Proteomics:Programmers Meeting on 2011-10-14

From BioAssist
Jump to: navigation, search

Location and time

  • Location: Hojel City Center, building D (5th floor), Graadt van Roggenweg 340, 3531 AH Utrecht
  • Date: Friday October 14th, 2011
  • Time: 9:00-10:30



  1. Action points and status updates
  2. Next meeting

Action points and status updates


  • Wim is finishing his work on the storage tools (refactoring, automatic integration testing and code cleanup).
  • He is aiming to create the production version by the end of November.
  • The source code can be made available via our Trac system.
  • The ms_lims system will be installed in Utrecht. This system should provide a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data. It is developed by Ghent University and VIB (The ms_lims website).


  • Tim has just started working on a BRS (Bioinformatics Research Support) project for Twan America (WUR) using Cytoscape. He has worked on it for half a week and is interested to see what the proteomics task force is working on.


  • Ishtiaq added the classification tool to Galaxy. It is a challenge to set the number of datasets to be used for training the system using the Galaxy UI.
  • The next step will be the report generator.
  • He also worked on getting msCompare running on the new NBIC Galaxy server. Berend Hoekman (RUG) will take a look at it.


  • Henk visited the PRIME-XS group in Belgium together with Bas van Breukelen (UU). The meeting was focused on quality control, the OpenMS team offered some suggestions. They plan to integrate with NIST guidelines.
  • Henk is participating in the group that works on the file format for quality control. The format might be xml based, but they could also decide to use SQLite.
  • He is also working with a vender on port processing of quantitation data (statistical analysis).
  • Salvatore Cappadona (UU) found some problems with pview and is discussing those with Zia Khan (the author of pview).
  • Salvatore is comparing pview to Progenisis LC-MS. The first results indicate that pview is a lot faster and these results appear to be better as well.


  • George established several pipelines and is now focussing on testing and improving scalability.
  • He is also working on running R scripts from Molgenis.
  • Finally, George is using Jan Bot's system or SSH-2 to work with the grid (DAF is not used).


  • Péter worked on msCompare in Galaxy with Ishtiaq.


  • Pieter Lukasse (WUR) has started in Wageningen.
  • Bas and Freek are organising a new PI/programmers meeting.
  • Elizabeth McClellan (EMC) sent a partial draft of her MS PRUNA publication to Bas for feedback.

Next meeting

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