User: Yassene

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Name: Yassene

Joined: Tuesday 14 June 2011 16:42:50 (UTC)

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Yassene has been credited 13 times

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Blob Example results from the UniProt Protein Protein Net...

Created: 2015-12-04 14:50:06

Credits: User Magnus Palmblad User Yassene

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example results from the UniProt Protein Protein Network workflow (http://www.myexperiment.org/workflows/4778.html) on Apolipoprotein A-I (P02647). The purpose of the igraph graph is to check that the workflow ran OK. For further exploration and visualization of the network, one of the output files can be opened in Cytoscape or similar tool.

File type: PNG image

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Workflow

Workflow Author Citation Network (1)

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Map citation/reference network for one author using Europe PMC Web services. This workflow is intended to show the integration of several Web services, XPath XML parsing and use of the igraph package in R. Although the workflow is functional, the information in PubMed is incomplete. This means the results may be a subset of the correct citation graph.

Created: 2015-12-04 | Last updated: 2015-12-04

Credits: User Magnus Palmblad User Yassene

Workflow

Workflow UniProt Protein Protein Network (1)

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This workflow uses the Europe PMC Web Services searchPublications and getDatabaseLinks to reconstruct a protein-protein network based on co-occurence in the scientific literature, arbitrary filtered by a PubMed query, e.g. the word "complex" appearing in the title or abstract. The workflow also looks up the second degree connections, i.e. proteins co-occuring with proteins co-occuring with the protein given as input, but not with this protein itself. The output is a (1) Pajek graph file, a GM...

Created: 2015-12-04

Credits: User Magnus Palmblad User Yassene

Workflow

Workflow connect to WoS Web services lite concept (1)

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This workflow is a concept for how Taverna could connect to the Thomson Reuters Web of Science (WoS) Web services lite. However, at this moment (2015-01-20), the authentication generate a session ID, but the other services (here search and closeSession) do not have an input port for this session ID. According to the documentation, this is required. The error message from the Web service also show this is missing. This workflow is "work in progress", but may nevertheless be of interest to an...

Created: 2015-08-19

Credits: User Magnus Palmblad User Yassene User Arzu Tugce Guler

Workflow

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Workflow Generate Spectral Library (1)

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This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License (CC BY-SA). Copyright© 2012 Yassene Mohammed Please send your feedback, questions, comments and suggestions for improvement to y.mohammed@lumc.nl 14 November 2012 Yassene

Created: 2013-08-16

Credits: User Yassene User Magnus Palmblad

Workflow

Workflow 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: User Sonja Holl User Yassene User Magnus Palmblad

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

Workflow

Workflow Optimization of retention time prediction (1)

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The workflow uses RTCalc from the TPP toolbox to perform two different retention time predictions. The third branch uses a linear retention time predictor (Palmblad et al., 2002). The workflow has a flag that switches on a specific branch.

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

Credits: User Sonja Holl User Yassene User Magnus Palmblad

Attributions: Workflow Retention Time Prediction with X!Tandem

Workflow

Workflow Comparison of Peptide and Protein Fraction... (1)

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This workflow was used to analyze the data in a manuscript by Mostovenko et al. (2013, submitted), comparing peptide and protein fractionation methods. The workflow identifies proteins by X!Tandem database search and validates the results using PeptideProphet. Additional information such as pI and fraction number is extracted and plotted for IEF and SCX data. For each protein identified in SDS-PAGE derived data sequences are downloaded from UniProt and plotted against the fraction number. Rs...

Created: 2013-03-27

Credits: User Kate Mostovenko User Yassene User Magnus Palmblad

Attributions: Workflow Plasma Precipitation Analysis

Workflow

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Workflow Cloud Parallel Processing of Tandem Mass S... (1)

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A workflow for searching LC−MS/MS mass spectrometry data using X!Tandem on the cloud. The workflow consists of 5 processors. The objectLogic processor prepares all inputs in the right format, i.e. keeping or converting strings into file object according to the following processor. The mzxmlDecomposer and pepxmlComposer run the decomposing/recomposing algorithms. objectLogic, mzxmlDecomposer and pepxmlComposer are Beanshell processors and they run locally. Xtandem runs X!Tandem on a remo...

Created: 2012-09-10

Credits: User Yassene

Workflow

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Workflow Cloud Parallel Processing of Tandem Mass S... (1)

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An advanced scientific workflow for searching LC−MS data using SpectraST on the cloud. Uploading the libraries is optimized to achieve better performance, which makes this workflow more suitable for processing mzXML spectra files from human samples, as the corresponding NIST library needed by SpectraST is larger than 2 GB. Here we connect 3 nested workflows, in which the first 2, i.e., decomposeMzxml and uploadToCloud, run in parallel, while the third nested workflow, i.e. runSpectrastO...

Created: 2012-09-10 | Last updated: 2015-08-19

Credits: User Yassene

Workflow

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Workflow Cloud Parallel Processing of Tandem Mass S... (1)

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A workflow for searching LC−MS/MS data using SpectraST on the cloud. The processor mzxmlDecomposer, pepxmlUnzip, and pepxmlComposer are identical to the one in the X!Tandem workflow (Figure 2). The only difference is that the Xtandem processor is exchanged with the Spectrast processor and the constant inputs are adjusted to SpectraST. This approach is also possible for other search engines as described in Data Decomposition and Recomposition Algorithms. More details can be found here:...

Created: 2012-09-10

Credits: User Yassene

Workflow

Workflow Retention Time Prediction with X!Tandem (1)

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This workflow identifies peptides from tandem mass spectra using X!Tandem as in a standard installation of the Trans-Proteomic Pipeline (TPP, version 4.6, but earlier versions should also work). The peptide-spectrum matches are validates using PeptideProphet (also from a standard installation of TPP) and peptides with at least a probability 0.95 are used to train a linear retention time predictor (Palmblad et al., 2002), whereby retention coefficients are also derived. These indirectly provid...

Created: 2012-09-03 | Last updated: 2012-09-03

Credits: User Magnus Palmblad User Yassene User Eleni

Attributions: Blob rt3.c

Workflow

Workflow Plasma Precipitation Analysis (1)

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ABOUT THE WORKFLOW This workflow was used to analyze the data in a manuscript by Mostovenko et al. (2012, submitted), comparing proteins in the precipitate with those left in solution after organic solvent precipitation. However, the workflow is generally applicable in comparisons of any binary fractionation method in proteomics, where the fractions are analyzed by liquid chromatography-tandem mass spectrometry. The workflow identifies proteins by SpectraST spectral library search and X!Ta...

Created: 2012-07-31 | Last updated: 2012-07-31

Credits: User Magnus Palmblad User Kate Mostovenko User Yassene

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