Proteomics:Programmers Meeting on 2013-01-11

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Location and time

  • Location: Hojel City Center, building D (5th floor), Graadt van Roggenweg 340, 3531 AH Utrecht
  • Date: Friday January 11th
  • Time: 9:00-10:30



  1. Action points and status updates
  2. Proteomics bioinformatics meeting on Thursday January 31st
  3. NPC progress meeting on Monday and Tuesday February 11th and 12th
  4. Year report 2012
  5. Next meeting

Action points and status updates


  • Pravin is working on installing and testing the NIST proteomics QC tool - with modifications made by Marcel Kempenaar (NBIC BRS). As part of the CTMM TraIT project, this QC tool will be used by VUmc.
  • At the moment he is testing with 200+ raw files.
  • Currently the pipeline supports 5 metrics, but we want to add more in the future.
  • The European PRIME-XS consortium has also developed a new proteomics QC tool as part of OpenMS. Pravin will compare the NIST/NBIC tool to the OpenMS one in the future.
  • Pravin is also working on a viewer for the QC reports.


  • Bas reviewed the documentation of our pipeline and tools in Galaxy and made a list of recommendations.
  • He and Pieter have already modified the documentation for some tools.
  • Bas has also created some guidelines that could be useful for other task forces. He will send it to the mailing list.
  • Freek remarks that it is a bit silly (but still very common) how we put a lot of effort into creating and/or integrating a tool in Galaxy, but we create only minimalistic documentation (if at all). While on the other hand everyone has experienced difficulties getting 3rd party tools to work without proper documentation...
  • Peter is looking at reorganizing the Galaxy menu for the proteomics tools.


  • Pieter is working on a new protein inference algorythm.
  • He also started writing an article on this topic.
  • Finally, Pieter is checking some strange results he got from ProteinLynx.


  • Work is focussing on adding 2D extension to msCompare.
  • Ishtiaq Ahmad is working on the article comparing several proteomics pipelines.
  • For the article, Ishtiaq needs to have all proteomics tools working again on the NBIC Galaxy server in the cloud.

Proteomics bioinformatics meeting on Thursday January 31st

Name: Proteomics bioinformatics meeting Date: Thursday January 31st Time: 12:00-15:30 Location: Kruytbuilding, Zuid room 613 (South wing), Padualaan 8, Utrecht Contact: Freek

The focus of the meeting will be on existing and new collaborations on proteomics bioinformatics.

On the agenda are the following topics:

  • 12:00-12:30 lunch
  • 12:30-13:30 short introductions (5-10 minutes for each group), for example: what do you do with proteomics, which bioinformatics tools do you use, what do you expect from collaborations
  • 13:30-15:10 discussion: who is already working together with whom, what is useful to collaborate on, what can be shared and what not
  • 15:10-15:30 conclusion: plans for the future, action points and schedule followup

NPC progress meeting on Monday and Tuesday February 11th and 12th

Name: NPC progress meeting 2013 Date: Monday and Tuesday February 11th and 12th Time: 9:00-22:00 and 9:00-17:00 Location: Media Plaza (Jaarbeurs Utrecht), Croeselaan 6, 3521 CA, Utrecht Web site: NPC progress meeting 2013

The meeting will be particular special, because it is dedicated to the 10th anniversary of the Netherlands Proteomics Centre. International and national scientists will present their views on the latest developments in proteomics with lectures, NPC project posters and an exhibition. The celebration will be completed with the NPC Anniversary Dinner on February 11th.

Official registration deadline is January 25th, but maybe you can still register if you ask very nicely... ;-)

Year report 2012

Freek is asking everyone's input to write the year report for 2012. The early part of the year is already filled in, so we only need to add the missing bits until December 31st. We can report on the following subjects:

  1. General issues (for example: contract renewals or major task force modifications)
  2. Recent progress/highlights (for example: integration of tools, large contributions to tools, important decisions, changes to short term plans, presentations, workshops or publications)
  3. Staff, collaborators, and students (any changes in the team members)
  4. Task force tools (updates or additions to our list of 3rd party/own developed tools)
  5. Valorization (opportunities we see or already seized)

Next meeting

Friday February 8th 9:00-10:30 will be our next programmer's meeting.