Proteomics:Programmers Meeting on 2011-03-18

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Location and time

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



  1. Presentation from Ishtiaq on DAF
  2. Action points and status updates
  3. Next meeting

Presentation from Ishtiaq on DAF

Ishtiaq held a presentation on DAF (Data Analysis Framework). This lead to an important discussion on whether it is better to add more functionality to your own system or to try to combine your software with existing, successful systems with (large) user communities.

Rob said that we have to keep working on adding more of our tools to Galaxy and connecting them. This way, we will have something to show.

Action points and status updates


  • Don is assisting Elizabeth with MS PRUNA. The script is finished now and it is running on the test server.
  • He is putting MS PRUNA on the production server. Later he will put it on the NBIC Galaxy server.


  • George is evaluating options to combine Molgenis with Galaxy or Taverna.
  • He will participate in a InforSense workshop organized at UMCG. InforSense is a competitor for Galaxy and Taverna. He expects the workshop will give good feedback for Molgenis.
  • Currently there are 15 developers working on Molgenis.


  • Henk is mapping peptides from proteomics experiments to genomes.


  • Pieter is combining PTMs from experiments & online databases and making motifs from that.


  • Wim is developing the storage and retrieval system for raw files.
  • A demo of the second version has been presented and discussed.
  • He is starting the third iteration during which he will overhaul the technical design and implement the remaining features.


  • Ishtiaq will finish the IBM pipeline.
  • After that, he will develop the light paths application. This will take about one month.
  • Finally, he will work on parameter optimization for msCompare.


  • Freek will plan the next gaining momentum meeting.
  • The NBIC hackathon will have a project on Galaxy. We expect two developers from the Galaxy team in the US to participate.

Next meeting

Friday April 15th 9:00-10:30 will be our next programmer's meeting.