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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 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 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 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 Demonstration of configurable iteration (1)

Created: 03/07/09 @ 14:32:26 | Last updated: 03/07/09 @ 14:33:01

Credits: User Stian Soiland-Reyes User Tomoinn

Attributions: Workflow Demonstration of configurable iteration

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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

Viewed: 92 times | Downloaded: 71 times

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Original Uploader

Workflow Execute cmd line app - unix - /bin/ls of t... (1)

Created: 27/09/08 @ 16:52:16

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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Note that this workflow only works on Unix systems. The get_temporary_directory beanshell returns the path to the directory in which temporary files are held. This value is passed to the args port of the execute_cmd_line_app service. The command port of that service has been defaulted to '/bin/ls'. The execute_cmd_line_app service runs the /bin/ls command on the temporary directory. The result is passed to its result port and then to the out port of the workflow.

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

Viewed: 52 times | Downloaded: 50 times

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Original Uploader

Workflow Dummy example of looping (2)

Created: 27/01/10 @ 15:52:50 | Last updated: 27/01/10 @ 15:56:10

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution 3.0 Unported License

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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. ...

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

Viewed: 168 times | Downloaded: 75 times

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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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