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Items tagged with "taverna" (70)

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Groups (7)

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. You do not need to join this group to see the shared items. If you are interested in contributing to myGrid or Taverna development or have questions about Taverna, then please email support@mygrid.org.uk

300 shared items   |   0 announcements

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Network-member Taverna 1.7.1 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 1.7.1 workflow workbench

17 shared items   |   0 announcements

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Network-member Taverna Help

Unique name: taverna-help
Created: Wednesday 07 January 2009 @ 14:54:33 (GMT)

Help and guides for using Taverna Workbench www.mygrid.org.uk/tools/taverna/taverna-2-0/download-taverna-2-0/

0 shared items   |   2 announcements

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Latest announcement:: Linux users

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Network-member Taverna 1 Tutorial

Unique name: taverna1tutorial
Created: Wednesday 14 January 2009 @ 15:10:18 (GMT)

This group was created for anyone who is currently undergoing Taverna 1 training. Please feel free to add your workflows, packs, and files as you wish.

0 shared items   |   0 announcements

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Network-member Newcastle MSc.

Unique name: NewcastleMsc
Created: Wednesday 04 March 2009 @ 14:53:45 (GMT)

This group was create for the Newcastle MSc.

1 shared item   |   0 announcements

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Network-member SADI

Unique name: sadi
Created: Thursday 07 January 2010 @ 00:57:16 (GMT)

No description

2 shared items   |   0 announcements

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Network-member IMPACT-myGrid-Hackathon


Created: Friday 04 November 2011 @ 13:29:38 (GMT)

Group for sharing workflows & resources for the IMPACT-myGrid-hackathon:  http://impact-mygrid-taverna-hackathon.wikispaces.com

15 shared items   |   0 announcements

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Files (8)
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Blob Taverna tutorial

Created: 03/03/08 @ 11:15:00 | Last updated: 03/03/08 @ 11:16:11

Credits: User Franck Tanoh User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported 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: PowerPoint presentation

Rating: 4.0 / 5 (1 rating) | Comments: 0 | Viewed: 102 times | Downloaded: 186 times

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Blob Taverna tutorial

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

Credits: User Franck Tanoh User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported 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: PowerPoint presentation

Rating: 4.0 / 5 (2 ratings) | Comments: 4 | Viewed: 256 times | Downloaded: 428 times

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Blob The Data Playground: An Intuitive Workflow Specifica...

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

Credits: User Katy Wolstencroft User Andrew Gibson

License: Creative Commons Attribution-Share Alike 3.0 Unported 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: Adobe PDF

Rating: 4.0 / 5 (1 rating) | Comments: 0 | Viewed: 107 times | Downloaded: 140 times

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Blob An Introduction to Taverna Tutorial

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

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: PowerPoint presentation

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 69 times | Downloaded: 140 times

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Blob EraSysBio Summer School Taverna Tutorial

Created: 24/07/09 @ 21:54:27

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial is an introduction to Taverna and myExperiment

File type: application/mspowerpoint

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 22 times | Downloaded: 34 times

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Blob Automated Workflows for Accurate Mass-based Putative...

Created: 03/03/11 @ 15:27:04 | Last updated: 03/03/11 @ 15:27:07

Credits: User Marie Brown

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Three workflows, together defined as PUTMEDID-LCMS, have been developed using the open source Taverna environment to perform putative metabolite identification based on accurate mass data acquired from liquid chromatography-electrospray mass spectrometry instruments. Three workflows perform the following steps. (Step 1) Generation of a list of pairwise peak correlations required for input to workflow 2 (workflow 1) (Step 2) Annotation of features to group different ion types of the same metab...

File type: application/x-zip-compressed

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 45 times | Downloaded: 24 times

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Blob Introduction to Taverna and HELIO presentation

Created: 19/04/12 @ 09:00:18

Credits: User Anja Le Blanc

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Introductorily presentation to Taverna for HELIO users. It was given as part of the Taverna workshop for HELIO.

