Workflows

blastn and blastx (1)

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This workflow accepts an url of a fasta file as input and performs an NCBI blastn at the EBI against the bacteria database and an NCBI blastx against the uniref90 database.  From the blast results of the blastx the hit with the lowest e-value is taken and the GO is returned. Output is blastx and blastn results and GO from the first hit of the blastx.   Based on Katy Wolstencroft & Hamish McWilliam EBI_NCBI_BLAST http://www.myexperiment.org/workflows/1765.html

Created: 2011-06-08 | Last updated: 2011-06-08

Credits: Niek

Bash example from the NGS community contri... (1)

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  BASH Simple workflow that executes "ls" on the command line in the directory "/".

Created: 2011-06-07

Credits: Baj

Download the ONS solubility data from Goog... (1)

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 Use the Bioclipse scripting langauge to authenticate with Google Docs, and download the Open Notebook Science solubility data into a local data structure.

Created: 2011-06-06 | Last updated: 2011-06-06

Credits: Egon Willighagen

DAS features retrieval and parsing with JDAS (2)

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Retrieve Protein or Genome features using the Distributed Annotation System (DAS) and create your own text output by modifying the JDAS component. To be able to use this workflow with JDAS copy this file … http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar … to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs.

Created: 2011-06-01 | Last updated: 2011-06-02

Credits: Rafael C. Jimenez

DAS features retrieval (2)

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Retrieve Protein or Genome features (annotations) using the Distributed Annotation System (DAS).

Created: 2011-06-01 | Last updated: 2011-06-01

Credits: Rafael C. Jimenez

DAS sequence retrieval and parsing with JDAS (1)

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Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS) and create your own text output by modifying the JDAS component. To be able to use this workflow with JDAS, copy this file … http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar … to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs.

Created: 2011-05-30 | Last updated: 2011-05-30

Credits: Rafael C. Jimenez

DAS sequence retrieval (2)

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Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS).

Created: 2011-05-30 | Last updated: 2011-05-30

Credits: Rafael C. Jimenez

Find Biological Models by GO. (1)

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Find Biological Models (Ids and Names) from Biomodels querying by Gene Ontology terms.

Created: 2011-05-29 | Last updated: 2011-05-29

Credits: Rafael C. Jimenez

Find Reactome pathways and reactions by GO (1)

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Find Reactome pathways and reactions (names and accessions) in Human querying by a Gene Ontology term. This is an example of how to use the Reactome Biomart service in Taverna. Many other possibilities are possible by modifying the filters and attributes options of the service.

Created: 2011-05-29 | Last updated: 2011-05-29

Credits: Rafael C. Jimenez

Find PRIDE experiments by GO (1)

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Find PRIDE experiments in Human with related information like Cell Type and Tissue location filtering results by Gene Ontology terms. This is an example of how to use the PRIDE Biomart service in Taverna. Many other options are possible by modifying the filters and attributes of this service.

Created: 2011-05-29 | Last updated: 2011-05-29

Credits: Rafael C. Jimenez