Proteomics:Programmers Meeting on 2011-06-17

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Location and time

  • Location: Hojel City Center, building D (5th floor), Graadt van Roggenweg 340, 3531 AH Utrecht
  • Date: Friday June 17th, 2011
  • Time: 9:00-10:30



  1. Action points and status updates
  2. Hands on collaboration: pview
  3. Next meeting

Action points and status updates


  • Wim is working on the client applications for the storage system.

Pieter (update by Wim):

  • Pieter will join the Molgenis team in Groningen!


  • Ishtiaq is getting started in the AMC.
  • His first task is to improve the APML to R ExpressionSet conversion tool.
  • After that, he will be working on the Quality Control tool.


  • George is writing articles in the coming weeks.
  • He is also writing code & tutorials and creating videos for the BOSC (Bioinformatics Open Source Conference).
  • He has finished the imputation and NGS pipelines in Molgenis.
  • An extra cluster will be installed for the Molgenis team in Groningen.
  • In the future, George plans to work on making it easier to install Molgenis, together with MySQL and Tomcat.
  • Book tip: George is reading "Genome: The Autobiography of a Species in 23 Chapters" written by Matt Ridley and is recommending it to everyone interested in learning more about Biology in an entertaining way. See for example the book on Amazon for more information (ISBN: 9780007635733).


  • Freek had a meeting with Bas van Breukelen (UU), Barend Mons (NBIC) and Rob Hooft (NBIC) to discuss our future plans for the proteomics task force.
  • Bas van Breukelen (UU) and Freek will visit Connie Jimenez and Thang Pham from the VUmc OncoProteomics Laboratory (Connie and Thang) to talk about possible collaboration for CTMM TraIT.
  • Machiel Jansen (SARA) has proposed putting DAF on e-BioGrid. Ishtiaq and Freek will visit Machiel and Irene Nooren (e-BioGrid) to talk about the possibilities.

Hands on collaboration: pview

  • We worked on getting pview to compile with NetBeans.
  • After the project was set up and compilation was possible, we started analyzing the structure of the code.

Next meeting

Friday July 15th 20th 9:00-10:30 will be our next programmer's meeting.