File type: PowerPoint presentation

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 9 times | Downloaded: 9 times

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Blob Bozeman Tutorial

Created: 22/08/12 @ 09:59:37

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial is an introduction to designing and using Taverna workflows and myExperiment. It was created for the workshop "Making Sense of Biological Systems:Using Knowledge Mining to Improve and Validate Models of Living Systems", at Montana State University Aug 2012

File type: PowerPoint presentation

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 5 times | Downloaded: 40 times

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Workflows (51)
Original Uploader

Workflow Example of a conditional execution workflow (1)

Created: 05/03/08 @ 13:55:45 | Last updated: 23/05/12 @ 11:18:50

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

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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. Note that this type of workflow is not suitable for Taverna 2. An alternative mechanism is recommended.

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

Viewed: 1708 times | Downloaded: 500 times

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Workflow BiomartAndEMBOSSAnalysis (4)

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

License: Creative Commons Attribution 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: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 1256 times | Downloaded: 421 times

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Workflow A workflow version of the EMBOSS tutorial (1)

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

Credits: User Tomoinn

License: Creative Commons Attribution 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: 419 times | Downloaded: 144 times

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Original Uploader

Workflow Fetch today's xkcd comic (1)

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

Credits: User Tomoinn User Stian Soiland-Reyes

Attributions:

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

Viewed: 514 times | Downloaded: 188 times

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Original Uploader

Workflow Fetch Dragon images from BioMoby (3)

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

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

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Fetch images and annotations of snapdragons

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

Viewed: 326 times | Downloaded: 112 times

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Original Uploader

Workflow Demonstration of configurable iteration (1)

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

Credits: User Tomoinn

License: Creative Commons Attribution 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: 4.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 296 times | Downloaded: 165 times

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Workflow Retrieve sequence in EMBL format (3)

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

Credits: User Franck Tanoh User Tomoinn User Stuart Owen

License: Creative Commons Attribution 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: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 330 times | Downloaded: 108 times

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Original Uploader

Workflow Fetch PDB flatfile from RCSB server (1)

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

Credits: User Tomoinn

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

Viewed: 307 times | Downloaded: 121 times

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Original Uploader

Workflow GBSeq test (2)

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

Credits: User Franck Tanoh

License: Creative Commons Attribution 3.0 Unported License

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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: 249 times | Downloaded: 93 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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Workflow Analysing workflows (3)

Created: 06/05/09 @ 08:49:59 | Last updated: 06/05/09 @ 08:50:29

Credits: User Wassinki User Pieter Neerincx User Katy Wolstencroft User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflows analyses workflows stored at the myExperiment site. It is used in the paper submitted to the Workshop on Scientific Workflow 2009. The workflow shows the task usage in the Taverna workflows stored at the myExperiment site The amount of services used The amount of local processors used The amount of scripting tasks The amount of sub workflows Furthermore it classifies the local services based on their intended function. The workflow has two inputs: ...

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

Viewed: 168 times | Downloaded: 64 times

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Original Uploader

Workflow Example 3 (1)

Created: 20/10/09 @ 17:00:59

Credits: User Ruben

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Search in the Datenbank SWISS the Sequence 1220173

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

Viewed: 82 times | Downloaded: 30 times

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Original Uploader

Workflow Find/show Taverna's home directory (1)

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

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 24 times | Downloaded: 14 times

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Workflow Get KEGG gene descriptions and pathways (1)

Created: 30/04/10 @ 16:09:29 | Last updated: 30/04/10 @ 16:12:02

Credits: User Nadia Cerezo User Paul Fisher

Attributions: Workflow Get Kegg Gene information

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes a list of KEGG gene identifiers and supplies descriptions associated to said genes + pathways including all genes and the descriptions associated to said pathways. The list_to_string local beanshell scripts merely transform a given list into a string of unique not-null elements separated by new lines (for batch btit use). Note that the input is a real taverna list : multiple values must be declared as multiple values instead of a single string value with distinct identif...

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

Viewed: 852 times | Downloaded: 33 times

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Workflow Sff2Fasta_Blast_ParseBlast (1)

Created: 22/09/10 @ 12:40:55 | Last updated: 22/09/10 @ 13:35:26

Credits: User Barbera van Schaik User Antoine van Kampen User Angela Luijf User Silvia Olabarriaga

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Blast Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blast sequences against a database Parse Blast results http://www.bioinformaticslaboratory.nl/      

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

Viewed: 39 times | Downloaded: 18 times

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Workflow Sff2Fasta_Blat (1)

Created: 22/09/10 @ 13:18:55 | Last updated: 22/09/10 @ 13:35:49

Credits: User Barbera van Schaik User Antoine van Kampen User Angela Luijf User Silvia Olabarriaga

