Workflows

Term Extraction with NaCTeM's TerMine Tool (2)

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Pass in text and retrieve a list of terms discovered ranked by their importance within the text.

Created: 2009-07-23

Credits: Brian Rea National Centre for Text Mining (NaCTeM)

Arabidopsis thaliana QTL Analysis (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Arabidopsis thaliana. 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 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 pathway database. ...

Created: 2009-07-08 | Last updated: 2009-12-14

Credits: Paul Fisher

Retrieve sequence in EMBL format (1)

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This workflow retrieves a sequence associated with its features in embl format

Created: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: Retrieve sequence in EMBL format

Demonstration of configurable iteration (1)

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This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2009-07-03 | Last updated: 2009-07-03

Credits: Stian Soiland-Reyes Tomoinn

Attributions: Demonstration of configurable iteration

Execute GWorkflowDL workflow using Taverna... (1)

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This workflow makes use of the "Grid Workflow Execution Service" (GWES) in order to exececute a GWorkflowDL workflow by means of the Taverna Workbench 2. As the GWES is deployed as a regular SOAP service, the WSDL can be imported as a normal service into the Taverna Workbench. This workflow contains all the input parameters as string constants, so it can be started right away without user inputs.

Created: 2009-06-30

Credits: Andreas Hoheisel

Attributions: Execute GWorkflowDL workflow using Taverna 2

Execute GWorkflowDL workflow using Taverna 2 (1)

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This workflow makes use of the "Grid Workflow Execution Service" (GWES) in order to exececute a GWorkflowDL workflow by means of the Taverna Workbench 2. As the GWES is deployed as a regular SOAP service, the WSDL can be imported as a normal service into the Taverna Workbench.

Created: 2009-06-30 | Last updated: 2009-06-30

Credits: Andreas Hoheisel

Query dbsnp, transform to HTML (1)

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Created: 2009-05-21 | Last updated: 2009-05-21

Credits: Pierre Lindenbaum

LINTUL crop model (1)

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Created: 2009-04-01

Credits: Robert Muetzelfeldt

Search InChI in NCBI eSearch (pccompound) (1)

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This workflow takes in a search term (e.g. InChI) for search in PubChem pccompound database. The result is an xml file containing summary information about the search term and also a compound image and the compound webpage fetched from Pubchem.

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

Download Entries from PubChem (1)

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Given a list of identifiers (e.g. CID) and their appropriate type (eID_CID - note that these differ slightly from the original identifier name -> CID <-> eID_CID), this workflow queries PubChem via PUG to retrieve a download URL for the resulting XML file containing the results. Adding support for downloading this XML file and writing it to filesystem is planned.

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich