GSoC/GCI Archive
GSoC/GCI Archive
Google Summer of Code 2014

BioJavaScript

License: Apache License, 2.0

Web Page: https://rostlab.org/services/biojs/gsoc.html

Mailing List: https://groups.google.com/forum/#!forum/biojs

BioJS is a community-based standard and repository of functional components to represent biological information on the web. Its modular architecture makes it easy for users to find a specific functionality without needing to know how it has been built. The BioJS community of developers currently provides a range of functionality that is open access and freely available. A registry has been set up that categorises and provides installation instructions and testing facilities at http://www.ebi.ac.uk/tools/biojs/.

Projects

  • A JavaScript library for an interactive visualization of sequence logos Sequence logos are very popular in life sciences. They reveal the evolutionary relationship of aligned sequences and are used to depict sequence patterns. Moreover they provide an illustration of the consensus sequence. The aim of this project is to create an extendable BioJS library for an interactive visualization of protein or DNA sequence logos.
  • BAM File Viewer BioJS currently has support for Feature Tracks and BigWIG files. Those are enough to provide a minimum genome browser that includes coverage from alignments. However, detailed information about the alignments from NGS is not supported yet. Most of the modern sequence aligners support BAM as the format output. The BAM format enables random queries, avoiding the necessity to load the whole alignment in memory. BAM File Viewer for BioJS will complement wigExplorer.
  • Human Genetic Variation Viewer With the advent of NGS techniques, though we have been able to generated tonnes of data, little has been done to make sense out of the available data by integrating data across different levels in an integrative manner or even otherwise. Inspite of being made available as open and available from different sources, however there is none a tool that acts as an integrated visualiser.
  • Phylogenetic Tree Viewer Phylogenetic Tree Viewer as described on the project idea page and why you should choose me to work on it!
  • Taxonomy Viewer A BioJS component to visualize Uniprot proteomes. The tool uses the NCBI taxonomy to explore Uniprot proteomes from different zoom levels.