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Blat Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blat sequences against a database http://www.bioinformaticslaboratory.nl/  

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

Viewed: 23 times | Downloaded: 16 times

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Workflow Sff2Fasta_Blast_Blat_ParseBlast (1)

Created: 22/09/10 @ 13:22:57 | Last updated: 22/09/10 @ 13:36:12

Credits: User Barbera van Schaik User Antoine van Kampen User Angela Luijf User Silvia Olabarriaga

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Blast and Blat Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blat sequences against a database Blast sequences against a database Parse Blast results http://www.bioinformaticslaboratory.nl/  

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

Viewed: 39 times | Downloaded: 21 times

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Original Uploader

Workflow [untitled] (1)

Created: 26/04/11 @ 14:50:37 | Last updated: 26/04/11 @ 15:04:28

Credits: User Dennis Leenheer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow allows the user to search for processes that are involved with a certain gene. Using microarray-files (CEL-files), consisting of wild type and KO mice to which a stimulant is induced, the user can get an idea of the processes involved. (This is done using the global test and the literature weighted global test.) The results are then given as a text-file. Warning: workflow is not working (needs some revisions), all input is currently hardcoded! (You will have to change the file...

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

Viewed: 22 times | Downloaded: 15 times

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Workflow BiomartAndEMBOSSDisease (2)

Created: 12/07/11 @ 12:54:05 | Last updated: 19/03/12 @ 15:31:14

Credits: User Katy Wolstencroft

Attributions: Workflow BiomartAndEMBOSSDisease

License: Creative Commons Attribution 3.0 Unported License

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

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

Viewed: 33 times | Downloaded: 21 times

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Workflow EBI_InterproScan_NewServices (1)

Created: 12/07/11 @ 13:02:49 | Last updated: 12/07/11 @ 13:02:50

Credits: User Alan Williams User Katy Wolstencroft

Attributions: Workflow EBI_InterproScan_NewServices

License: Creative Commons Attribution 3.0 Unported License

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text, xml or png. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.

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

Viewed: 21 times | Downloaded: 9 times

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Original Uploader

Workflow Example workflow for REST and XPath activi... (1)

Created: 12/07/11 @ 13:07:58 | Last updated: 12/07/11 @ 13:07:59

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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This workflow fetches weather forecast for the user-specified location. First of all it uses the provided location name to obtain a WOEID ("Where On Earth ID") of that location, then uses that unique identifier to fetch the weather forecast from Yahoo server. Multiple results may be obtained in case there is no unique translation of the location to a WOEID. REST activity is used to perform HTTP requests and fetch data from remote servers; XPath activity is then used to parse the XML data a...

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

Viewed: 29 times | Downloaded: 18 times

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Workflow Multiple choice quiz (1)

Created: 12/07/11 @ 13:46:40 | Last updated: 12/07/11 @ 13:46:42

Credits: User Alan Williams User George

Attributions: Workflow Multiple choice quiz

License: Creative Commons Attribution 3.0 Unported License

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A fun example workflow showing user-interaction and service looping

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

Viewed: 15 times | Downloaded: 11 times

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Original Uploader

Workflow Fetch Dragon images from BioMoby (1)

Created: 12/07/11 @ 13:52:04 | Last updated: 12/07/11 @ 13:52:05

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

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Fetch images and annotations of snapdragons

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

Viewed: 9 times | Downloaded: 8 times

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Workflow Spreadsheet Import Example (1)

Created: 12/07/11 @ 13:57:34 | Last updated: 12/07/11 @ 13:57:36

Credits: User David Withers

Attributions: Workflow Spreadsheed Data Import Example

License: Creative Commons Attribution 3.0 Unported License

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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date. The source data is from http://data.gov.uk/

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

Viewed: 34 times | Downloaded: 27 times

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Workflow Retrieve sequence in EMBL format (1)

Created: 12/07/11 @ 14:01:17 | Last updated: 12/07/11 @ 14:01:18

Credits: User Franck Tanoh

Attributions: Workflow Retrieve sequence in EMBL format

License: Creative Commons Attribution 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: 0 | Citations: 0

Viewed: 10 times | Downloaded: 12 times

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Workflow Pipelined list iteration (1)

