Proteomics:Gaining Momentum Meeting on 2010-03-05

Location

Biomolecular Mass Spectrometry and Proteomics Group, Hugo R. Kruyt Building, Padualaan 8, 3584CA Utrecht, NL, room Z612

Time

10:00 – 15:00, lunch included

Attendees

• Bas van Breukelen (UU)
• Pieter Neerincx (UU)
• Henk van den Toorn (UU)
• Perry Moerland (AMC)
• Péter Horvatovich (RUG)
• Morris Swertz (RUG)
• User:Huub Hoefsloot (UvA)
• Carsten Byrman (UvA)
• Twan America (WUR)
• Dmitry Katsubo (NBIC)
• Thang V. Pham (VU)

Agenda

1. What did or did we not do form the action points made in the previous meeting
   • Not so may tools have been submitted so far
2. Discussion on the proposed data standards by Twan America
3. DAF, does it work, how to use it..
4. Programmers need to meet regularly, how to set this up.
5. new action points

Minutes notes

• Introduction
• Thang: Cancer centre Amsterdam, using LS-MS platform for research
• Bas: Review of previous action points
• Twan: Presenting the information that we need to add to the format
  • Corra is functional framework with working workflow. Should be taken into consideration
  • Corra workflow is something representing a flow based in information from a publication
  • On NBIC flow yellow = RUG, red = UvA, green = WUR, purple = EMC, light purple = UU tools
  • For creatly we share the login that can modify flows
  • Morris: PeakML originally developed for metabolomics, and it misses certain information
  • Twan: Needs XSD from Richard
  • Twan: Is not efficient, misses some things, but that can be added
  • Twan: Are we going to implement Corra?
  • Pieter: need to play with Corra
  • Wiki page to discuss APML
  • We need better examples, including statistics data
• Morris: we need to organize parallel sessions on NBIC bioassist meeting.
• Péter: reports the status on DAF and lightpath, team is implementing converters
• Morris: update on DAF-related developments (job execution on cloud/cluster)
• Bas: If APML can handle big amount of data, is it scalable?
• Pieter: The first test should show, if there are scalability problems with it. If we fit a memory limit, that means either the format is not efficient or parsers are not efficient.
• Twan: Mentioned TIQAM
• Next meeting: 14th of May
• Henk: presented CAStor. CAStor is a cloud-based store.

Action points

Twan:

• Provide raw data for Pieter/Morris to test Corra
• Communicate to Corra community (ask questions on APML, make proposals for improvement)
• Check/analyse the results from Corra (are they complete? is all necessary information present?)

Morris:

• Setup Corra and provide access for Twan / Pieter. Give a feedback on how easy is to setup it and run a workflow.

Pieter:

• Try to implement workspace with OMSSA
• Test machine for Galaxy

Dmitry:

• Parallel session for programmers meeting in Utrecht

Bas:

• Draw a workflow for UU.