Group: Taverna 1.7.1 workflow workbench examples

Original Uploader

Alan Williams

Example of a conditional execution workflow (v1)

Created: 05/03/08 @ 13:55:45 | Last updated: 25/03/08 @ 14:46:12

Credits: Tomoinn

License: Creative Commons Attribution 3.0 Unported License

If the input is true then the string 'foo' is emited, if false then 'bar'. Just a simple example to show how the monster works, so to speak.

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Viewed: 927 times | Downloaded: 279 times

Original Uploader

Alan Williams

BiomartAndEMBOSSAnalysis (v4)

Created: 15/09/09 @ 15:11:11

License: Creative Commons Attribution 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.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 640 times | Downloaded: 251 times

Original Uploader

Alan Williams

A workflow version of the EMBOSS tutorial (v1)

Created: 05/03/08 @ 14:05:20 | Last updated: 25/03/08 @ 14:43:35

Credits: Tomoinn

License: Creative Commons Attribution 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: 303 times | Downloaded: 104 times

Original Uploader

Alan Williams

Fetch today's xkcd comic (v1)

Created: 05/03/08 @ 14:08:52 | Last updated: 07/04/08 @ 13:54:04

Credits: Tomoinn Stian Soiland-Reyes

Attributions:

License: Creative Commons Attribution 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: 4.5 / 5 (2 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 324 times | Downloaded: 125 times

Original Uploader

Alan Williams

Fetch Dragon images from BioMoby (v3)

Created: 05/03/08 @ 14:09:35 | Last updated: 14/07/10 @ 16:46:37

Credits: Tomoinn

License: Creative Commons Attribution 3.0 Unported License

Fetch images and annotations of snapdragons

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 230 times | Downloaded: 77 times

Original Uploader

Alan Williams

Demonstration of configurable iteration (v1)

Created: 05/03/08 @ 14:10:51 | Last updated: 25/03/08 @ 14:40:27

Credits: Tomoinn

License: Creative Commons Attribution 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.

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Viewed: 203 times | Downloaded: 121 times

Original Uploader

Alan Williams

Retrieve sequence in EMBL format (v3)

Created: 17/06/09 @ 16:51:32

Credits: Franck Tanoh Tomoinn Stuart Owen

License: Creative Commons Attribution 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 246 times | Downloaded: 77 times

Original Uploader

Alan Williams

Fetch PDB flatfile from RCSB server (v1)

Created: 05/03/08 @ 14:13:24 | Last updated: 31/03/08 @ 16:01:41

Credits: Tomoinn

License: Creative Commons Attribution 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: 3.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 224 times | Downloaded: 82 times

Original Uploader

Alan Williams

GBSeq test (v2)

Created: 05/03/08 @ 14:15:35 | Last updated: 31/03/08 @ 15:55:09

Credits: Franck Tanoh

License: Creative Commons Attribution 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: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 188 times | Downloaded: 69 times

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

Comments: 0 | Viewed: 325 times | Downloaded: 153 times

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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Uploader:

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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Uploader:

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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Uploader:

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

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 28 times | Downloaded: 131 times

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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

Comments: 0 | Viewed: 44 times | Downloaded: 3 times

Creator:

Franck Tanoh

Example workflow for KEGG web service

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

14 items in this pack

Comments: 0 | Viewed: 163 times | Downloaded: 26 times

Original Uploader

Katy Wolstencroft

BioMart and Emboss Analysis (T2) (v1)

Created: 15/09/09 @ 15:05:11

Credits: Katy Wolstencroft Alan Williams

Attributions: BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is the Taverna 2 version of the Biomart and Emboss Analysis workflow http://www.myexperiment.org/workflows/158   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. Previous versions of this workflow only returned sequences with an ID mapped to a MIM_morbid_accession. This was primarily to reduce the numbe...

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

Viewed: 176 times | Downloaded: 35 times