Difference between revisions of "Proteomics:Gaining Momentum Meeting on 2010-03-05"

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* [[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|Peter Horvatovich]] ([[RUG]])
+
* [[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

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
  • 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?)

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.