Proteomics:Programmers Meeting on 2011-07-15

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Location and time

  • Location: Hojel City Center, building D (5th floor), Graadt van Roggenweg 340, 3531 AH Utrecht
  • Date: Friday July 15th, 2011
  • Time: 9:00-10:30



  1. Action points and status updates
  2. Next meeting

Action points and status updates


  • Statistical classification model - carsten, learned R; model fitting, different parameters per optimization done, running on the grid, combine results files into one.
  • Clustering by splitting into eg. 100 parameter, cluster desktop boonex grid, but also on a normal grid ls-grid (Angela), .Rdata results files.
  • This will be run in Galaxy, now the cluster is called by a shell script.
  • APML to expressionset -> classification model -> QC report (todo).
  • Looking for reporting tool for HTML and how to display in Galaxy.
  • Searching is done in external search engines, mzIdentML is imported.
  • OMSSA? some instrument settings are missing, couldn't make it run.


  • Comparative genomics course, nice presentations about distant homology and tricks.
    • Creating trees is easy, consequently, creating bad trees is very easy!
    • Network mapping: how to map networks between species.
    • Genome duplication.
    • Endosymbiosis.
    • Tree of life actually is only valid for eukaryots, prokariots.
  • Storage client, cloud storage 'gateway', merged the two clients into one with different views.


  • We bought progenesis from Nonlinear dynamics, we think we need to continue working on pview.
  • Who's going to do what? Write XML? Henk asks Salvatore which parameters should be set by command line.
  • I uploaded the code to TRAC.
  • RockerBox -> ASMS, response; Who will continue the project, SARA?? Probably not.

Next meeting

Friday August 12th 9:00-10:30 will be our next programmer's meeting.