Workflows

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: 2009-12-15

Credits: Alan Williams

EBI_InterProScan_T2 (1)

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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: 2009-12-15

Credits: Alan Williams

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2009-12-15

Credits: Alan Williams

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: 2009-12-15

Credits: Alan Williams

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: 2009-12-15

Credits: Alan Williams

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2009-12-15

Credits: Alan Williams

Retrieve sequence in EMBL format (1)

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

Created: 2009-12-15

Credits: Alan Williams

Fetch Dragon images from BioMoby (2)

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Fetch images and annotations of snapdragons

Created: 2009-12-15 | Last updated: 2010-07-14

Credits: EdwardKawas

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: Stian Soiland-Reyes

Dummy example of looping (3)

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Example of looping over asynchronous services. The dummy beanshell scripts represents the operations of an asynchronous submit-status-results style service, such as EBI's InterProScan and NCBI Blast. createJob creates a temporary file with the content "0". Filename retuirned as a "job ID". checkStatus reads the job, and return state "RUNNING" as long as the content is less than 10, increasing the number for each call. (As no actual job is being run) getResults reads the file content, with...

Created: 2010-01-27 | Last updated: 2013-10-08

Credits: Stian Soiland-Reyes

Rdfise Riken SciNes Database Repository [m... (1)

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This workflow rdfise Riken SciNes Database Repository available at https://database.riken.jp/sw/links/en/crib151s2i/. There is a bug with main page listing databases: version 2p and 3p are similar to 1p.

Created: 2010-02-01 | Last updated: 2010-02-01

Credits: Francois Belleau

SBML to SBML shortand converter (1)

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converts SBML document to SBML shorthand via BASIS web services BASIS: www.basis.ncl.ac.uk:81/Basis SBML shorthand: http://www.staff.ncl.ac.uk/d.j.wilkinson/software/sbml-sh/

Created: 2010-02-03 | Last updated: 2010-02-03

SBML shorthand to SBML converter (1)

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converts SBML shorthand to SBML document via BASIS web services BASIS: www.basis.ncl.ac.uk:81/Basis SBML shorthand: http://www.staff.ncl.ac.uk/d.j.wilkinson/software/sbml-sh/

Created: 2010-02-03 | Last updated: 2010-02-03

CaliBayes_Client (1)

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A workflow for consuming CaliBayes web services. CaliBayes: www.calibayes.ncl.ac.uk

Created: 2010-02-03 | Last updated: 2010-02-03

Get Gene Ids for Human (1)

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This workflow gets a list of gene ids (number depending on Ret_Max_value variable) for Homo sapiens. The species may be changed according to that desired, by altering the term_value string constant

Created: 2010-02-04 | Last updated: 2010-02-04

Credits: Paul Fisher

PDB2KEGG step 1done during BH2010 (1)

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No description

Created: 2010-02-13

Credits: Francois Belleau

LipidMaps Query (1)

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This workflow retrieves database entries from LipidMaps for given exact mass and tolerance inputs.

Created: 2010-02-16