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!

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

• Systems Bioinformatics Workshop 2011
• Gaggle Workshop 2009, Presentations
• Gaggle Workshop 2008 wiki; workshop web pages
• 2007 Workshop agenda; Gaggle Workshop 2007.

See also:2011 Gaggle workshop planning