Workflows

EBI_InterProScan for Taverna 2 (2)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to t...

Created: 2010-01-26 | Last updated: 2010-11-24

Credits: Stian Soiland-Reyes Katy Wolstencroft Paolo Hamish McWilliam

Attributions: EBI_InterProScan for Taverna 2 EBI InterproScan T2 EBI_InterProScan EBI InterProScan

EBI_InterProScan for Taverna 2 (2)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2010-01-26 | Last updated: 2010-01-26

Credits: Stian Soiland-Reyes Paolo Katy Wolstencroft Hamish McWilliam

Attributions: EBI InterproScan T2 EBI_InterProScan

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.

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

Credits: Stian Soiland-Reyes

Attributions: Fetch PDB flatfile from RCSB server Fetch PDB flatfile from RCSB server

A workflow version of the EMBOSS tutorial (1)

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Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.

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

Credits: Stian Soiland-Reyes

Attributions: A workflow version of the EMBOSS tutorial

Fetch today's xkcd comic (1)

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Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: Fetch today's xkcd comic

Biomart and EMBOSS analysis (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: 2009-07-03 | Last updated: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: BiomartAndEMBOSSAnalysis

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

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2009-07-03

Credits: Stian Soiland-Reyes Ian Dunlop

GBSeq test (1)

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: GBSeq test