Workflows

Pathways and Gene annotations for RefSeq ids (1)

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This workflow searches for genes which were found to be differentially expressed from a microarray study in the mouse, Mus musculus. The workflow requires an input of gene ref_seq identifiers. Data is then extracted from BioMart to annotate each of the genes found for each ref_seq id. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to search for pathways in the KEGG pathway database.

Created: 2010-11-15 | Last updated: 2010-11-15

Credits: Paul Fisher

Pathways and Gene annotations for QTL region (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path...

Created: 2010-11-15 | Last updated: 2010-11-16

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

Search OpenTox data sets by title. (1)

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 Use of an OpenTox ontology server to find data sets with a particular string in the title, such as 'EPA' as in this case.

Created: 2010-11-14 | Last updated: 2010-11-14

Credits: Egon Willighagen

Run OpenTox models on local data. (1)

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 Runs a remote OpenTox model to predict properties for local data which is uploaded on the fly.

Created: 2010-11-13 | Last updated: 2010-11-13

Credits: Egon Willighagen

BiomartAndEMBOSSAnalysis (1)

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Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Created: 2010-11-12

Credits: Krisztina

BiomartAndEMBOSSAnalysis (1)

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Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Created: 2010-11-12 | Last updated: 2010-11-12

Credits: Krisztina

[untitled] (1)

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A tutorial workflow of Taverna.

Created: 2010-11-12 | Last updated: 2010-11-12

Credits: Sukhdeep Singh

retry-example (1)

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This workflow executes a local beanshell script that has been programmed to fail on some iterations. It demonstrates the advantages of setting retries in your workflows to make them more robust

Created: 2010-11-08 | Last updated: 2010-11-08

Credits: Alan Williams

Async WPS example (2)

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Example on how to work with an async service, where the statusURL is used to check for Example on how to work with an async service, where the statusURL is used to check for if the process has finished or not

Created: 2010-11-04 | Last updated: 2011-04-27

Credits: Jorgejesus

Sacs Gene Muation Analysis (1)

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This workflow was created to predict the effect of the mutation on the primary and the secondary structure of a mutated sacsin protein. The genomic sequence bearing the mutation should be pasted on FASTA format as input for the Transeq tool. This sequence will be translated to protein and compared to the wild type protein, already extracted from NCBI database, through the Supermatcher tool. Variation(s) will be verified by multiple alignment using Blastp and ClustalW tools. Prediction of th...

Created: 2010-11-03 | Last updated: 2010-11-03

Credits: Yosr Bouhlal