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User: Stian Soiland-Reyes

Workflow 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: User Stian Soiland-Reyes

Attributions: Workflow BiomartAndEMBOSSAnalysis

Workflow 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: User Stian Soiland-Reyes

Attributions: Workflow Retrieve sequence in EMBL format

Workflow 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: User Stian Soiland-Reyes User Tomoinn

Attributions: Workflow Demonstration of configurable iteration

Workflow Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2009-07-03

Credits: User Stian Soiland-Reyes User Ian Dunlop

Workflow 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: User Stian Soiland-Reyes

Attributions: Workflow GBSeq test

Pack Visualize PAV provenance as SVG


Created: 2013-04-05 09:18:51 | Last updated: 2018-01-04 11:39:09

A workflow that converts PAV provenance to SVG by inferring PROV-O statements.VoID descriptions following the Open PHACTS Dataset descriptions specification are fetched as Turtle, cleaned up to be valid OWL2 ontology and include useful labels, processed through the OWL reasoner Pellet; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox, generating an SVG visualization of the provenance.Note that this workflow downloads CWM, Pellet and ProvToolbox on dema...

11 items in this pack

Comments: 0 | Viewed: 80 times | Downloaded: 10 times

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Workflow Pattern: Return errors instead of null (1)

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 As Taverna can't (currently) handle null (see http://www.mygrid.org.uk/dev/issues/browse/TAV-653) - in Taverna 2 one can instead return exceptions on individual ports and inside lists. Exceptions are registered as error documents by Taverna, and are passed along. The ErrorBounce layer of processors downstream will prevent execution if they see this 'null'-exception - as showed in this example that the string concatination is just run for the two list elements that are not exceptio...

Created: 2010-01-04 | Last updated: 2010-01-04

Credits: User Stian Soiland-Reyes

Workflow Hello World in CWL (1)

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Puts a message into a file using echo

Created: 2017-11-03

Credits: User Stian Soiland-Reyes

Blob Workflow run bundle of helloabcd

Created: 2016-03-16 00:57:14

Credits: User Stian Soiland-Reyes

Attributions: Workflow Hello abcd

License: Creative Commons Attribution 3.0 Unported License

See https://gist.github.com/stain/fa63a3527bd09be2a42d

File type: ZIP archive

Comments: 0 | Viewed: 19 times | Downloaded: 0 times

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Workflow Hello abcd (1)

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Example of using the same inserted nested workflow twice, iterating over it twice, which should mean 4 distinct calls to the inner "concatenate" process. This workflow is mainly useful for provenance testing purposes.

Created: 2016-03-15

Credits: User Stian Soiland-Reyes

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