Group: myGrid

Creator:

Jiten Bhagat

Everything You Need To Know About myExperiment...

Created: 02/07/08 @ 22:31:12 | Last updated: 02/07/08 @ 23:11:22

9 items in this pack

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Creator:

Alan Williams

Taverna 1.7 starter pack

Created: 17/07/08 @ 21:06:12 | Last updated: 26/06/09 @ 10:40:01

16 items in this pack

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Uploader:

Alan Williams

Example Genbank data

Created: 25/09/08 @ 15:00:28

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Alan Williams

Example SwissProt Data

Created: 25/09/08 @ 15:09:03

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Alan Williams

Example XML file

Created: 26/09/08 @ 12:12:41

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

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Alan Williams

Example XSLT file

Created: 26/09/08 @ 12:13:31

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Binary data

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Creator:

Alan Williams

Taverna localworker example pack

Created: 27/09/08 @ 17:57:39 | Last updated: 27/09/08 @ 18:23:50

103 items in this pack

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Creator:

Franck Tanoh

Example workflows for annotated web services

Created: 29/09/08 @ 11:57:45 | Last updated: 29/09/08 @ 11:59:09

1 item in this pack

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Creator:

Franck Tanoh

Example workflow for KEGG web service

Created: 29/09/08 @ 13:28:02

14 items in this pack

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Creator:

Stian Soiland-Reyes

Taverna 2.1 beta 2 example workflows

Created: 26/06/09 @ 13:59:43 | Last updated: 17/12/09 @ 17:08:41

9 items in this pack

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Original Uploader

Stian Soiland-Reyes

EBI_InterProScan for Taverna 2 (v2)

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

Credits: Stian Soiland-Reyes Paolo Katy Wolstencroft Hamish McWilliam

Attributions: EBI InterproScan T2 EBI_InterProScan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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: 83 times | Downloaded: 60 times

Creator:

Stian Soiland-Reyes

Taverna 2.1 beta 2

Created: 02/07/09 @ 12:51:11 | Last updated: 03/07/09 @ 15:39:08

6 items in this pack

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Original Uploader

Stian Soiland-Reyes

EBI_InterProScan for Taverna 2 (v2)

Created: 26/01/10 @ 14:45:46

Credits: Stian Soiland-Reyes Katy Wolstencroft Paolo Hamish McWilliam

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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: 139 times | Downloaded: 81 times

Original Uploader

Stian Soiland-Reyes

Biomart and EMBOSS analysis (v1)

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

Credits: Stian Soiland-Reyes

Attributions: BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

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Original Uploader

Stian Soiland-Reyes

Demonstration of configurable iteration (v1)

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

Credits: Stian Soiland-Reyes Tomoinn

Attributions: Demonstration of configurable iteration

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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: 62 times | Downloaded: 52 times

Original Uploader

Stian Soiland-Reyes

Fetch PDB flatfile from RCSB server (v1)

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

Credits: Stian Soiland-Reyes

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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: 32 times | Downloaded: 17 times

Original Uploader

Stian Soiland-Reyes

Fetch today's xkcd comic (v1)

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

Credits: Stian Soiland-Reyes

Attributions: Fetch today's xkcd comic

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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Original Uploader

Stian Soiland-Reyes

GBSeq test (v1)

Created: 03/07/09 @ 14:48:38

Credits: Stian Soiland-Reyes

Attributions: GBSeq test

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

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

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Original Uploader

Stian Soiland-Reyes

Retrieve sequence in EMBL format (v1)

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

Credits: Stian Soiland-Reyes

Attributions: Retrieve sequence in EMBL format

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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This Workflow has no tags!

Original Uploader

Stian Soiland-Reyes

A workflow version of the EMBOSS tutorial (v1)

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

Credits: Stian Soiland-Reyes

Attributions: A workflow version of the EMBOSS tutorial

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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: 71 times | Downloaded: 21 times

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Original Uploader

Stian Soiland-Reyes

Pipelined list iteration (v1)

Created: 03/07/09 @ 14:59:53

Credits: Stian Soiland-Reyes Ian Dunlop

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Perform multiple iterations of services in order to show pipelining

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

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Original Uploader

Stian Soiland-Reyes

Dummy example of looping (v2)

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

Credits: Stian Soiland-Reyes

License: Creative Commons Attribution 3.0 Unported License

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: 62 times | Downloaded: 14 times

Original Uploader

Stian Soiland-Reyes

Find/show Taverna's home directory (v1)

Created: 12/04/10 @ 15:11:47 | Last updated: 12/04/10 @ 15:17:57

Credits: Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Find Taverna's home directory and open that folder using Explorer/Finder/Gnome. This is the folder that is typically something like C:\Users\stain\AppData\Roaming\taverna-2.1.2, C:\Documents and settings\stain\taverna-2.1.2, /home/stain/.taverna-2.1.2 or /Users/stain/Library/Application support/taverna-2.1.2 This workflow should work on both Taverna 1 and Taverna 2. For Taverna 2 the beanshell script uses reflection to try to call ApplicationRuntime.getInstance().getApplicationHome() ...

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

Viewed: 8 times | Downloaded: 3 times

Creator:

Alan Williams

Taverna 2.2 starter pack

Created: 11/06/10 @ 13:40:05 | Last updated: 07/07/10 @ 12:06:58

16 items in this pack

Comments: 0 | Viewed: 20 times | Downloaded: 8 times

Uploader:

Marco Roos

From biologist to web service to Taverna to myExperiment to biologist

Created: 21/03/08 @ 19:00:12 | Last updated: 23/03/08 @ 10:39:27

Credits: Marco Roos Martijn Schuemie AID myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: AVI video

Rating: 1.0 / 5 (1 rating) | Comments: 1 | Viewed: 143 times | Downloaded: 158 times