Gb User: Alan Williams Admin_badge

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Name: Alan Williams

Joined: Monday 23 July 2007 13:06:43 (UTC)

Last seen: Monday 10 May 2021 10:31:05 (UTC)

Email (public): alan.r.williams [at] manchester.ac.uk

Website: http://www.taverna.org.uk

Location: Manchester, United Kingdom

Alan Williams has been credited 237 times

Alan Williams has an average rating of:

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Description/summary not set


Other contact details:

Not specified

Interests:

Workflows, web services, data handling

Field/Industry: Computer science

Occupation/Role(s): Technical manager

Organisation(s):

University of Manchester

 

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Blob Multiple selection

Created: 2015-03-31 11:23:55 | Last updated: 2015-03-31 11:37:25

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

An interaction page that allows multiple selections from a list of values.There is a single input port of depth one called selectionValuesThere is a single output port of depth one called answers

File type: htm

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Blob Importing data from spreadsheets into Taverna workflows

Created: 2015-01-22 13:00:28

Credits: User Aleksandra Pawlik User Katy Wolstencroft User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: PowerPoint 2007 presentation

Comments: 0 | Viewed: 22 times | Downloaded: 10 times

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Blob Using REST services from Biocatalogue

Created: 2015-01-22 12:40:34 | Last updated: 2015-01-22 12:42:14

Credits: User Aleksandra Pawlik User Stian Soiland-Reyes User Katy Wolstencroft User Alan Williams User Christian

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: PowerPoint 2007 presentation

Comments: 0 | Viewed: 24 times | Downloaded: 11 times

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Blob Building simple workflow in Taverna

Created: 2015-01-22 12:38:13

Credits: User Aleksandra Pawlik User Stian Soiland-Reyes User Katy Wolstencroft User Alan Williams User Christian

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: PowerPoint 2007 presentation

Comments: 0 | Viewed: 27 times | Downloaded: 14 times

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Blob Short introduction to Taverna 2.5

Created: 2015-01-22 12:37:00

Credits: User Aleksandra Pawlik User Stian Soiland-Reyes User Katy Wolstencroft User Alan Williams User Christian

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: PowerPoint 2007 presentation

Comments: 0 | Viewed: 29 times | Downloaded: 25 times

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Blob Example Newick file

Created: 2013-12-02 20:05:47

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A file containing example Newick format data

File type: Plain text

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Blob Bonn 2014 Help links

Created: 2014-09-03 08:19:52 | Last updated: 2014-09-03 08:20:20

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Many useful links accurate Sept 2014

File type: Adobe PDF

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Blob XPath tutorial presentation

Created: 2014-07-16 12:16:48

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a tutorial introducing how to use Taverna's XPath capabilities

File type: Adobe PDF

Comments: 0 | Viewed: 26 times | Downloaded: 20 times

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Blob Taverna Workbench introduction presentation

Created: 2014-07-16 12:15:19

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a tutorial designed to introduce the basic features of Taverna Workbench

File type: Adobe PDF

Comments: 0 | Viewed: 19 times | Downloaded: 13 times

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Blob Help presentation

Created: 2014-07-16 12:13:54

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a presentation of information on where to find help on myGrid tools

File type: Adobe PDF

Comments: 0 | Viewed: 16 times | Downloaded: 13 times

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Blob Introduction to using components presentation

Created: 2014-07-16 12:12:13

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a quick tutorial on how to use components within a workflow

File type: Adobe PDF

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Blob Advanced Taverna Features Presentation

Created: 2014-07-16 12:09:47 | Last updated: 2014-07-16 12:10:55

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a tutorial on some of Taverna's advanced features.

File type: Adobe PDF

Comments: 0 | Viewed: 19 times | Downloaded: 15 times

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Blob Gene spreadsheet for VPH-Share workshop

Created: 2014-07-13 17:31:59

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: Excel workbook

Comments: 0 | Viewed: 16 times | Downloaded: 17 times

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Blob Genes for VPH-Share workshop

Created: 2014-07-13 17:18:43

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: Plain text

Comments: 0 | Viewed: 21 times | Downloaded: 19 times

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Blob An introduction to Taverna components

Created: 2014-02-11 16:15:52 | Last updated: 2014-02-11 16:27:15

Credits: User Norman Morrison User Alan Williams User Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: PowerPoint 2007 presentation

Comments: 0 | Viewed: 29 times | Downloaded: 17 times

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Blob Introduction to building workflows with Taverna

Created: 2014-01-22 13:28:47

Credits: User Aleksandra Pawlik User Katy Wolstencroft User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Introduction to building workflows with Taverna for the Cranfield University course.

