/group/genome-informatics). Candidate students need to start discussing application ideas with Genome Informatics as soon as possible. The application period for students is March 28 to April 8. All student proposals will be matched with a mentor by April 22, and the final list of accepted students and their projects will be announced on April 25 (3pm EST).

“Google Summer of Code (GSoC, http://socghop.appspot.com<http://socghop.appspot.com/>) is a global program that offers student developers stipends to write code for various open source software projects. We have worked with several open source, free software, and technology-related groups to identify and fund several projects over a three month period. Since its inception in 2005, the program has brought together over 4,500 students and more than more than 4,000 mentors & co-mentors from over 85 countries worldwide, all for the love of code. Through Google Summer of Code, accepted student applicants are paired with a mentor or mentors from the participating projects, thus gaining exposure to real-world software development scenarios and the opportunity for employment in areas related to their academic pursuits. In turn, the participating projects are able to more easily identify and bring in new developers. Best of all, more source code is created and released for the use and benefit of all."

Wormbase (http://www.wormbase.org<http://www.wormbase.org/>)
An online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. The database is constantly updated and new versions are released on a monthly basis. WormBase is a collaboration among the Wellcome Trust Sanger Institute, Ontario Institute for Cancer Research, Washington University in St. Louis, and the California Institute of Technology.

Reactome (http://www.reactome.org<http://www.reactome.org/>)
A manually curated database of core pathways and reactions in human biology that functions as a data mining resource and electronic textbook. The Reactome data model describes diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, signal transduction, and high-level processes, such as the cell cycle. Reactome software uses only freely available (and often open source) components and has been created with cross-platform compatibility and wide usability in mind. Data is stored in a MySQL database, the web site is implemented in Perl and data entry tool in Java programming language. The Reactome team is composed of individuals who are both biologists and programmers at the Ontario Institute for Cancer Research, New York University Langone Medical Center, Cold Spring Harbor Laboratory, and The European Bioinformatics Institute.

Generic Model Organism Database (GMOD, http://www.gmod.org<http://www.gmod.org/>)
An open source project to develop a complete set of software for creating and administering a model organism database. Components of this project include genome visualization and editing tools, literature curation tools, a robust database schema, biological ontology tools, and a set of standard operating procedures. This project is collaboration of several database projects, including WormBase, FlyBase, Mouse Genome Informatics, Gramene, the Rat Genome Database, TAIR, EcoCyc, and the Saccharomyces Genome Database.

Contact Information
Email: robin.haw at oicr.on.ca<mailto:robin.haw at oicr.on.ca> - contact me to find out more about a project or your potential mentor(s).
Website: http://www.gmod.org/wiki/GSoC
Discussion mailing lists: Genome Informatics Google Groups (http://groups.google.com/group/genome-informatics) - ask about our projects; join the community!