- DLSG cluster at University of Groningen. Contact persons: Isthiaq Ahmad, Peter Horvatovich, Rainer Bischoff.
- DLSG cluster at Academic Medical Center. Contact persons: Mark Santcroos, Silvia Olabarriaga, Perry Moerland, Antoine van Kampen.
- DLSG cluster at Delft University. Contact persons: Jan Bot.
- DLSG cluster at SARA. Contact persons: Tom Visser, Coen Schrijvers.
Involved laboratory and contact persons:
Isthiaq Ahmad, Peter Horvatovich (Analytical Biochemistry, University of Groningen) and Frank Suits (IBM Watson Center)
Short description of the pipeline: TAPP is abbreviation of Threshold Avoiding Proteomics Pipeline developed by Frank Suits scientists working at IBM Watson Center. TAPP is preprocessing pipeline for label-free LC-MS proteomics data of multiple chromatograms, and provide a quantitative peak matrix amenable for statistical analysis. It consist of for tools:
- Meshing is reconstructing the raw data in grid with constant resolution.
- Centroid is performing peak detection and quantification and provide a quantitative peak lists.
- Warp2D time alignment tool correct for non linear retention time shifts between peaks of different chromatograms.
- Metamatch tool is clustering the same peaks in multiple chromatograms resulting the quantitative peak matrix.
- 7*5=35 files of qTOF single stage MS data in line mode (~30 MB/files and ~1.050 GB in total) obtained from porcine CSF spiked at various concentration of horse heart Cytochrom C. The expected size of all output file is ~1 GB.
- 7*5=35 files of qTOF single stage MS data in profile mode (25 GB/files and 1.050 TB in total)obtained from porcine CSF spiked at various concentration of horse heart Cytochrom C. The expected size of all output file is ~1 GB.
Testing methods: Testing will be performed using TAPP pipeline and the two datasets with the following two methods:
- raw starting files at RUG DLSG cluster and processing at XXX cluster using the complete TAPP pipeline.
- raw starting files at RUG DLSG cluster and processing at other locations having the dynamic lightpath connection with work load distributed between the different sites.
Implementation: This use case will use TAPP pipeline implemented in DAF and will using DRAC API to switch on and off dynamic lightpath during file transfer between DLSG clusters. Main programmer: Isthiaq Ahmad.
Skype meeting on 10 May 2011
- I will describe our use case with data in NBIC Wiki (done)
- Peter Hinrich will subject sites to perform testing of DLP in DLSG
- Isthiaq will start implementing DLP in DAF and will use TAPP pipeline as use(test) case.
- Jan Bot will submit application for EYR 3
- Isthiaq Ahmad will start (or incorporate into DAF project) a trac project for DLP implementation