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X!Tandem and PeptideProphet on the Grid (1)

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The workflow performs the execution of X!Tandem and PeptideProphet from the TPP toolbox on the Grid. The execution is performed by the UNICORE Plugin for Taverna. mzXMLDecomposer/Composer is used to run the execution of X!Tandem in parallel. extract_values extract relevant information from thetandem.interact.pep.xml File. The file can then remain on the remote storage.

Created: 2013-08-13 | Last updated: 2013-09-04

Credits: Sonja Holl Yassene Magnus Palmblad

Attributions: de Bruin et al. Workflow 1 Cloud Parallel Processing of Tandem Mass Spectrometry Based Proteomics Data: X!Tandem

Biomarker Identification via RFE on the Grid (2)

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The first two components split the original data set into several sub-sampling sets. The RFE component performs the machine learning approach by executing several instances of a SVM, each of which consuming one sub-sample data set. The execution of the SVM takes place in a distributed computing environment, using the UNICORE-Taverna Plugin. The calc_objFunc component calculates the F-measure of the ranked gene list compared to a 'gold standard'.

Created: 2013-08-13 | Last updated: 2013-09-24

Credits: Sonja Holl

Attributions: Biomarker Identification via EFS on the Grid