Proteomics:Programmers Meeting on 2011-09-16

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Location and time

  • Location: Hojel City Center, building D (5th floor), Graadt van Roggenweg 340, 3531 AH Utrecht
  • Date: Friday September 16th, 2011
  • Time: 9:00-10:30



  1. Action points and status updates
  2. Next meeting

Action points and status updates


  • Ishtiaq is working on putting the R scripts in Galaxy. Currently trying to ignore errors when the script writes to the standard error stream.
  • When this issue is fixed, he will put the scripts in the NBIC Galaxy.


  • Pieter Lukasse will start on October 1st. He studied computer science and was working as a general programmer. After a few years he started studying bioinformatics (VU) in his spare time and now has almost finished that.
  • Twan has found an interesting alternative for OMSSA, which he will evaluate for his lab.


  • Berend is sick and it is unclear when he will be back.
  • The work on msCompare is finished. Péter is working on publication.
  • At HUPO a poster on msCompare was presented. There was a lot of interest in comparing pipelines.
  • Péter will test the installation of msCompare and describe test cases. These test cases will be used by George to include msCompare as a pipeline in Molgenis.


  • Two NGS pipelines have been added to Molgenis.
  • George is experimenting with using GPUs fro some tasks. It can be very much faster.
  • He agreed on a format for running tasks on a grid with Jan Bot (TU Delft) and Barbera van Schaik (AMC).


  • Wim is working on the storage tools (one tool to enter all metadata and one tool to run queries). He is doing a final iteration before going to production.
  • The tools are intended as a small, lightweight solution for some practical problems.
  • George suggests to take a look at the Molgenis data model and he will send the link to Wim. It would be interesting to compare the different approaches to metadata storage:
    • Develop some small tools like in Utrecht.
    • Use one of the existing systems like Molgenis, GSCF, ms-lims or openBIS for Proteomics (ETH Zurich). (The group of Matthias Mann has also developed a custom lims, which might be available for others.)
  • Wim reports that pview is being compared to MSQuant and Progenesis LC-MS in Utrecht.


  • CTMM TraIT will start in October. The proteomics team in VUmc is looking for a postdoc/programmer to help.
  • During the first six months different tools will be evaluated. After this initial phase, the best tools will be consolidated into an integrated system.
  • Depending on the part of the system, a tool should be in the range from good enough to very good. The tools can be open source and should be practical for a running lab.


  • The NBIC Galaxy system was moved to a different server. Thanks to Ishtiaq and Pieter Neerincx for migrating tools!
  • We had a meeting with people from NPC, NBIC and Erasmus MC regarding collaboration in the task force and for CTMM TraIT.
  • There will be a HPC for Life Sciences / e-BioGrid workshop on November 10th in Amsterdam.

Next meeting

Friday October 14th 9:00-10:30 will be our next programmer's meeting.