Proteomics:Programmers Meeting on 2010-11-19

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Location and time

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



  1. Action points and status update
  2. Hands on collaboration
  3. Next meeting

Action points and status update


  • Have been working on restoring hardware failures, supporting Urology, etc.
  • Action point: planning to work and collaborate in UU for one day every week/two weeks. Expect this to be valuable, UU is interesting for EMC.


  • Silvia had an accident and is in hospital (AMC). She will have an operation.
  • Visit from RUG has been successful, focused on grids and work flows.
  • Visit to UU with Joost was successful too, Pieter explained a lot about adding tools to Galaxy (fixed issues like problems with output from R to error and standard output, using capital letters in file extensions, etc.).
  • Action point: next step will be differential analysis.
  • Action point: web service for quality control.


  • Time alignment service is finished.
  • Conversion from and to APML format is working.
  • Action point: split up conversion from and to APML format in separate parts.
  • Action point: add proper error handling to pipeline, hopefully before demo next Friday.
  • Action point: protein identification engine.
  • Action point: light paths in DAF for fast transport of large amounts of data.


  • Paper "Towards a MOLGENIS based computational framework" is accepted and will be presented at the 19th Euromicro International Conference on Parallel, Distributed and Network-Based Computing, PDP 2011.
  • MCF (Molgenis Computation Framework) site is ready (MCF). It contains architecture, design, data model, code examples.
  • Warp2D pipeline (3 first steps) is implemented in MCF. Pipeline is started from MOLGENIS-generated interface (MolgenisServlet running on Tomcat locally): jobs are sent to the Millipede (Gr.) Cluster and monitored using MCF.
  • Action point: develop a data structure for Warp2D to store/retrieve it from Molgenis DBMS (collaboration with P. Horvatovich), it will be used in DAF as well.
  • Action point: advanced graphical web-interface to show jobs progress.


  • Joost de Groot was our proteomics programmer in Wageningen. Last Monday, his funeral was attended by a lot of family members, friends and colleagues. There was much music and speeches from numerous people. Roeland van Ham - who was Joost's boss - told stories from colleagues about working with him.
  • Last week, Rob and I met with Carsten, Perry and Silvia in AMC.
  • Meetings are planned for UU (November 26th) and WUR (December 7th).
  • Action point: plan meetings with RUG and EMC.


  • Migrated from old Mascot server to new version. This version has a better UI for users (no changes for pipeline/automation).
  • Worked on the storage tool to put raw files on storage cluster.
  • Various scripting work.
  • Action point: work on a new version of the storage upload tool.


  • Most of the msCompare tools are now in Galaxy (NBIC Galaxy).
  • Action point: work on 2D-LC-MS (liquid chromatography mass spectrometry).


  • Helping out Carsten and Joost with Galaxy.
  • Planning collaboration with Don and Elizabeth.
  • Action point: on a quest to find the perfect quantitation tool that is pipelinable/can be in a work flow and is open source. Currently users in UU work with GUI based tool and replacing it has a fluctuating priority (from very low to extremely high). Looking at three candidates: 2 closed source, 1 open source but in bad shape. OpenMS is open source and can be used in a pipeline, currently the algorithms are not good enough.
  • Action point: Pieter and Henk will take turns attending our meetings in the future.

Hands on collaboration

Both Carsten and Ishtiaq and also Berend and Pieter used the opportunity for some hands on collaboration.

Next meeting

Friday December 17th 9:00-10:30 will be our next programmer's meeting.