Proteomics:Programmers Meeting on 2010-12-17

From BioAssist
Jump to: navigation, search

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 updates
  2. Next meetings

Action points and status updates

The snow caused lots of problems to get to Utrecht this time, so we only had four attendees and started the meeting late. Ishtiaq Ahmad (RUG) and Wim Spee (UU) were able to reach the Hojel City Center later in the morning.


  • Henk has finished the article on his RockerBox tool for the Journal of Proteome Research and it should be published soon. RockerBox (see Trac) can filter the search results obtained from the Mascot search engine using statistics and machine learning. This way, large files (around 4 GB is possible) can be reduced to a size that can be processed by other tools again.
  • Action point: Henk is now working on proteogenomics for a new organism. Pieter has already been working on this and he is now joined by Henk. Henk is for example comparing peptide spectra to genome reads in order to complement (and maybe challenge) the genomics data found so far.

Henk reporting for Pieter:

  • Jack Leunissen (WUR) is interested in adding a talk/demo/poster on Galaxy to the IB2011 symposium.
  • Bas van Breukelen (UU) has found a very interesting option for quantitation: the Princeton LC-MS viewer developed by Zia Khan contains good quantification functionality. Bas has contacted the maker of the software and cooperation and modification seems to be possible.
  • Mao Peng (UU) is a new PhD student in the UU research group working on spectral counting/quantification.


  • Carsten has found out more about Galaxy and how to integrate his tools: increase usability, add more input validation and add example input files. The goal is to expand the group of potential users beyond Berend and Carsten.
  • Carsten has some additional questions for Pieter and will contact him (using Skype).
  • Action point: Carsten is working with Berend on a poster for the NPC Progress Meeting (Thursday January 13th).
  • Action point: Carsten is working on connecting to the grid. An extra API for MOTEUR may be needed.


  • Rob and Freek have visited UU, WUR and UMCG/RUG. The meetings were very valuable and brought a much better understanding of the needs of the different research groups.
  • One of the subjects that was discussed with Peter Horvatovich (RUG) is the infrastructure proposal that he and Perry Moerland (AMC) have sent to TI-COAST (Top Institute Comprehensive Analytical Science and Technology). The required infrastructure for TI-COAST is very similar to work the groups in RUG and AMC have already done, so cooperation would be interesting and benificial for both parties.
  • Rob has informed Ruben Kok (NBIC) and Barend Mons (NBIC) about the proposal that Peter and Perry have sent to TI-COAST. Ruben will contact Oscar van den Brink (TI-COAST and AkzoNobel) in January.
  • A gaining momentum meeting was held on Friday November 26th.
  • Action point: Freek will write the annual report for the proteomics task force this year.
  • Action point: Freek will ask Bas whether everything goes according to plan for the NPC Progress Meeting (Thursday January 13th).

Next meetings

Thursday January 13th 9:00-18:00 will be the NPC Progress Meeting (venue: Media Plaza (Jaarbeurs), Croeselaan 6, Utrecht). See NPC Progress Meeting for more information.

Friday January 21th 9:00-10:30 will be our next programmer's meeting.