Proteomics:Programmers Meeting on 2011-02-18

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Location and time

  • Location: Hojel City Center, building D (5th floor), Graadt van Roggenweg 340, 3531 AH Utrecht
  • Date: Friday February 18th, 2011
  • Time: 9:00-10:30



  1. Presentation from George on MOLGENIS
  2. Action points and status updates
  3. Next meeting

Presentation from George on MOLGENIS

George held a presentation on MOLGENIS (see File:Programmers-Meeting-on-2011-02-18-George-Byelas-MOLGENIS.pdf for the slides). There were discussions of interesting topics, like how to handle a variable number of output files and how to give external tools access to data on a cluster.

Action points and status updates


  • Carsten came to say goodbye. He had a temporary contract with AMC and although there was still one year left, he decided to accept a new challenge with a technical consulting company. Keywords: water management, open source software and located in Utrecht (biking distance). AMC is making plans for continuing the work with the remaining funding.
  • He has transferred knowledge to collegues, wiki, etc.
  • He has also sent some example code on how to call the AMC tools in Galaxy to Elizabeth (EMC).
  • Thanks for the great collaboration, Carsten!

General update:

  • Elizabeth received data from Javier Munoz (UU) to test MS PRUNA.
  • Peter suggests to combine msCompare and OMSSA in Galaxy. Pieter (UU) is planning to look at this later.

Wim (update by Henk):

  • Wim is working on software for quantative analysis of overlapping isotopes. The aim is being able to predict overlaps and do a correction for this.

Pieter (update by Henk):

  • Pieter is mainly busy with phosphorylation site motifs. He is using the MEME suite and TOMTOM tool to search for motifs. Pieter plans to add support for proteins.


  • He is analyzing Trichoplax with proteogenomics tools.


  • Ishtiaq is integrating msCompare in DAF, which requires OpenMS. It is a lot of hassle to recompile it for a different Linux distribution.
  • He is also planning to work on adding more checks for input files for the DAF web service.

Berend (update by Peter):

  • 2D LCMS is almost added to msCompare.
  • Light paths will be installed in AMC (it turned out to be impossible in Wageningen).

Next meeting

Friday March 18th 9:00-10:30 will be our next programmer's meeting.