File type: PowerPoint presentation

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Blob Cranfield - Introduction to webservices and workflows

Created: 2014-01-22 13:27:41

Credits: User Aleksandra Pawlik User Katy Wolstencroft User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Introduction to workflows, web services and Taverna for the Cranfield University.

File type: PowerPoint presentation

Comments: 0 | Viewed: 16 times | Downloaded: 16 times

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Blob Help information powerpoint

Created: 2013-12-06 10:01:54

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A set of slides about where to seek help

File type: PowerPoint presentation

Comments: 0 | Viewed: 19 times | Downloaded: 15 times

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Blob Introduction to Taverna Online & Interaction

Created: 2013-09-06 09:04:41

Credits: User Aleksandra Pawlik User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is an introductory tutorial for Taverna Online and Interaction service. To be used for the workshop at Bonn University 4-6 September 2013

File type: PowerPoint presentation

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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

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Blob XPath service Tutorial

Created: 2013-09-05 12:26:15

Credits: User Katy Wolstencroft User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

XPath Service tutorial to be used for the workshop at Bonn University, 4-6 September 2013

File type: PowerPoint presentation

Comments: 0 | Viewed: 39 times | Downloaded: 38 times

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Blob REST Service Tutorial

Created: 2013-09-05 12:12:56

Credits: User Katy Wolstencroft User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

REST Services Tutorial to be used for the workshop at Bonn University 2013

File type: PowerPoint presentation

Comments: 0 | Viewed: 39 times | Downloaded: 34 times

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Blob Introduction to Taverna -part2 - Bonn 2013

Created: 2013-09-03 22:28:51

Credits: User Katy Wolstencroft User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Introduction to Taverna workflows: myExperiment, nested workflows, Spreadsheet import, BioMart, exploring workflow engine. This is a tutorial for the workshop at Bonn University 4-6 September 2013

File type: PowerPoint presentation

Comments: 0 | Viewed: 51 times | Downloaded: 58 times

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Blob Introduction to Taverna - Bonn 2013

Created: 2013-09-03 20:22:55

Credits: User Katy Wolstencroft User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Introduction to building workflows with Taverna - tutorial for the workshop at Bonn University, 4-6 September 2013

File type: PowerPoint presentation

Comments: 0 | Viewed: 46 times | Downloaded: 53 times

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Blob Nested UnigeneID_to_KEGG in Import and Convert

Created: 2013-08-29 14:09:53

Credits: User Katy Wolstencroft User Alan Williams User Paul Fisher

Attributions: Workflow UnigeneID to KEGG Pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is an example of a nested workflow, created for the training purposes.

File type: Trident (Package)

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Blob Species in Excel

Created: 2013-07-16 15:31:29

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: Excel workbook

Comments: 0 | Viewed: 14 times | Downloaded: 8 times

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Blob Species names

Created: 2013-07-16 14:55:56 | Last updated: 2013-07-16 14:56:06

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A list of species

File type: Trident (Package)

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Blob BioVel Taverna Tutorial

Created: 2011-12-05 11:07:46 | Last updated: 2011-12-05 11:07:49

Credits: User Katy Wolstencroft User Alan Williams User Robert Haines User Biomobst

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial gives an introduction to Taverna, myExperiment and BioCatalogue, using a case study from ecological niche modelling.

