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'''Google Summer of Code is a global program that offers student developers stipends to write code for various open source software projects. We work with many open source, free software, and technology-related groups to identify and fund projects over a three month period. Since its inception in 2005, the program has brought together over 7,500 successful student participants from 97 countries and over 7,000 mentors from over 100 countries worldwide to produce over 50 million lines 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.''' | '''Google Summer of Code is a global program that offers student developers stipends to write code for various open source software projects. We work with many open source, free software, and technology-related groups to identify and fund projects over a three month period. Since its inception in 2005, the program has brought together over 7,500 successful student participants from 97 countries and over 7,000 mentors from over 100 countries worldwide to produce over 50 million lines 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.''' | ||
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GSoC has several goals: | GSoC has several goals: | ||
Revision as of 21:58, 17 January 2014
Contents
Welcome to the Genome Informatics Google Summer of Code
from the Google Summer of Code website:
Google Summer of Code is a global program that offers student developers stipends to write code for various open source software projects. We work with many open source, free software, and technology-related groups to identify and fund projects over a three month period. Since its inception in 2005, the program has brought together over 7,500 successful student participants from 97 countries and over 7,000 mentors from over 100 countries worldwide to produce over 50 million lines 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.
GSoC has several goals:
- get more open source code created and released for the benefit of all
- inspire young developers to begin participating in open source development
- help open source projects identify and bring in new developers and committers
- provide students the opportunity to do work related to their academic pursuits during the summer
- give students more exposure to real-world software development scenarios.
Member Projects
The Genome Informatics group is organizing the joint efforts of Galaxy, GBrowse, GMOD, JBrowse, Reactome, SeqWare, and Wormbase (see below). This is a great opportunity for students to contribute to the work of any of eight established bioinformatics projects.
- Galaxy
- An open, web-based platform for accessible, reproducible, and transparent computational biomedical research. The public Galaxy service 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. Galaxy is implemented in Python. Links: Website.
- Generic Model Organism Database (GMOD)
- 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. Links: Website, GMOD Blog
- GBrowse
- The Generic Genome Browser (GBrowse) is a web application for searching and displaying annotations on genomes. GBrowse was designed from the bottom up for portability, extensibility, and modularity. It relies on no proprietary software, but only readily available open source software such as MySQL and the BioPerl libraries. GBrowse is implemented in Perl. Link: Website.
- JBrowse
- JBrowse is being developed as the successor to GBrowse. It is a modern, fast genome browser implemented almost entirely in JavaScript, with some server-side formatting code in Perl. Link: Website.
- PortEco
- PortEco project unifies web access to information and tools about the biology of E. coli, its bacteriophages, plasmids, and mobile genetic elements. PortEco partners include EcoCyc, EcoliWiki, the Stanford Microarray Database, and PANTHER protein families database. PortEco is responsible for maintaining the Gene Ontology annotation of E. coli genes.
- Reactome
- 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. Links: Website, ReactomeWiki .
- SeqWare
- SeqWare is a multi-faceted project that includes a developer-friendly workflow development and execution engine (SeqWare Pipeline) along with a NoSQL variant database (SeqWare Query Engine). The system is used by OICR to automate the analysis of a large percentage of the NGS samples processed by the institute. It's our intention to share these workflow with the community and we're using the SeqWare workflow format and reference VM on Amazon to do this. For the GSoC we're interested in integrating the project with Galaxy to use that terrific application as a frontend. We also are interested in exposing the Query Engine HBase variant database through a nice REST API and web app for interacting with this highly scalable variant storage and analysis system. The SeqWare team is based at OICR and includes developers at UNC and other locations. Links: [1]
- WormBase
- 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. Links: Website.
Contact Us
- Email: robin.haw[AT]oicr.on.ca - contact me to find out more about a project or your potential mentor(s).
- Discussion mailing lists: Genome Informatics Google Groups - ask about our projects; join the community!
- IRC channel: #genomeinformatics on Freenode.
How to apply
We would like to know who you are and how you think. Incorporate the following into your application:
- Your information
- Name, email, and website (optional)
- Brief background: education and relevant work experience
- Your programming interests and strengths
- What are your languages of choice?
- Any prior experience with open source development?
- Your interest and background in biology or bioinformatics
- Any prior exposure to biology or bioinformatics?
- Your ideas for a project (an original idea or one expanded from our Ideas Page)
- Provide as much detail as possible
- Strong applicants include an implementation plan and timeline (hint!)
- Refer to and link to other projects or products that illustrate your ideas
- Identify possible hurdles and questions that will require more research/planning
- What can you bring to the team?
Resources
Guides
For Students
For Mentors
Project Ideas
These projects include a broad set of skills, technologies and domains, such as GUIs, database integration and algorithms. You are also encouraged to propose your own ideas related to our projects. If you have strong computer skills and have an interest in biology or bioinformatics, then you should definitely apply!
(your idea here)
Please feel very free to propose your own idea. As long as it is relevant to one of our projects, we will give it serious consideration. Creativity and self-motivation are great traits for open source programmers. Do not hesitate to propose your own project idea: some of the best applications we see are by students that go this route.
