Workflows

FunctionalClusterDavid (1)

• Download

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: Katy Wolstencroft

ImportConvertEnsembl (1)

• Download

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: Katy Wolstencroft

entreztoKeggImage (1)

• Download

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: Katy Wolstencroft

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

• Download

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

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

Credits: Markus Plangg

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

• Download

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

Created: 2014-09-07

Credits: Markus Plangg

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

• Download

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

Created: 2014-09-07

Credits: Markus Plangg

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

• Download

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

Created: 2014-09-07

Credits: Markus Plangg

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

• Download

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

Created: 2014-09-07

Credits: Markus Plangg

Optimization of retention time prediction (1)

• Download

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: Sonja Holl Yassene Magnus Palmblad

Attributions: Retention Time Prediction with X!Tandem

X!Tandem and PeptideProphet on the Grid (1)

• Download

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