Workflows

EBI_CiteXplore (1)

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Perform a literature search using the EBI's CiteXplore service (http://www.ebi.ac.uk/citexplore/), and get the results in a minimal XML format containing the citation information (i.e. title, author, journal, etc.), the identifier of the citation in the source database (PubMed/Medline, Agricola, Patent Abstracts, CBA, CiteSeer, etc.) and information about abstract and full article availablity including URLs.

Created: 2008-07-09

Credits: Hamish McWilliam

EBI_ScanPS (1)

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Perform a Smith-Waterman sequence similarity search using the ScanPS tool (see http://www.compbio.dundee.ac.uk/Software/Scanps/scanps.html). In the case the EBI's WSScanPS web service (see http://www.ebi.ac.uk/Tools/webservices/services/scanps) is used to run the tool. Note: the WSScanPS service used by this workflow was retired 27th January 2010. Equivalent functionality is available in the EBI's FASTA (REST or SOAP) and PSI-Search (REST or SOAP) services.  

Created: 2008-06-03 | Last updated: 2010-12-06

Credits: Hamish McWilliam

Indigo-pains-recursive (2)

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*** Update 20151130 - using KNIME 3 nodes and the 'RDKit' version of PAINS queries ***The old Indigo library (1.1.13) could not take advantage of the parallelizing nodes in KNIME the way the RDKit library could. One way to speed up the PAINS workflow when using the Indigo library was to use a recursive loop that constantly shrank the list of structures being presented to the next PAINS query as structures were knocked out of the main list.Using the WEHI-10k reference set (embedded in ...

Created: 2013-08-13 | Last updated: 2015-12-01

Credits: sauberns

Attributions: Indigo-pains RDKit-pains-parallel

A Basic example R workflow (3)

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This workflow uses an R service running on localhost to calculate sin(0.45)

Created: 2010-11-26 | Last updated: 2014-08-20

Credits: Alan Williams

Split multi-sequence FASTA file into list (1)

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Splits a flat file containing multiple fasta sequences into a list of fasta sequences.

Created: 2010-03-16

Transform XML - explicit output file (1)

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The get_xml_file_from_web service downloads an example xml from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xml_file. The path to the temporary file is passed to the inFileURL port of Transform_XML. The get_xslt_file_from_web service downloads an example xslt file from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xslt_file. The path to the temporary file is passed to the xslFileURL port...

Created: 2008-09-27

Credits: Alan Williams

Test always fails - two parameters (1)

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The test always fails service generates a service failure when two parameter values are supplied.

Created: 2008-09-27

Credits: Alan Williams

Test always fails - one parameter (1)

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The test always fails service generates a service failure when one parameter value is supplied.

Created: 2008-09-27

Credits: Alan Williams

Split string into string list by regular e... (1)

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The split string into string list by regular expression takes the string 'boo:and:foo' and using the specified regular expression 'o' splits it into the list ['b','',':and:f']

Created: 2008-09-27

Credits: Alan Williams

Split string into string list by regular e... (1)

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The split string into string list by regular expression takes the string 'boo:and:foo' and using the specified regular expression ':' splits it into the list ['boo','and','foo']

Created: 2008-09-27

Credits: Alan Williams