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Items tagged with "taverna" (19)

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Packs (1)

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Pack Everything You Need To Know About myExperiment...

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

... but were afraid to ask. This is the pack to go to for all information about myExperiment and the people involved in this project!

9 items in this pack

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Groups (3)

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Network-member myGrid

Unique name: myGrid Created: Friday 30 November 2007 @ 12:19:26 (GMT)

People working or contributing to the myGrid project, including the Taverna developers

11 shared items

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Network-member Taverna workflow workbench examples

Unique name: tavernaExamples Created: Wednesday 05 March 2008 @ 13:45:09 (GMT)

The workflows visible from this group correspond to the examples from the Taverna workflow workbench

11 shared items

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Network-member Taverna 2 beta tester programme

Unique name: t2beta Created: Tuesday 05 August 2008 @ 10:51:32 (BST)

Members of this groups are the participants of the Taverna 2 beta tester programme. If you want to be a beta tester and are not already a member of the group, use the request membership of the group link above.  

6 shared items

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Files (4)

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Blob Taverna tutorial

Created: 03/03/08 @ 11:15:00 | Updated: 03/03/08 @ 11:16:11

Credits: User Franck Tanoh User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 License

A step by step guide on how to build workflows in Taverna.  Biology oriented but  should be ok with other background with a 'tiny'  Biology knowledge.  I welcome your comments and suggestions.

File type: application/vnd.ms-powerpoint

Rating: 4.0 / 5 (1 rating) | Comments: 0 | Viewed: 267 times | Downloaded: 304 times

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Blob Taverna tutorial

Created: 03/03/08 @ 11:05:24 | Updated: 03/03/08 @ 11:20:45

Credits: User Franck Tanoh User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 License

A step by step guide on how to build workflows in Taverna. This tutorial is designed for any background. i welcome your comments and suggestions.

File type: application/vnd.ms-powerpoint

Rating: 4.0 / 5 (2 ratings) | Comments: 3 | Viewed: 365 times | Downloaded: 448 times

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Blob The Data Playground: An Intuitive Workflow Specification Environment

Created: 02/06/08 @ 14:46:40 | Updated: 02/06/08 @ 14:46:40

Credits: User Katy Wolstencroft User Andrew Gibson

License: Creative Commons Attribution-Share Alike 3.0 License

This is a copy of the paper we wrote for the 3rd International Conference on e-Science and Grid Computing 2007 (http://www.escience2007.org/index.asp). It won the Best Paper award!  

File type: application/pdf

Rating: 4.0 / 5 (1 rating) | Comments: 0 | Viewed: 137 times | Downloaded: 139 times

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Blob An Introduction to Taverna Tutorial

Created: 17/06/08 @ 14:17:20 | Updated: 17/06/08 @ 14:17:20

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 License

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File type: application/vnd.ms-powerpoint

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 126 times | Downloaded: 175 times

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Workflows (11)

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Workflow Example of a conditional execution workflow (v1)

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

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 License

Example_of_a_conditional_execution_workflow_7882_1
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.

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

Viewed: 354 times | Downloaded: 247 times

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Workflow BiomartAndEMBOSSAnalysis (v2)

Created: 05/03/08 @ 14:01:16 | Updated: 27/03/08 @ 12:14:09

License: Creative Commons Attribution 3.0 License

Biomartandembossanalysis_32163_2
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: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow A workflow version of the EMBOSS tutorial (v1)

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

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 License

A_workflow_version_of_the_emboss_tutorial_32367_1
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

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Workflow Fetch today's xkcd comic (v1)

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

Credits: User Tomoinn User Stian Soiland-Reyes

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License: Creative Commons Attribution 3.0 License

Fetch_today_s_xkcd_comic_5577_1
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: 4.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 395 times | Downloaded: 262 times

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Workflow Fetch Dragon images from BioMoby (v2)

Created: 05/03/08 @ 14:09:35 | Updated: 25/03/08 @ 14:41:59

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 License

Fetch_dragon_images_from_biomoby_1077_2
Fetch images and annotations of snapdragons

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

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Workflow Demonstration of configurable iteration (v1)

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

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 License

Demonstration_of_configurable_iteration_12320_1
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

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Workflow Retrieve sequence in EMBL format (v2)

Created: 05/03/08 @ 14:11:18 | Updated: 31/03/08 @ 15:19:06

Credits: User Franck Tanoh User Tomoinn

License: Creative Commons Attribution 3.0 License

Retrieve_sequence_in_embl_format_22581_2
This workflow retrieves a sequence associated with its features in embl format given a sequence id.

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

Viewed: 395 times | Downloaded: 299 times

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Workflow Retrieve SNPs from regions around known genes (v1)

Created: 05/03/08 @ 14:12:32 | Updated: 29/07/08 @ 15:18:38

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 License

Retrieve_snps_from_regions_around_known_genes_12046_1
Given a list of Gene IDs this workflow will query against the Ensembl human genome data to fetch the genomic region for each gene, extend that region by 1000bp in each direction and use this set of ranges, one per gene, to build a query against dbSNP to return the SNP identifier and location information (chromosome name, strand and position)

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

Viewed: 175 times | Downloaded: 140 times

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Workflow Fetch PDB flatfile from RCSB server (v1)

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

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 License

Fetch_pdb_flatfile_from_rcsb_server_27474_1
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: 402 times | Downloaded: 458 times

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Workflow GBSeq test (v2)

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

Credits: User Franck Tanoh

License: Creative Commons Attribution 3.0 License

Gbseq_test_23328_2
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: 461 times | Downloaded: 314 times

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Workflow Staged iteration strategy (v1)

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

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 License

Staged_iteration_strategy_11879_1
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: 334 times | Downloaded: 158 times

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