GSoC/GCI Archive
Google Summer of Code 2012

Genome Informatics

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The Genome Informatics group is organizing the joint efforts of Galaxy, GBrowse, GMOD, JBrowse, Reactome, Wormbase, and ProtEco. This is a great opportunity for students to contribute to the work of any of seven 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.


  • Phyloviz: Interactive Phylogenetic Tree Visualizer for Galaxy PhyloViz is an interactive phylogenetic tree visualizer built for Galaxy to give its users a more effective way to access, manipulate, analyze and present data of phylogenetic tree data on galaxy.
  • Reactome Pathway Summary Visualization This project would produce a replacement for the old "Sky" View of the Reactome Project. Pathways would be represented as Nodes and their relationships (common entities and reactions etc.) would be represented as arcs which would be visualized on a Canvas Interface. It would also show expression and species comparison information in a multi-pathway context, by plotting the output of common proteins on this interface.