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Research Software

Software for Research

Software in this section is focused on a specific research goal. Most have been described in greater detail in one of our publications.
  • ChromoZoom is a web-based genome browser currently hosting tracks for the yeast and human genomes.
  • FuncBase is web-based software for browsing quantitative gene function assignments for yeast, mouse and human genes.
  • FuncAssociate 2.0 takes a list of genes as input and produces a ranked list of the Gene Ontology terms enriched in an input list.
    • Python and Perl clients for the FuncAssociate 2.0 web service are available here
    • An older beta version, FuncAssociate 1.5 is also available, but is now deprecated.
    • The original FuncAssociate 1.0 is still available, but GO annotations are out of date. (Download Source Code: here.)
  • SILVER assists the analysis of tandem mass spectra by displaying the predicted mass spectrum of a given peptide, and scoring consistency between predicted and observed spectra. You can access SILVER through a web interface.
    • Download Source Code: here.
  • ChIPper: a tool for analysis of ChIP-chip data.
    • Download Source Code: here.
  • ClusterJudge. Not sure which clustering algorithm to use with your gene expression data? ClusterJudge scores the results from any clustering algorithm, using existing annotation, so you can see which one best groups genes by function.
    • Download Source Code: here.
  • The Synergizer is a database of gene, protein, and other biological identifiers. The Synergizer web interface allows users to translate gene names from one naming scheme ("namespace") to another. For more information about the Synergizer and to download applications allowing programmatic access, please visit the Synergizer help page.
    • Download our Synergizer Perl Client: here.
    • Download our Synergizer Java Client: here.
  • Query Chem is a Web program that integrates chemical structure and text-based searching using publicly available chemical databases and Google's Web Application Program Interface (API). Query Chem makes it possible to search the Web for information about chemical structures without knowing their common names or identifiers. Query Chem's search results can retrieve many interesting structure-property relationships of biomolecules on the Web.
  • GoFish!. This program (available as a Java applet) allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes.
    • Download Binaries with Source Code: here.
  • Complexpander used a confidence-weighted graph of protein interactions to predict new members of protein complexes.
    • NOTE: This implemented our first attempt at this problem. Improved methodology has since been described in (H Huang, LV Zhang, FP Roth & JS Bader. Probabilistic paths in protein interaction networks. Proceedings of the RECOMB Conferences on Systems Biology and Computational Proteomics (2007) [PDF])

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Donnelly Centre for Cellular & Biomolecular Research, University of Toronto Samuel Lunenfeld Research Institute, Mt. Sinai Hospital