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Items tagged with "taverna" (89)

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Files (9)
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Blob Taverna tutorial

Created: 2008-03-03 11:15:00 | Last updated: 2008-03-03 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

Comments: 0 | Viewed: 164 times | Downloaded: 258 times

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Uploader

Blob Taverna tutorial

Created: 2008-03-03 11:05:24 | Last updated: 2008-03-03 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

Comments: 4 | Viewed: 431 times | Downloaded: 638 times

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

Created: 2008-06-02 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

Comments: 0 | Viewed: 187 times | Downloaded: 214 times

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Blob An Introduction to Taverna Tutorial

Created: 2008-06-17 14:17:20

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: PowerPoint presentation

Comments: 0 | Viewed: 88 times | Downloaded: 208 times

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Blob EraSysBio Summer School Taverna Tutorial

Created: 2009-07-24 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

Comments: 0 | Viewed: 41 times | Downloaded: 52 times

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

Created: 2011-03-03 15:27:04 | Last updated: 2011-03-03 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

Comments: 0 | Viewed: 111 times | Downloaded: 83 times

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Blob Introduction to Taverna and HELIO presentation

Created: 2012-04-19 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

Comments: 0 | Viewed: 35 times | Downloaded: 43 times

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Blob Bozeman Tutorial

Created: 2012-08-22 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

Comments: 0 | Viewed: 27 times | Downloaded: 55 times

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Blob Introduction to Taverna Components - Bonn 2013

Created: 2013-09-06 07:39:49

Credits: User Aleksandra Pawlik User Stian Soiland-Reyes User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is an introductory tutorial about Taverna Components to be used for the workshop at Bonn University 4-6 September 2013. Please note that as components are still under development some details presented in this tutorial may change in the future.

File type: PowerPoint 2007 presentation

Comments: 0 | Viewed: 31 times | Downloaded: 47 times

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Groups (10)

Network-member myGrid

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

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

376 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 (UTC)

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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Owner

Network-member Taverna Help

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

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

Members (1):

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Latest announcement:: Linux users

Owner

Network-member Taverna 1 Tutorial

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

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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Owner

Network-member Newcastle MSc.

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

This group was create for the Newcastle MSc.

1 shared item   |   0 announcements

Members (23):

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Network-member SADI

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

No description

2 shared items   |   0 announcements

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Owner

Network-member IMPACT-myGrid-Hackathon


Created: Friday 04 November 2011 13:29:38 (UTC)

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

11 shared items   |   0 announcements

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Network-member BioVel Training 5-6 Dec 2013 Manchester

Unique name: biovel-5-12-2013
Created: Thursday 21 November 2013 16:02:27 (UTC)

This is a group for all participants of the BioVel training workshop in Manchester, 5-6 December 2013. You should have Taverna Workbench installed on your machines. There is also a discipline-specific Taverna Workbench version which can be downloaded from here. Timetable:Thursday, 5th December 10.00 - 10.30 Arrival, Setup and Coffee10.30 - 11.00 Introductions: round tab...

24 shared items   |   0 announcements

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Network-member BioVel Workshop June 2014

Unique name: biovel-jun14
Created: Thursday 08 May 2014 10:32:28 (UTC)

This group is for BioVel training 4-5 June 2014 in Manchester

1 shared item   |   0 announcements

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Network-member Bonn Workshop Sep 2014

Unique name: Bonn2014
Created: Wednesday 27 August 2014 13:24:58 (UTC)

This group is for the attendees of the lab course "In silico experimentation using e-labs" at BonnUniversity, September 2014

33 shared items   |   0 announcements

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Packs (9)
Creator

Pack Everything You Need To Know About myExperiment...


Created: 2008-07-02 22:31:12 | Last updated: 2008-07-02 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!

9 items in this pack

Comments: 0 | Viewed: 281 times | Downloaded: 62 times

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Creator

Pack Carole's Keynotes


Created: 2008-09-27 19:52:17 | Last updated: 2010-05-08 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

Comments: 0 | Viewed: 446 times | Downloaded: 39 times

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Creator

Pack Trial Pack for UT UCD


Created: 2012-06-11 12:06:57 | Last updated: 2012-06-17 14:46:28

 This is a trial for usability testing.

