WebDev 2009.07.22-Agenda and Minutes

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1. Administration Update (Todd; 5 minutes)

  • Mercurial / DVCS overview

From last week's call, here is how to run a series of commands on a firewalled machine:

ssh gatewayhost.com "ssh firewalled_node.com 'cd /into/some/path; chown -R todd:todd *'"

2. Development update (Norie; 10 minutes)

  • GBrowse2
  • GFF2 to GFF3 converter
  • Working on modularization, which features to export
  • nBrowse2 update
  • Bug and feature enhancements

3. GFF3 Validator (Todd, Zheng; 10 minutes)

4. modENCODE update (Marc, Peter, Zheng; 10 minutes)


  • New data from Waterston group
  • Developmental series and organ
  • Formats: Wiggle and GFF3
  • TH : what groups are provided SAM format?
  • PR: So far only Waterston (and Celniker, but in fly)


  • Submitted MacAlpine data to geo


  • Away for the next two weeks

5. BioMart (Zheng)

  • Talking with BioMart people (on vacations, at meetings)
  • Assign a person for code development; automatic chado2schema mapping

6. Open Table