Workflows

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

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: 2009-12-15

Credits: Alan Williams

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: 2014-07-09

Credits: Alan Williams

Attributions: Demonstration of configurable iteration

EBI_InterproScan_broken (1)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text and xml. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration. Note that this workflow is deliberately broken

Created: 2014-07-09

Credits: Alan Williams Katy Wolstencroft Hamish McWilliam

Attributions: EBI_InterproScan_NewServices

BiomartAndEMBOSSMouseRat (1)

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions of the mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

Created: 2012-04-05

Credits: Alan Williams

BiomartAndEMBOSSMouseRat (1)

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions of the mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

Created: 2012-04-05

Credits: Katy Wolstencroft

Hello Anyone (1)

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An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".

Created: 2012-01-03 | Last updated: 2014-03-03

Credits: Stian Soiland-Reyes

Attributions: Hello World

Hello World (1)

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One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".

Created: 2012-01-03 | Last updated: 2014-03-03

Credits: Stian Soiland-Reyes

Example of explicit looping (1)

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This workflow demonstrates how a nested workflow can be called an explicit number of times. Note that the loop iterator does not need to be used in the logic of the loop contents. It can be used as a sentinel (see the conditional workflow)

Created: 2011-11-15 | Last updated: 2011-11-15

Credits: Alan Williams

Example of conditional invocation (1)

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This workflow demonstrates how nested workflows can be conditionally invoked

Created: 2011-11-15 | Last updated: 2011-11-15

Credits: Alan Williams