Created: 12/07/11 @ 14:04:39 | Last updated: 12/07/11 @ 14:04:41

Credits: User Ian Dunlop User Stian Soiland-Reyes

Attributions: Workflow Pipelined list iteration

License: Creative Commons Attribution 3.0 Unported License

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Perform multiple iterations of services in order to show pipelining

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

Viewed: 11 times | Downloaded: 6 times

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Workflow GBSeq test (1)

Created: 12/07/11 @ 14:08:40 | Last updated: 12/07/11 @ 14:08:41

Credits: User Franck Tanoh

Attributions: Workflow GBSeq test

License: Creative Commons Attribution 3.0 Unported License

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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

Viewed: 12 times | Downloaded: 6 times

Tags (2):

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Workflow Fetch today's xkcd comic (1)

Created: 12/07/11 @ 14:13:35 | Last updated: 12/07/11 @ 14:13:36

Credits: User Tomoinn User Stian Soiland-Reyes

Attributions: Workflow Fetch today's xkcd comic

License: Creative Commons Attribution 3.0 Unported License

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Use the local services 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: 34 times | Downloaded: 17 times

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Workflow Fetch PDB flatfile from RCSB server (1)

Created: 12/07/11 @ 14:37:08 | Last updated: 12/07/11 @ 14:37:10

Credits: User Alan Williams User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

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Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

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

Viewed: 24 times | Downloaded: 10 times

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Workflow Demonstration of configurable iteration (1)

Created: 12/07/11 @ 14:40:22 | Last updated: 12/07/11 @ 14:40:24

Credits: User Alan Williams User Tomoinn

License: Creative Commons Attribution 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: 17 times | Downloaded: 4 times

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Workflow BioMoby tutorial workflow (1)

Created: 12/07/11 @ 15:50:21 | Last updated: 12/07/11 @ 15:50:22

Credits: User EdwardKawas

License: Creative Commons Attribution 3.0 Unported License

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A workflow from part of the BioMoby tutorial

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

Viewed: 19 times | Downloaded: 12 times

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Workflow A workflow version of the EMBOSS tutorial (1)

Created: 12/07/11 @ 15:55:06 | Last updated: 12/07/11 @ 15:55:08

Credits: User Tomoinn

Attributions: Workflow A workflow version of the EMBOSS tutorial

License: Creative Commons Attribution 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: 21 times | Downloaded: 8 times

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Workflow Unix tool service using string replacement (1)

Created: 13/07/11 @ 10:19:35 | Last updated: 13/07/11 @ 10:19:37

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The tool service outputs a message that greets using the names specified on Greet's input ports.

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

Viewed: 14 times | Downloaded: 10 times

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Workflow Unix tools with zip, unzip and diff (1)

Created: 13/07/11 @ 10:21:10 | Last updated: 13/07/11 @ 10:22:52

Credits: User Alan Williams User Steffen Möller

Attributions: Workflow Example for external tools with gzip and gunzip

License: Creative Commons Attribution 3.0 Unported License

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This workflow only works on a Unix machine. This workflow takes a fixed URL from which a text file is downloaded (output as Original_file). That file is zipped (output as Zipped_File) and then unzipped again (output as Unzipped_File). The orginal file and the unzipped version are then diff'd/

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Workflow Unix tool for numerically adding two values. (1)

Created: 13/07/11 @ 10:24:40 | Last updated: 13/07/11 @ 10:25:37

Credits: User Alan Williams User Steffen Möller

License: Creative Commons Attribution 3.0 Unported License

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This workflow relies on a Unix system. It wraps the "bc" command line calculator. It downloads the calculation script from a URL.

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

Viewed: 30 times | Downloaded: 14 times

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Workflow Secure REST service call example (1)

Created: 14/07/11 @ 15:01:03 | Last updated: 14/07/11 @ 15:01:05

Credits: User Alex Nenadic

License: Creative Commons Attribution 3.0 Unported License

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This is an example of a workflow that contains a call to a secure REST service that requires user to authenticate with HTTP Basic Authentication. You can use testuser/testpasswd as username and password for authentication when running the workflow.

