Genome Informatics

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

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

Open Source Bioinformatics Projects - The Genome Informatics group is organizing the joint efforts of WormBase, Reactome, and GMOD.

Wormbase is 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.

Reactome is 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.

Generic Model Organism Database (GMOD) is 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 is a great opportunity for undergraduate students to contribute to the work of these bioinformatics projects, to participate in open source development and to do work related to their academic pursuits during the summer. If you have any questions or queries, please feel free to send a post to the Genome Informatics Google Groups.

To access our GSoC Code Repository, please follow this link: http://code.google.com/p/google-summer-of-code-2011-genomeinformatics/

Projects

• HTML 5 Canvas based Pathway Visualization Tool The project involves the development of a canvas-based network interaction visualization prototype for biological interaction networks and pathways having various common nodes of metabolism. Majority of the pathway visualization tools involve Flash. The project developed would have more features like real-time collaboration etc., as well as utilize HTML 5 features allowing it to be light-weight and that can run in both modern browsers in a full-fledged computer, or in a tablet (e.g. ipad).
• IDEA 6: Reactome RESTful API My idea is to implement a lightweight, easy to use, and well-documented RESTful API for Reactome. It will allow Reactome annotated data to be used programmatically and integrated in other web applications.
• Reactome and Bioconductor Integration Proposal Here I propose to create a Reactome R package for the purposes of pathway enrichment analysis. The process of pathway analysis can be greatly enhanced with the integration of existing Bioconductor packages and the implementation of the R statistical programming language. The deliverables expected by this project would include a Reactome R library with a pathway enrichment analysis package, R-based pathway diagrams visualization function, Vignettes, and User guide documents.