Difference between revisions of "Proteomics:Gaining Momentum Meeting on 2010-03-05"
From BioAssist
m |
m |
||
| Line 13: | Line 13: | ||
* [[User:Henkvandentoorn|Henk van den Toorn]] ([[UU]]) | * [[User:Henkvandentoorn|Henk van den Toorn]] ([[UU]]) | ||
* [[User:Perry|Perry Moerland]] ([[AMC]]) | * [[User:Perry|Perry Moerland]] ([[AMC]]) | ||
| − | * [[User:Horvatovich| | + | * [[User:Horvatovich|Péter Horvatovich]] ([[RUG]]) |
* [[User:Mswertz|Morris Swertz]] ([[RUG]]) | * [[User:Mswertz|Morris Swertz]] ([[RUG]]) | ||
* [[User:Huub Hoefsloot]] ([[UvA]]) | * [[User:Huub Hoefsloot]] ([[UvA]]) | ||
| Line 37: | Line 37: | ||
* Bas: Review of previous action points | * Bas: Review of previous action points | ||
* Twan: Presenting the information that we need to add to the format | * 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]] is functional framework with working workflow. Should be taken into consideration |
| − | ** Corra workflow is something representing a flow based in information from a publication | + | ** [[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 | ** 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 | ** For creatly we share the login that can modify flows | ||
| Line 44: | Line 44: | ||
** Twan: Needs XSD from Richard | ** Twan: Needs XSD from Richard | ||
** Twan: Is not efficient, misses some things, but that can be added | ** Twan: Is not efficient, misses some things, but that can be added | ||
| − | ** Twan: Are we going to implement Corra? | + | ** Twan: Are we going to implement [[Corra]]? |
| − | ** Pieter: need to play with Corra | + | ** Pieter: need to play with [[Corra]] |
| − | ** Wiki page to discuss APML | + | ** Wiki page to discuss [[APML]] |
** We need better examples, including statistics data | ** We need better examples, including statistics data | ||
* Morris: we need to organize parallel sessions on NBIC bioassist meeting. | * Morris: we need to organize parallel sessions on NBIC bioassist meeting. | ||
* Peter: reports the status on [[DAF]] and lightpath, team is implementing converters | * Peter: reports the status on [[DAF]] and lightpath, team is implementing converters | ||
* Morris: update on [[DAF]]-related developments (job execution on cloud/cluster) | * Morris: update on [[DAF]]-related developments (job execution on cloud/cluster) | ||
| − | * Bas: If APML can handle big amount of data, is it scalable? | + | * 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. | * 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 | * Next meeting: 14th of May | ||
* Henk: presented CAStor. CAStor is a cloud-based store. | * Henk: presented CAStor. CAStor is a cloud-based store. | ||
| Line 58: | Line 59: | ||
=== Action points === | === Action points === | ||
| − | Twan: | + | [[User:TwanAmerica|Twan]]: |
| − | * Provide raw data for Pieter/Morris to test Corra | + | * Provide raw data for Pieter/Morris to test [[Corra]] |
| − | * Communicate to Corra community (ask questions on APML, make proposals for improvement) | + | * 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?) | + | * Check/analyse the results from [[Corra]] (are they complete? is all necessary information present?) |
| − | Morris: | + | [[User:Mswertz|Morris]]: |
| − | * Setup Corra and provide access for Twan / Pieter. Give a feedback on how easy is to setup it and run a workflow. | + | * Setup [[Corra]] and provide access for Twan / Pieter. Give a feedback on how easy is to setup it and run a workflow. |
| − | Pieter: | + | [[User:Pneerincx|Pieter]]: |
* Try to implement workspace with OMSSA | * Try to implement workspace with OMSSA | ||
* Test machine for Galaxy | * Test machine for Galaxy | ||
| − | Dmitry: | + | [[User:Dmitry Katsubo|Dmitry]]: |
* Parallel session for programmers meeting in Utrecht | * Parallel session for programmers meeting in Utrecht | ||
| − | Bas: | + | [[User:Bvanbreukelen|Bas]]: |
* Draw a workflow for [[UU]]. | * Draw a workflow for [[UU]]. | ||
[[Category:Proteomics:Meeting|Gaining Momentum]] | [[Category:Proteomics:Meeting|Gaining Momentum]] | ||
Revision as of 22:48, 8 March 2010
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
- 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
Minutes notes
- Introduction
- 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.
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?)
- 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
Bas:
- Draw a workflow for UU.
