Proteomics:Gaining Momentum Meeting on 2011-11-14
Location and time
- Location: Kruytbuilding (6th floor, east wing), Padualaan 8, 3584 CH Utrecht
- Date: Monday November 14th, 2011
- Time: 13:00-17:00
- Andrew Stubbs (EMC)
- Bas van Breukelen (UU)
- Henk van den Toorn (UU)
- Ishtiaq Ahmad (AMC)
- Péter Horvatovich (RUG)
- Pieter Lukasse (WUR)
- Rob Hooft (NBIC)
- Thang Pham (VUmc)
- Twan America (WUR)
- Freek de Bruijn (NBIC)
- Status updates
- Action points
- Next meeting
- Pieter presented the new plans from Wageningen for the task force pipeline.
- Bas explained more about pview and what makes it an interesting tool.
- Péter showed mcCompare. We discussed the possibility to include pview in msCompare (this would require the functionality to be divided for the two phases).
- Ishtiaq gave an update on the statistical tools from AMC.
- We talked about proteomics search tools that we can use in Galaxy: X! Tandem, OMSSA and Mascot. Pieter will investigate Mascot and X! Tandem.
- Bas advised Thang to consider using massQC (approx. 5,000 euro) as a short term solution for quality control and switching to PRIME-XS tools in the long term.
- November 2011 - Ishtiaq: help EMC with VM updates and report generation.
- November 2011 - Andrew: supply data to Pieter and Twan.
- November 2011 - Péter: supply data to Pieter and Twan.
- November 2011 - Andrew, Bas and Henk: exchange information on pview CLI, functional requirements.
- November 2011 - Pieter: get data & Galaxy workflow from Péter and get it running.
- November 2011 - Freek: create overview page of available test data on the wiki, plan next meeting and create minutes.
- December 2011 - Berend: documentation and test data for msCompare.
- December 2011 - Pieter: integrate SetMat in the pipeline, database search and feature alignment.
- December 2011 - Thang: put VUmc statistical tool on NBIC Galaxy server (with help from Ishtiaq and Freek).
- December 2011 - Henk: look at possibilities for splitting pview in two phases to fit msCompare model.
- December 2011 - Bas: get quality control (QC) list from PRIME-XS plans (file formats, reference implementation).
- January 2012 - Henk, Ishtiaq, Ivo Palli (EMC) and Freek: command-line interface for pview, integration in Galaxy.
The NPC Progress Meeting 2012 is coming up on 7 February 2012 in Media Plaza (Jaarbeurs), Utrecht. We will have our Gaining Momentum Meeting from 9:30 until 12:30 (as one of the theme sessions for NPC project groups). The whole day runs from 9:00 until 18:00.
For more information: http://www.netherlandsproteomicscentre.nl/