2 items in this pack

Comments: 0 | Viewed: 29 times | Downloaded: 11 times

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Pack Provenance of a Taverna and Vistrails workflows


Created: 2012-08-06 11:02:31 | Last updated: 2012-08-07 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.

5 items in this pack

Comments: 0 | Viewed: 36 times | Downloaded: 10 times

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Creator

Pack Astronomy Taverna 2.5 starter pack


Created: 2014-03-03 17:02:08 | Last updated: 2014-03-03 17:16:57

This is a set of small snippets using Astronomy Taverna. The purpose of this pack is to make the design and development of astronomy Virtual Observatory workflows easier, learning by the example. Additionally, you can find other Astronomy related workflows and snippets related to general functionalities of Taverna. 

45 items in this pack

Comments: 0 | Viewed: 61 times | Downloaded: 7 times

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Creator

Pack Taverna 2.5 Bioinformatics Starter Pack


Created: 2014-04-02 12:44:47 | Last updated: 2017-01-09 13:08:53

This is a Starter Pack for Taverna 2.5 Bioinformatics edition - it contains a number of example workflows to showcase various features of Taverna 2.5 Bioinformatics and help you get started using it.Workflows from this Starter pack can also be found in the myExperiment perspective of the Taverna Workbench.Tutorials for Taverna are available under the Taverna 2.x documentation on the Taverna Web site.Also check out the Taverna User Manual.

18 items in this pack

Comments: 0 | Viewed: 48 times | Downloaded: 15 times

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Creator

Pack Taverna 2.5 Biodiversity Starter Pack


Created: 2014-04-02 12:40:42 | Last updated: 2017-01-09 13:09:17

This is a Starter Pack for Taverna 2.5 Biodiversity edition - it contains a number of example workflows to showcase various features of Taverna 2.5 Biodiversity and help you get started using it.Workflows from this Starter pack can also be found in the myExperiment perspective of the Taverna Workbench.Tutorials for Taverna are available under the Taverna 2.x documentation on the Taverna Web site.Also check out the Taverna User Manual.

14 items in this pack

Comments: 0 | Viewed: 42 times | Downloaded: 7 times

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Creator

Pack Taverna 2.5 Core Starter Pack


Created: 2014-04-02 11:32:18 | Last updated: 2017-01-09 13:09:40

This is a Starter Pack for Taverna 2.5 Core edition - it contains a number of example workflows to showcase various features of Taverna 2.5 Core and help you get started using it.Workflows from this Starter pack can also be found in the myExperiment perspective of the Taverna Workbench.Tutorials for Taverna are available under the Taverna 2.x documentation on the Taverna Web site.Also check out the Taverna User Manual.

14 items in this pack

Comments: 0 | Viewed: 60 times | Downloaded: 8 times

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Creator

Pack Taverna 2.5 Enterprise Starter Pack


Created: 2014-04-02 12:54:33 | Last updated: 2017-01-09 12:01:51

This is a Starter Pack for Taverna 2.5 Enterprise edition - it contains a number of example workflows to showcase various features of Taverna 2.5 Enterprise and help you get started using it.Workflows from this Starter pack can also be found in the myExperiment perspective of the Taverna Workbench.Tutorials for Taverna are available under the Taverna 2.x documentation on the Taverna Web site.Also check out the Taverna User Manual.

18 items in this pack

Comments: 1 | Viewed: 160 times | Downloaded: 131 times

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Workflows (61)

Workflow Example of a conditional execution workflow (1)

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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.

Created: 2008-03-05 | Last updated: 2012-05-23

Credits: User Tomoinn

Workflow BiomartAndEMBOSSAnalysis (4)

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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.

Created: 2009-09-15 | Last updated: 2015-01-26

Workflow A workflow version of the EMBOSS tutorial (1)

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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.

Created: 2008-03-05 | Last updated: 2008-03-25

Credits: User Tomoinn

Workflow Fetch today's xkcd comic (1)

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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.

Created: 2008-03-05 | Last updated: 2008-04-07

Credits: User Tomoinn User Stian Soiland-Reyes

Attributions:

Workflow Fetch Dragon images from BioMoby (3)

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Fetch images and annotations of snapdragons

Created: 2008-03-05 | Last updated: 2010-07-14

Credits: User Tomoinn

Workflow Demonstration of configurable iteration (1)

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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.

