Stian Soiland-Reyes' Workflows

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Workflow EBI_InterProScan for Taverna 2 (2)

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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 t...

Created: 2010-01-26 | Last updated: 2010-11-24

Credits: User Stian Soiland-Reyes User Katy Wolstencroft User Paolo User Hamish McWilliam

Attributions: Workflow EBI_InterProScan for Taverna 2 Workflow EBI InterproScan T2 Workflow EBI_InterProScan Workflow EBI InterProScan

Workflow EBI_InterProScan for Taverna 2 (2)

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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: 2010-01-26 | Last updated: 2010-01-26

Credits: User Stian Soiland-Reyes User Paolo User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EBI InterproScan T2 Workflow EBI_InterProScan

Workflow 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: User Stian Soiland-Reyes

Workflow Using CQL to query protein sequence data (1)

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To query protein sequence infomation out of 3 caGrid data services: caBIO, CPAS and GridPIR Adapted from http://www.myexperiment.org/workflows/600

Created: 2009-05-07

Credits: User Stian Soiland-Reyes

Attributions: Workflow Using CQL to query protein sequence data

Workflow Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.

Created: 2009-07-03 | Last updated: 2009-07-03

Credits: User Stian Soiland-Reyes

Attributions: Workflow Fetch PDB flatfile from RCSB server Workflow Fetch PDB flatfile from RCSB server

Workflow REST access of xml.nig.ac.jp (WABI) (1)

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This workflow has a beanshell script for composing the REST URL for the services at xml.nig.ac.jp  (WABI) This URL is passed to the local worker Get_web_page_from_URL that fetches the requested data. Note: This is a proof of concept of accessing REST services through Taverna. All of WABI's services can more easily be browsed and used in Taverna by adding their WSDL, for instance http://xml.nig.ac.jp/wsdl/GetEntry.wsdl The example invokes the getDDBJEntry(accession) method of the getE...

Created: 2008-10-14 | Last updated: 2008-10-14

Credits: User Stian Soiland-Reyes

Workflow Staged iteration strategy (1)

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Consider two lists A and B, of equal size 3. A[1] corresponds to B[1], A[2] to B[2], etc, for instance A are image scans from 2007 and B from 2008, and the index indicates the patient number. A = [a0, a1, a2] B = [b0, b1, b2] There's then two lists of possible parameters P and Q, of different lengths, P has 2 and Q has 4 items. P = [p0, p1] Q = [q0, q1, q2, q3] Each of the A items should be processed in ap using each of the P parameters, and each of the B items ...

Created: 2008-05-07 | Last updated: 2008-05-07

Credits: User Stian Soiland-Reyes

Workflow 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: 2009-07-03 | Last updated: 2009-07-03

Credits: User Stian Soiland-Reyes

Attributions: Workflow A workflow version of the EMBOSS tutorial

Workflow 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: 2009-07-03

Credits: User Stian Soiland-Reyes

Attributions: Workflow Fetch today's xkcd comic

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

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