Proteomics:Programmers Meeting on 2011-10-14
Location and time
- Location: Hojel City Center, building D (5th floor), Graadt van Roggenweg 340, 3531 AH Utrecht
- Date: Friday October 14th, 2011
- Time: 9:00-10:30
- George Byelas (UMCG)
- Henk van den Toorn (UU)
- Ishtiaq Ahmad (AMC)
- Péter Horvatovich (RUG)
- Tim te Beek (NBIC BRS)
- Wim Spee (UU)
- Freek de Bruijn (NBIC)
- Action points and status updates
- Next meeting
Action points and status updates
- Wim is finishing his work on the storage tools (refactoring, automatic integration testing and code cleanup).
- He is aiming to create the production version by the end of November.
- The source code can be made available via our Trac system.
- The ms_lims system will be installed in Utrecht. This system should provide a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data. It is developed by Ghent University and VIB (The ms_lims website).
- Tim has just started working on a BRS (Bioinformatics Research Support) project for Twan America (WUR) using Cytoscape. He has worked on it for half a week and is interested to see what the proteomics task force is working on.
- Ishtiaq added the classification tool to Galaxy. It is a challenge to set the number of datasets to be used for training the system using the Galaxy UI.
- The next step will be the report generator.
- He also worked on getting msCompare running on the new NBIC Galaxy server. Berend Hoekman (RUG) will take a look at it.
- Henk visited the PRIME-XS group in Belgium together with Bas van Breukelen (UU). The meeting was focused on quality control, the OpenMS team offered some suggestions. They plan to integrate with NIST guidelines.
- Henk is participating in the group that works on the file format for quality control. The format might be xml based, but they could also decide to use SQLite.
- He is also working with a vender on port processing of quantitation data (statistical analysis).
- Salvatore Cappadona (UU) found some problems with pview and is discussing those with Zia Khan (the author of pview).
- Salvatore is comparing pview to Progenisis LC-MS. The first results indicate that pview is a lot faster and these results appear to be better as well.
- George established several pipelines and is now focussing on testing and improving scalability.
- He is also working on running R scripts from Molgenis.
- Finally, George is using Jan Bot's system or SSH-2 to work with the grid (DAF is not used).
- Péter worked on msCompare in Galaxy with Ishtiaq.
- Pieter Lukasse (WUR) has started in Wageningen.
- Bas and Freek are organising a new PI/programmers meeting.
- Elizabeth McClellan (EMC) sent a partial draft of her MS PRUNA publication to Bas for feedback.
Friday November 18th 9:00-10:30 will be our next programmer's meeting.