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Workflow Secure Web service call example (1)

Created: 14/07/11 @ 15:02:36 | Last updated: 14/07/11 @ 15:02:38

Credits: User Alex Nenadic

License: Creative Commons Attribution 3.0 Unported License

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This is an example of a workflow that contains a call to a secure Web service that runs behind HTTPS and requires user to authenticate. The first thing you can expect to see is a pop up dialog asking if you trust the Web service to be invoked over HTTPS. You can use testuser/testpasswd as username and password for authentication when running the workflow. To see where the security is being configured, right-click the service in the diagram and select "Configure security" from the menu.

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Workflow Example of Execute_SQL_Query with parameters (1)

Created: 16/03/12 @ 14:12:35 | Last updated: 16/03/12 @ 14:16:18

Credits: User Helen Hulme

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow connects to a mysql on localhost, queries the "world" database which is one of the test databases on MySQL 5.5, queries it about which countries have Dutch as a language, and emits answers in both Lists and in xml. This workflow is intended as an example to help you see the syntax for the various inputs to this local service beanshell. see: http://www.mygrid.org.uk/dev/wiki/display/taverna/Execute+SQL+Query for instructions on jars, dependencies etc. The jar used he...

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Workflow Run sextractor using a votable (2)

Created: 26/07/12 @ 11:23:30 | Last updated: 07/09/12 @ 12:25:41

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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It runs sextractor and adjust the paramenters specified. This workflow has a dependency on the stil library (http://www.star.bris.ac.uk/~mbt/stil/). Sextractor is called by an bash script as 'sex'. Sextractor is called for every row in the votable. Columns where the configuration file and the image file name are defined must be especified. These files should be accesibles from taverna. ExperimentFolder provides the root folder for the experiment. If the configuration files contain refer...

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

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Workflow Create votable from sextractor results (2)

Created: 26/07/12 @ 11:39:53 | Last updated: 21/08/12 @ 08:20:36

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The workflow creates a votable from the results provided by sextractor (votables). It returns this table and an aditional table that is joined to the input table. It requires a votable that contains a column with the file name resulting from running sextractor and such files accesible from taverna. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/).

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

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Workflow Ajusting galaxy paramenters using sextractor (5)

Created: 26/07/12 @ 12:02:48 | Last updated: 07/09/12 @ 12:29:00

Credits: User Julian Garrido

Attributions: Workflow Create configuration files from a template and a votable Workflow Run sextractor using a votable Workflow Create votable from sextractor results Workflow Add columns to a votable resulting from executing sextractor.

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow creates configuration files for sextractor, it runs sextractor using this configuration files, it adds sextractor results to the input votable and adds new calculated columns. This task requires a votable as input, a template, a vocabulary and the specification of the column names that contain some required files (configuration files, image files, ...). These files must be accesible from taverna. Sextractor is called by an bash script as 'sex'. Every row in the votable cotains ...

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

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Workflow Run galfit using a votable (2)

Created: 26/07/12 @ 12:20:52 | Last updated: 07/09/12 @ 12:39:42

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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It runs galfit and adjust the paramenters specified. This workflow has a dependency on the stil library (http://www.star.bris.ac.uk/~mbt/stil/). Galfit is called by a bash script as 'galfit'. Galfit is called for every row in the votable. Columns where the result file name and the configuration file name are defined must be especified. These files should be accesibles from taverna. ExperimentFolder provides the root folder for the experiment. If the configuration files contain references to o...

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

Viewed: 9 times | Downloaded: 8 times

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Workflow Create votable from galfit results (4)

Created: 26/07/12 @ 12:27:41 | Last updated: 07/09/12 @ 12:47:12

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The workflow creates a votable from the results provided by galfit. It returns this table and an aditional table that is joined to the input table. It requires a votable that contains a column with the file name resulting from running galfit and such files must be accesible from taverna. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/) and it has a dependency on stil library (http://www.star.bris.ac.uk/~mbt/stil/).

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

Viewed: 11 times | Downloaded: 7 times

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Workflow Create galfit configuration files with par... (1)

Created: 26/07/12 @ 12:41:51 | Last updated: 26/07/12 @ 12:44:09

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow creates galfit configuration files using a partition criteria. The resulting configuration files are different depending on whether the galaxy has o doesn't have a bar. They are created (one for every row in the votable) using a template whose keys are replaced by data from a votable. Keys must appear also in the vocabulary file and match column names in the votable. A column in the votable must contain the name of the result configuration file. This workflow uses astrotaverna ...

