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User: Stian Soiland-Reyes
Original Uploader

Workflow EBI_InterProScan for Taverna 2 (2)

Created: 26/01/10 @ 14:45:46 | Last updated: 24/11/10 @ 10:04:09

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 456 times | Downloaded: 210 times

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Original Uploader

Workflow EBI_InterProScan for Taverna 2 (2)

Created: 26/01/10 @ 14:46:07 | Last updated: 26/01/10 @ 14:46:08

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

Attributions: Workflow EBI InterproScan T2 Workflow EBI_InterProScan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 sig...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 198 times | Downloaded: 129 times

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Original Uploader

Workflow Using CQL to query protein sequence data (1)

Created: 07/05/09 @ 14:28:59

Credits: User Stian Soiland-Reyes

Attributions: Workflow Using CQL to query protein sequence data

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 178 times | Downloaded: 76 times

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Original Uploader

Workflow Staged iteration strategy (1)

Created: 07/05/08 @ 12:10:27 | Last updated: 07/05/08 @ 12:32:36

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 106 times | Downloaded: 50 times

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Original Uploader

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

Created: 14/10/08 @ 16:17:58 | Last updated: 14/10/08 @ 16:39:03

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution 3.0 Unported License

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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...

Rating: 4.0 / 5 (1 rating) | Versions: 1 | Reviews: 1 | Comments: 2 | Citations: 0

Viewed: 195 times | Downloaded: 58 times

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Original Uploader

Workflow Fetch PDB flatfile from RCSB server (1)

Created: 03/07/09 @ 14:37:14 | Last updated: 03/07/09 @ 14:53:40

Credits: User Stian Soiland-Reyes

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 93 times | Downloaded: 87 times

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Original Uploader

Workflow Biomart and EMBOSS analysis (1)

Created: 03/07/09 @ 14:18:28 | Last updated: 03/07/09 @ 14:19:32

Credits: User Stian Soiland-Reyes

Attributions: Workflow BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 98 times | Downloaded: 25 times

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Original Uploader

Workflow Fetch today's xkcd comic (1)

Created: 03/07/09 @ 14:40:25

Credits: User Stian Soiland-Reyes

Attributions: Workflow Fetch today's xkcd comic

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 126 times | Downloaded: 81 times

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Original Uploader

Workflow A workflow version of the EMBOSS tutorial (1)

Created: 03/07/09 @ 14:50:54 | Last updated: 03/07/09 @ 14:51:15

Credits: User Stian Soiland-Reyes

Attributions: Workflow A workflow version of the EMBOSS tutorial

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 106 times | Downloaded: 35 times

This Workflow has no tags!

Original Uploader

Workflow Retrieve sequence in EMBL format (1)

Created: 03/07/09 @ 14:49:48

Credits: User Stian Soiland-Reyes

Attributions: Workflow Retrieve sequence in EMBL format

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 52 times | Downloaded: 29 times

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