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Showing 2916 results. Use the filters on the left and the search box below to refine the results.
Taverna 2
Uploader
3739?size=60x60 Yassene

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

Taverna 2
Uploader
3505?size=60x60 At Markus Plangg

Workflow Imagemagick convert - tiff2tiff - compression (1)

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Converts tiff to tiff using imagemagick convert with the provided compression

Created: 2013-08-15

Credits: User Markus Plangg

Taverna 2
Uploader
Avatar De Sonja Holl

Workflow Biomarker Identification via EFS on the Grid (2)

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The first two components split the original data set into several sub-sampling sets. The EFS component performs the machine learning approach by executing several instances of a SVM, each of which consuming one sub-sample data set. Another level of SVM execution is added by taking bootstapping into account. The execution of all SVMs 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 ...

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

Credits: User Sonja Holl

Attributions: Workflow Biomarker Identification via RFE on the Grid

Taverna 2
Uploader
Avatar De Sonja Holl

Workflow 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: User Sonja Holl

Attributions: Workflow Biomarker Identification via EFS on the Grid

Taverna 2
Uploader
Avatar De Sonja Holl

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

Taverna 2
Uploader
Avatar De Sonja Holl

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

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Integral Projection Model for Demographic ... (1)

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This workflow constructs and analyses an IPM with only continuous stages and without ramet production based on the IPMpack (R). Information about the Input file: The data must be organized in a table (in .csv format), where each row represents one observation of an organism in the population at one census time t with the following column names: size: size of individuals in census time t sizeNext: size of individuals in census time t +1 surv: survival of individuals from census time t to t...

Created: 2013-08-13

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Matrix Population Model analysis v12 (2)

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The Matrix Population Models Workflow provides an environment to perform several analyses on a stage-matrix with no density dependence: - Eigen analysis; - Age specific survival; - Generation time (T); - Net reproductive rate (Ro); - Transient Dynamics; - Bootstrap of observed census transitions (Confidence intervals of lambda); - Survival curve; - Keyfitz delta; - Cohen's cumulative distance. This workflow requires an instance of Rserve on localhost This workflow has been created by the Bi...

Created: 2013-08-13 | Last updated: 2014-07-09

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population Workflow Eigen analysis Workflow Age specific analysis Workflow Transient Dynamics. Workflow Generation time (T) Workflow Net reproductive rate (Ro) Blob Demographic data Gentiana pneumonanthe 1987-1988 from Terschelling File.

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Matrix Population Model construction and a... (3)

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The Matrix Population Models Workflow provides an environment to create stage-matrices with no density dependence and to perform several analyses on them: - Eigen analysis; - Age specific survival; - Generation time (T); - Net reproductive rate (Ro); - Transient Dynamics; - Bootstrap of observed census transitions (Confidence intervals of lambda); - Survival curve; - Keyfitz delta; - Cohen's cumulative distance. If multiple year transitions are selected, the results will be ordered by year. ...

Created: 2013-08-13 | Last updated: 2014-07-04

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population Workflow Matrix Population Model construction and analysis Workflow Eigen analysis Workflow Age specific analysis Workflow Transient Dynamics. Workflow Generation time (T) Workflow Net reproductive rate (Ro) Workflow Bootstrap of observed census transitions. Blob Demographic data Gentiana pneumonanthe 1987-1988 from Terschelling File.

Bioclipse Scripting Language
Uploader
4506?size=60x60 Nl Egon Willighagen

Workflow Extracts metabolites from a GPML pathway d... (1)

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This Groovy scripts starts with a WikiPathways identifier, downloads the GPML, and uses the Groovy XmlParser to extract metabolites for which it reports the label, and if available, database and identifier.

Created: 2013-08-11 | Last updated: 2013-08-11

Credits: User Egon Willighagen

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Funded by: BioVeL, EPSRC, JISC, Microsoft

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