[Computational-biology] Genome Informatics - Student Recruitment for Google Summer of Code 2011

Robin Haw via comp-bio%40net.bio.net (by Robin.Haw from oicr.on.ca)
Sun Mar 27 22:58:48 EST 2011

The Genome Informatics group, encompassing Reactome, Wormbase and GMOD will=
 be participating in Google Summer of Code 2011. This is a great opportunit=
y for students to contribute to the work of one of three bioinformatics pro=
jects. More information on project ideas and the program is published at th=
e GMOD website (http://www.gmod.org/wiki/GSoC). If you have any questions o=
r queries, please feel free to send a post to the Genome Informatics Google=
 Groups (http://groups.google.com/group/genome-informatics). Candidate stud=
ents 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 Ap=
ril 25 (3pm EST).

=93Google Summer of Code (GSoC, http://socghop.appspot.com<http://socghop.a=
ppspot.com/>) is a global program that offers student developers stipends t=
o write code for various open source software projects. We have worked with=
 several open source, free software, and technology-related groups to ident=
ify and fund several projects over a three month period. Since its inceptio=
n in 2005, the program has brought together over 4,500 students and more th=
an more than 4,000 mentors & co-mentors from over 85 countries worldwide, a=
ll for the love of code. Through Google Summer of Code, accepted student ap=
plicants are paired with a mentor or mentors from the participating project=
s, thus gaining exposure to real-world software development scenarios and t=
he opportunity for employment in areas related to their academic pursuits. =
In turn, the participating projects are able to more easily identify and br=
ing in new developers. Best of all, more source code is created and release=
d 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 or=
ganism Caenorhabditis elegans and related nematodes. It is used by the C. e=
legans research community both as an information resource and as a mode to =
publish and distribute their results. The database is constantly updated an=
d new versions are released on a monthly basis. WormBase is a collaboration=
 among the Wellcome Trust Sanger Institute, Ontario Institute for Cancer Re=
search, Washington University in St. Louis, and the California Institute of=

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 Reac=
tome data model describes diverse processes in the human system, including =
the pathways of intermediary metabolism, regulatory pathways, signal transd=
uction, 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 dat=
a entry tool in Java programming language. The Reactome team is composed of=
 individuals who are both biologists and programmers at the Ontario Institu=
te for Cancer Research, New York University Langone Medical Center, Cold Sp=
ring Harbor Laboratory, and The European Bioinformatics Institute.

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

Contact Information
Email: robin.haw from oicr.on.ca<mailto:robin.haw from oicr.on.ca> - contact me to fi=
nd 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.g=
oogle.com/group/genome-informatics) - ask about our projects; join the comm=

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