Genome Informatics

Web Page: http://gmod.org/wiki/GSoC

Mailing List: mailto:genome-informatics@googlegroups.com

The Genome Informatics group is organizing the joint efforts of Galaxy, GBrowse, GMOD, JBrowse, Reactome, Wormbase, ProtEco, and SeqWare. 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. 
• GBrowse: The Generic Genome Browser (GBrowse) is a web application for searching and displaying annotations on genomes. 
• Generic Model Organism Database: An open source project to develop a complete set of software for creating and administering a model organism database. 
• JBrowse: The 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.
• Reactome: A manually curated database of core pathways and reactions in human biology that functions as a data mining resource and electronic textbook. 
• Wormbase: An online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. 
• PortEco: The PortEco project unifies web access to information and tools about the biology of E. coli, its bacteriophages, plasmids, and mobile genetic elements.
• SeqWare: 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), which is used by automate the analysis of Next-Generation Sequencing data.

Projects

• eQTL Pipeline and Visualisation For The Galaxy Project Establish an eQTL pipeline in Galaxy for various tools, pack them in a workflow for comparison and implement visualisation heatmaps and scatter plots using d3.js.
• Genome Informatics - Improving UX of GMOD Extensions for MediaWiki (widget, skin and feedback extension)
• Reactome Smartphone Application This project aims to bring Reactome to the smartphones. Reactome’s REST API is quite diverse and exposes lots of data. This data can be utilized to develop a smartphone app which would allow users to access pathways and other data easily. The technology is advancing at a rapid rate and the count of smartphones is increasing everyday. A good app is necessary to allow users to access the data from anywhere. My objective is to develop a user friendly app which gives access to data anywhere. I will use jQuery mobile to design the UI and it will be wrapped into Phonegap to make it a native app.
• WormBase iOS App/Mobile web site Development of a mobile web application and a HTML5 App for accessing the WormBase.org database.