Systems Bioinformatics Workshop 2012

The Institute for Systems Biology
401 Terry Ave North - South Lake Union
Seattle, WA 98109

September 10 & 11, 2012

The Systems Bioinformatics Workshop 2012 will be held at the Institute for Systems Biology in Seattle, WA on September 11 & 12, 2012.

Sessions and discussions will cover:

  • analysis of biological networks
  • software engineering for biological data analysis
  • visualization

Note: Please feel free to add notes, agenda items or further discussion topics.


Potential topics

  • network analysis using Python and networkX or R and igraph
  • graph databases with neo4j
  • Want to lead a tutorial? Let us know!


  • Be ready to code!

Connecting Network Portal, Python cMonkey and KBase

We’d like to focus some time at the workshop on connecting our network inference algorithms and the Network Portal to KBase. We’re hoping to get a few KBase developers together in a room and spec out some APIs, and possibly hack up some quick prototypes. Some data types and queries we might want to support are listed here:

  • inferred regulons (lists of co-regulated genes)
  • whole or partial regulatory networks
  • KBase as a data source for cMonkey/Inferelator
  • export of cMonkey/Inferelator results to KBase?
  • linking regulatory networks with fitness data?
  • queries:
    • What regulates these genes?
    • What genes does this TF regulate?
    • Find co-regulated genes by promoter motif
    • Find co-regulated genes enriched for a particular function
    • Find genes with a ‘hit’ for a given promoter motif

Previous Systems Bioinformatics and Gaggle Workshops

workshop.txt · Last modified: 2012/06/15 11:53 by
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