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Viewed: 85 times | Downloaded: 8 times

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Workflow Adjusting galaxy parameters using galfit (4)

Created: 26/07/12 @ 12:56:18 | Last updated: 07/09/12 @ 12:57:59

Credits: User Julian Garrido

Attributions: Workflow Create configuration files from a template and a votable Workflow Run galfit using a votable Workflow Create votable from galfit results Workflow Create votable from different galfit paramenter adjustments Workflow Create galfit configuration files with partition criteria using votable

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow creates galfit configuration files using data from a votable, it runs galfit, its results is added to the votable, it creates new config files for galfit using the previous results, it runs galfit a second time considering galaxies that have and do not have bars in order to adjust the objective parameters and it finally includes the results into the votable. It requires the specification of the columns that contain file names (these files should be accesibles from taverna). If t...

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

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Workflow Create votable from different galfit param... (2)

Created: 21/08/12 @ 09:15:17 | Last updated: 07/09/12 @ 12:56:08

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The workflow creates a votable from the results provided by galfit. It returns this table and an aditional table that is joined to the input table. It requires a votable that contains a column with the file name resulting from running galfit and such files must be accesible from taverna. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/) and it has a dependency on stil library (http://www.star.bris.ac.uk/~mbt/stil/). The galfit files may come from adjusting 'disk, bulb, ba...

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

Viewed: 9 times | Downloaded: 6 times

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Workflow Read file from S3 bucket (1)

Created: 23/08/12 @ 15:46:21

Credits: User Robert Haines

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow simply loads a text file that is stored in an AWS S3 bucket. It is provided as an example of how to do this, rather than be a complete, reusable solution. You need to have s3fs installed and configured with your AWS credentials to use this workflow (see http://code.google.com/p/s3fs/).

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

Viewed: 17 times | Downloaded: 1 time

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Workflow Write file to S3 bucket (1)

Created: 23/08/12 @ 15:50:50

Credits: User Robert Haines

Attributions: Workflow Read file from S3 bucket

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow simply writes a text file to an AWS S3 bucket. It is provided as an example of how to do this, rather than be a complete, reusable solution. You need to have s3fs installed and configured with your AWS credentials to use this workflow (see http://code.google.com/p/s3fs/).

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

Viewed: 7 times | Downloaded: 0 times

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Workflow Add columns to a votable resulting from ex... (1)

Created: 30/08/12 @ 09:33:55

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Addcolumns that are needed to run galfit and ellipse. it requires columns coming from sextractor and the astrotaverna plugin.

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Workflow Build plots from galfit and ellipse results (2)

Created: 30/08/12 @ 09:51:58 | Last updated: 07/09/12 @ 13:33:55

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Build plots from galfit and ellipse results (http://www.myexperiment.org/workflows/3068.html, http://www.myexperiment.org/workflows/3052.html).

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

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Workflow Detect ellipse failures and get votable wi... (1)

Created: 07/09/12 @ 13:26:05

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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It detects if ellipse has failed by checking if the resulting data file exists. It adds a column (validellipse) that contains 1 if ellipse didn't fail and 0 if ellipse failed. It returns a votable that contains all the data with the new column and a votable that contains only the rows where ellipse didn't failed. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/).

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Viewed: 11 times | Downloaded: 3 times

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Packs (4)
Creator

Pack Everything You Need To Know About myExperiment...


Created: 02/07/08 @ 22:31:12 | Last updated: 02/07/08 @ 23:12:37

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

8 items in this pack

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Pack Carole's Keynotes


Created: 27/09/08 @ 19:52:17 | Last updated: 08/05/10 @ 20:24:47

Carole Goble's 2008 keynote talks that feature myExperiment, in PowerPoint 97-2003 format. All myExperiment presentation can be found on the wiki on http://wiki.myexperiment.org/index.php/Presentations  

5 items in this pack

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Pack Trial Pack for UT UCD


Created: 11/06/12 @ 12:06:57 | Last updated: 17/06/12 @ 14:46:28

 This is a trial for usability testing.

1 item in this pack

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Pack Provenance of a Taverna and Vistrails workflows


Created: 06/08/12 @ 11:02:31 | Last updated: 07/08/12 @ 19:45:23

 This Packs contains the specification of a workflow that retrieves pathways given gene identifiers in both Taverna and Vistrails. The pack also contains provenance traces of those workflows.

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