Created: 2008-03-05 | Last updated: 2008-03-25

Credits: User Tomoinn

Workflow Retrieve sequence in EMBL format (3)

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

Created: 2009-06-17

Credits: User Franck Tanoh User Tomoinn User Stuart Owen

Workflow Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.

Created: 2008-03-05 | Last updated: 2008-03-31

Credits: User Tomoinn

Workflow GBSeq test (2)

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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.

Created: 2008-03-05 | Last updated: 2008-03-31

Credits: User Franck Tanoh

Workflow Staged iteration strategy (1)

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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 ...

Created: 2008-05-07 | Last updated: 2008-05-07

Credits: User Stian Soiland-Reyes

Uploader

Workflow Analysing workflows (3)

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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: ...

Created: 2009-05-06 | Last updated: 2009-05-06

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

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Workflow Example 3 (1)

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Search in the Datenbank SWISS the Sequence 1220173

Created: 2009-10-20

Credits: User Ruben

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

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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() ...

Created: 2010-04-12 | Last updated: 2010-04-12

Credits: User Stian Soiland-Reyes

Workflow Get KEGG gene descriptions and pathways (1)

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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...

Created: 2010-04-30 | Last updated: 2010-04-30

Credits: User Nadia Cerezo User Paul Fisher

Attributions: Workflow Get Kegg Gene information

Workflow Sff2Fasta_Blast_ParseBlast (1)

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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/      

Created: 2010-09-22 | Last updated: 2010-09-22

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

Workflow Sff2Fasta_Blat (1)

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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/  

Created: 2010-09-22 | Last updated: 2010-09-22

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

Workflow Sff2Fasta_Blast_Blat_ParseBlast (1)

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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/  

Created: 2010-09-22 | Last updated: 2010-09-22

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

Workflow [untitled] (1)

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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...

Created: 2011-04-26 | Last updated: 2011-04-26

Credits: User Dennis Leenheer

Workflow BiomartAndEMBOSSDisease (2)

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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.

Created: 2011-07-12 | Last updated: 2012-03-19

Credits: User Katy Wolstencroft

Attributions: Workflow BiomartAndEMBOSSDisease

Workflow EBI_InterproScan_NewServices (1)

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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.

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Alan Williams User Katy Wolstencroft

Attributions: Workflow EBI_InterproScan_NewServices

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

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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...

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Alan Williams

Workflow Multiple choice quiz (1)

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A fun example workflow showing user-interaction and service looping

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Alan Williams User George

Attributions: Workflow Multiple choice quiz

Workflow Fetch Dragon images from BioMoby (1)

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Fetch images and annotations of snapdragons

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Tomoinn

Workflow Spreadsheet Import Example (1)

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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/

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User David Withers

Attributions: Workflow Spreadsheed Data Import Example

Workflow Retrieve sequence in EMBL format (1)

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

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Franck Tanoh

Attributions: Workflow Retrieve sequence in EMBL format

Workflow Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Ian Dunlop User Stian Soiland-Reyes

Attributions: Workflow Pipelined list iteration

Workflow GBSeq test (1)

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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.

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Franck Tanoh

Attributions: Workflow GBSeq test

Workflow Fetch today's xkcd comic (1)

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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.

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Tomoinn User Stian Soiland-Reyes

Attributions: Workflow Fetch today's xkcd comic

Workflow Fetch PDB flatfile from RCSB server (1)

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

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Alan Williams User Tomoinn

Workflow Demonstration of configurable iteration (1)

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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.

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Alan Williams User Tomoinn

Workflow BioMoby tutorial workflow (1)

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A workflow from part of the BioMoby tutorial

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User EdwardKawas

Workflow A workflow version of the EMBOSS tutorial (1)

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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.

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Tomoinn

Attributions: Workflow A workflow version of the EMBOSS tutorial

Workflow Unix tool service using string replacement (1)

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

Created: 2011-07-13 | Last updated: 2011-07-13

Credits: User Alan Williams

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

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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/

Created: 2011-07-13 | Last updated: 2011-07-13

Credits: User Alan Williams User Steffen Möller

Attributions: Workflow Example for external tools with gzip and gunzip

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

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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.

