Proteomics:Gaining Momentum Meeting on 2010-03-05
Revision as of 22:48, 8 March 2010 by Dmitry Katsubo
Biomolecular Mass Spectrometry and Proteomics Group, Hugo R. Kruyt Building, Padualaan 8, 3584CA Utrecht, NL, room Z612
10:00 – 15:00, lunch included
- 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)
- 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
- Discussion on the proposed data standards by Twan America
- DAF, does it work, how to use it..
- Programmers need to meet regularly, how to set this up.
- new action points
- 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.
- Peter: 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.
- 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?)
- Setup Corra and provide access for Twan / Pieter. Give a feedback on how easy is to setup it and run a workflow.
- Try to implement workspace with OMSSA
- Test machine for Galaxy
- Parallel session for programmers meeting in Utrecht
- Draw a workflow for UU.