Workflows

Generate Atom Signatures of molecules give... (1)

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Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re...

Created: 2011-05-13 | Last updated: 2011-05-13

Credits: Kalai

InterproScan without Looping (1)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text or png. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. This workflow will not work properly until we add looping.

Created: 2011-03-16 | Last updated: 2012-08-29

Credits: Katy Wolstencroft

[deprecated] Probabilistic Model Checking ... (1)

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This is a Taverna 1 version; if you're using latest Taverna 2 workbench please use: www.myexperiment.org/workflows/2267 . Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) Mathematica plotting Web service operation. This is a second-part for the computationaly exhaustive PMC: compute results workflow (http://www.myexperiment.org/workflows/1790).

Created: 2011-01-26 | Last updated: 2011-07-20

Credits: trybik

[deprecated] Probabilistic Model Checking ... (1)

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This is a Taverna 1 version; if you're using latest Taverna 2 workbench please use: www.myexperiment.org/workflows/2266.html . Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) PRISM model translation and model checking Web service operations.

Created: 2011-01-26 | Last updated: 2011-07-20

Credits: trybik

[deprecated] Simulate SBML-derived ODEs (1)

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This is a Taverna 1 version; if you're using latest Taverna 2 workbench please use: www.myexperiment.org/workflows/2264.html . Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) ODEs simulation and plotting Web service operations.

Created: 2011-01-26 | Last updated: 2011-07-20

Credits: trybik

EBI_InterproScan_NewServices (2)

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This workflow performs an interproscan on provided sequencesThis workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text, xml or png. 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.

Created: 2011-01-17 | Last updated: 2011-01-17

Credits: Katy Wolstencroft Hamish McWilliam Stian Soiland-Reyes

Attributions: EBI_InterProScan for Taverna 2 EBI_InterProScan for Taverna 2 EBI_InterProScan

retry-example (1)

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This workflow executes a local beanshell script that has been programmed to fail on some iterations. It demonstrates the advantages of setting retries in your workflows to make them more robust

Created: 2010-11-08 | Last updated: 2010-11-08

Credits: Alan Williams

Async WPS example (2)

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Example on how to work with an async service, where the statusURL is used to check for Example on how to work with an async service, where the statusURL is used to check for if the process has finished or not

Created: 2010-11-04 | Last updated: 2011-04-27

Credits: Jorgejesus

Polygon buffer - Using pyWPS (1)

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Basic example on how to integrate a Web Processing Service (WPS) using  PyWPS's WSDL/SOAP The workflow will accept a GML file with featureCollection where polyon is described using gml:coordinate element structure. This GMl is easely generated with GDAL. The coodinate structure will be converted to WKT and used to create a polygon using shapely, the output will be a buffer polygon with a defined width. Output polygon will replace the orginal polygon and the existing XML will be return...

Created: 2010-10-26 | Last updated: 2010-10-26

Credits: Jorgejesus

Testing caBIG workflow (1)

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An example workflow to test the installation of caGrid Workflow Suite and the submission of a workflow to a caGrid workflow service.

Created: 2010-08-17 | Last updated: 2010-08-17

Credits: Wei Tan