Created: 2011-07-13 | Last updated: 2011-07-13

Credits: User Alan Williams User Steffen Möller

Workflow Secure REST service call example (1)

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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.

Created: 2011-07-14 | Last updated: 2011-07-14

Credits: User Alex Nenadic

Workflow Secure Web service call example (1)

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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.

Created: 2011-07-14 | Last updated: 2011-07-14

Credits: User Alex Nenadic

Workflow Example of Execute_SQL_Query with parameters (1)

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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...

Created: 2012-03-16 | Last updated: 2012-03-16

Credits: User Helen Hulme

Workflow Run sextractor using a votable (2)

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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...

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: User Julian Garrido

Workflow Create votable from sextractor results (2)

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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/).

Created: 2012-07-26 | Last updated: 2012-08-21

Credits: User Julian Garrido

Workflow Ajusting galaxy paramenters using sextractor (5)

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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 ...

Created: 2012-07-26 | Last updated: 2012-09-07

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.

Workflow Run galfit using a votable (2)

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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...

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: User Julian Garrido

Workflow Create votable from galfit results (4)

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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/).

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: User Julian Garrido

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

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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 ...

Created: 2012-07-26 | Last updated: 2012-07-26

Credits: User Julian Garrido

Workflow Adjusting galaxy parameters using galfit (4)

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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...

Created: 2012-07-26 | Last updated: 2012-09-07

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

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

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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...

Created: 2012-08-21 | Last updated: 2012-09-07

Credits: User Julian Garrido

Workflow Read file from S3 bucket (1)

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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/).

Created: 2012-08-23

Credits: User Robert Haines

Workflow Write file to S3 bucket (1)

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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/).

Created: 2012-08-23

Credits: User Robert Haines

Attributions: Workflow Read file from S3 bucket

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

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

Created: 2012-08-30

Credits: User Julian Garrido

Workflow Build plots from galfit and ellipse results (2)

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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).

Created: 2012-08-30 | Last updated: 2012-09-07

Credits: User Julian Garrido

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

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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/).

Created: 2012-09-07

Credits: User Julian Garrido

Workflow GET statuses/home_timeline | Twitter (1)

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Returns a collection of the most recent tweets and retweets posted by the authenticating user and the users they follow. Uses the OAuth plugin for Taverna Workbench.

Created: 2013-01-22

Credits: User Mark Borkum

Workflow raw2nexus taverna 2 workflow using pt-mapr... (5)

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No description

Created: 2013-12-12 | Last updated: 2014-06-20

Credits: User Alastairduncan

Workflow Simple FASTA workflow (1)

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A simple Taverna workflo

Created: 2014-01-22

Credits: User Aleksandra Pawlik User Katy Wolstencroft User Alan Williams

Workflow simple fasta workflow (1)

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workflow using services

Created: 2014-01-22

Credits: User Ruth Eberhardt User Aleksandra Pawlik

Workflow P15409 (1)

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worflow to demostrate how to use Taverna with service anel or catalogue

Created: 2014-01-22

Credits: User Lilly Hueber

Workflow PDF Read (1)

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Read a PDF from a URL

Created: 2014-01-24

Credits: User Robert Haines User Alan Williams

Workflow Empty list output and a value (1)

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Simply returns a port, depth 1, with nothing in it and a port, depth 0, with a constant.

Created: 2014-01-24

Credits: User Robert Haines User Alan Williams

Workflow Empty list output (1)

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Simply returns a single port, depth 1, with nothing in it.

Created: 2014-01-24

Credits: User Robert Haines User Alan Williams

Workflow Visualize PAV provenance as SVG (1)

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VoID descriptions are fetched as Turtle, cleaned up to be valid OWL ontology and include useful labels, processed through the OWL reasoner Pellet; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox, generating an SVG visualization of the provenance. Note that this workflow downloads CWM, Pellet and ProvToolbox on demand, and uses UNIX command line tools like wget and md5 which are unlikely to work in Windows. This workflow has been tested on Ubuntu 12.10 wit...

Created: 2014-05-08

Credits: User Katy Wolstencroft User Aleksandra Pawlik

Workflow Taverna wf vs compss wf (1)

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No description

Created: 2015-03-24

Credits: User Pablo Martin

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Linked Data

Non-Information Resource URI: http://www.myexperiment.org/tags/663


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