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Showing 1566 results. Use the filters on the left and the search box below to refine the results.
Taverna 2
Uploader
1780?size=60x60 Gb Donal Fellows

Workflow myExperiment Group Activity Report (1)

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Prepares a report (three CSV files) on the activity of a group on myExperiment.

Created: 2014-08-26

Credits: User Donal Fellows

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

Workflow Calculate and Plot abundance over the years (1)

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This workflow calculates and plots the abundance per stage per year. This workflow has been created by the Biodiversity Virtual e-Laboratory (BioVeL http://www.biovel.eu/) project. BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359. This workflow was created using and based on Package ‘popbio’ in R. (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011). ================================================================================== Literature Caswell, H. 20...

Created: 2014-08-28

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

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

Workflow Variance matrix (1)

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This workflow estimates the variance matrix from a list of matrices. This workflow has been created by the Biodiversity Virtual e-Laboratory (BioVeL http://www.biovel.eu/) project. BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359. This workflow was created using and based on Package ‘popbio’ in R. (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011). ================================================================================== Literature Caswell, H. 20...

Created: 2014-08-28

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

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

Workflow Elasticity and Sensitivity of the Vital rates (1)

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This workflow calculates the Elasticity and Sensitivity of population growth rate with respect to various vital rates. The goal in both cases is to determine which vital rates has/ve the most influence on population growth rate (?). Elasticity and Sensitivity: Sensitivity and elasticity analyses are prospective analyses. a) The sensitivity matrix: The sensitivity describes the effect on ? of changes in vital rates of the matrix. The derivative tells what would happened to ? if aij was to c...

Created: 2014-08-29

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

Taverna 2
Uploader
9?size=60x60 Gb Stian Soiland-Reyes

Workflow Example dbfetch (2)

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Run EBI's dbfetch

Created: 2014-09-03 | Last updated: 2014-09-03

Credits: User Stian Soiland-Reyes User Katy Wolstencroft

Attributions:

Taverna 2
Uploader
71?size=60x60 Nl Katy Wolstencroft

Workflow FunctionalClusterDavid (1)

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This workflow takes a list of Entrez Gene IDs as input and submits them to the DAVID REST API for functional clustering using OG annotaiton, biological pathways and disease associations. Used for analysing a set of genes (i.e. those differentially expressed for a particular disease condition).

Created: 2014-09-05

Credits: User Katy Wolstencroft

Taverna 2
Uploader
71?size=60x60 Nl Katy Wolstencroft

Workflow ImportConvertEnsembl (1)

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This workflow accepts a spreadsheet file as input and extracts a list of ENSEMBL Gene IDs from column A. The hsapiens_gene_ensembl service converts these IDs to Entrez_geneIds

Created: 2014-09-05

Credits: User Katy Wolstencroft

Taverna 2
Uploader
71?size=60x60 Nl Katy Wolstencroft

Workflow entreztoKeggImage (1)

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This workflow accepts a list of Entrez Gene IDs. It dentifies which KEGG pathway each gene is involved with and displays the pathway diagrams

Created: 2014-09-05

Credits: User Katy Wolstencroft

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

Workflow Photohawk SSIM tiff/png/jpeg-jp2 (3)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk SSIM.

Created: 2014-09-07 | Last updated: 2014-09-07

Credits: User Markus Plangg

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

Workflow Photohawk MSE tiff/png/jpeg-jp2 (1)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk MSE.

Created: 2014-09-07

Credits: User Markus Plangg

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

Workflow Photohawk AE tiff/png/jpeg-jp2 (1)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk AE.

Created: 2014-09-07

Credits: User Markus Plangg

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

Workflow Photohawk MAE tiff/png/jpeg-jp2 (1)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk MAE.

Created: 2014-09-07

Credits: User Markus Plangg

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

Workflow Photohawk PAE tiff/png/jpeg-jp2 (1)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk PAE.

Created: 2014-09-07

Credits: User Markus Plangg

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
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 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 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
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
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
1780?size=60x60 Gb Donal Fellows

Workflow SCAPE Assess Metrics (1)

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Assesses whether a set of metrics satisfy some provided Quality Level Definition (QLD). The QLD is given as a Schematron schema, and is evaluated by the Java tool library Jing. Jing (http://www.thaiopensource.com/relaxng/jing.html) is assumed to be installed in the current directory.

Created: 2013-08-22 | Last updated: 2013-08-22

Taverna 2
Uploader
Avatar De Sonja Holl

Workflow EBI NCBI BLAST filter e-value and length (1)

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The workflow queries the NCBI BLAST web service and extracts the e-values and length of the results. One of the sub-workflows filters the length first and afterwards the e-value and the other sub-workflow filters first the e-value and then the length. As the result may be different, this workflow was used for optimization purposes to find the sub-workflow performing best.

Created: 2013-08-23 | Last updated: 2014-02-06

Credits: User Sonja Holl

Attributions: Workflow EBI_NCBI_BLAST

Taverna 2
Uploader
4185?size=60x60 Nl Eleni

Workflow Get concept suggestions from term (1)

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This workflow suggests concept ids that match the query term. The user can run this workflow with any term of interest as for example "human", "htt", "Transcription" etc, and will get suggestions for concept ids together with descriptions. Then can choose the concept id that matches the best to her/his needs and use it to the rest of the CPA workflows.

Created: 2013-08-31

Credits: User Eleni Network-member BioSemantics

Taverna 2
Uploader
4080?size=60x60 Renato De Giovanni
Project Biovel

Workflow Bioclim workflow (6)

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This workflow takes as input a file containing species occurrence points to create a model with the openModeller Web Service using the Bioclim algorithm. Environmental layers and mask are selected during the workflow. Points are filtered so that only environmentally unique points are used to create the model. You can use this workflow to either filter a set of species occurrence points excluding redundant points with the same environmental conditions (you can get the result in the output "se...

Created: 2013-09-02 | Last updated: 2015-04-04

Credits: User Renato De Giovanni Network-member BioVeL

Taverna 2
Uploader
4059?size=60x60 Gb Aleksandra Pawlik

Workflow UnigeneID to KEGG Pathways (1)

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This workflow accepts a list of Unigene gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in (plus pathway image) from the KEGG database. This workflow replaces the earlier SOAP version with the new KEGG REST services

Created: 2013-09-03

Credits: User Katy Wolstencroft User Alan Williams User Paul Fisher

Attributions: Workflow NCBI Gi to Kegg Pathways

Taverna 2
Uploader
4059?size=60x60 Gb Aleksandra Pawlik

Workflow Pathway to Pubmed (1)

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This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2013-09-03

Credits: User Alan Williams User Paul Fisher

Attributions: Workflow Pathway to Pubmed

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Funded by: BioVeL, EPSRC, JISC, Microsoft

Affiliates: myGrid, Taverna, BioCatalogue
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