File type: PowerPoint presentation

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Blob testModel.xslt

Created: 2011-11-22 17:59:12

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: Trident (Package)

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

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Blob testModel.xml

Created: 2011-11-22 17:58:08

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: XML

Comments: 0 | Viewed: 13 times | Downloaded: 7 times

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Blob projectModel.xslt

Created: 2011-11-21 14:50:08

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: Trident (Package)

Comments: 0 | Viewed: 18 times | Downloaded: 11 times

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Blob projectModel.xml

Created: 2011-11-21 13:49:41

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: XML

Comments: 0 | Viewed: 17 times | Downloaded: 12 times

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Blob createModel.xslt

Created: 2011-11-21 13:47:13 | Last updated: 2011-11-21 13:47:14

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: Trident (Package)

Comments: 0 | Viewed: 15 times | Downloaded: 9 times

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Blob createModel.xml

Created: 2011-11-21 13:44:44 | Last updated: 2011-11-21 13:44:45

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: XML

Comments: 0 | Viewed: 22 times | Downloaded: 15 times

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Blob addthem.sh

Created: 2011-07-13 10:15:22

Credits: User Alan Williams User Steffen Möller

Attributions: Workflow External Tool: Numerically adding two values with 'bc'.

License: Creative Commons Attribution 3.0 Unported License

Shell script to be downloaded for tool

File type: UNIX script

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Blob Example text file

Created: 2008-10-23 12:06:50

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: Plain text

Comments: 0 | Viewed: 37 times | Downloaded: 20 times

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Blob Example XSLT file

Created: 2008-09-26 12:13:31

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

XSLT file to be used for example workflows

File type: Binary data

Comments: 0 | Viewed: 142 times | Downloaded: 257 times

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Blob Example XML file

Created: 2008-09-26 12:12:41

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

XML file to be used for example workflows

File type: XML

Comments: 0 | Viewed: 184 times | Downloaded: 353 times

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Blob Example SwissProt Data

Created: 2008-09-25 15:09:03

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example SwissProt data to be used for Taverna examples.

File type: Plain text

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Blob Example Genbank data

Created: 2008-09-25 15:00:28

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example file containing GenBank data so that it can be used for example Taverna workflows

File type: Plain text

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Pack

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Pack IBISBA workflows


Created: 2018-01-28 19:40:56 | Last updated: 2018-01-28 19:43:39

Initial set of IBISBA WP7 workflows

2 items in this pack

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Workflow

Workflow

Workflow Metabolite pathway search (1)

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The workflow searches for metabolomic pathways that match the entered keywords and returns information about the chosen pathway

Created: 2014-12-18

Credits: User Alan Williams

Workflow

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Project Biovel

Workflow Ecological niche modelling workflow (28)

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This workflow takes as input a file containing species occurrence points to create a model with the openModeller Web Service. Algorithm, environmental layers and mask are selected during the workflow. The model is tested (internal test and optional cross validation external test) and then projected one or more times. All points from the input file are used to create a single model, even if there are differences in the scientific names. Cross validation calculates the mean AUC. Model projectio...

Created: 2013-01-07 | Last updated: 2015-06-11

Credits: User Renato De Giovanni User Alan Williams User Robert Kulawik User Francisco Quevedo User Vhernand Network-member BioVeL

Attributions:

Workflow

Workflow Increment an integer (1)

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This workflow uses R to increment the input integer

Created: 2014-10-03

Credits: User Alan Williams

Workflow

Workflow Species chooser (1)

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In your browser, choose between marmots and horseshoe crabs

Created: 2014-10-03

Credits: User Alan Williams

Workflow

Workflow Get weather information (1)

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Get the weather forcast of the day for you city. Info display: wind, visibility, temperature, sky conditions and pressure.

Created: 2014-10-03

Credits: User Alan Williams User Franck Tanoh

Attributions: Workflow Get weather information

Workflow

Workflow Species Occurrence (1)

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Retrieve the first 100 occurrences of a species in Darwin format

Created: 2014-10-03

Credits: User Alan Williams

Workflow

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: 2014-07-09

Credits: User Alan Williams

Attributions: Workflow Demonstration of configurable iteration

Workflow

Workflow Construct viewparams (1)

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Construct the viewparams parameter to OBIS services

Created: 2014-10-02

Credits: User Alan Williams

Workflow

Workflow A Basic example R workflow (3)

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This workflow uses an R service running on localhost to calculate sin(0.45)

Created: 2010-11-26 | Last updated: 2014-08-20

Credits: User Alan Williams

Workflow

Workflow EBI_InterproScan_broken (1)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text and xml. 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. Note that this workflow is deliberately broken

Created: 2014-07-09

Credits: User Alan Williams User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EBI_InterproScan_NewServices

Workflow

Workflow Download images for gene (3)

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This workflow downloads the first few images corresponding to experiments for the specified gene

Created: 2014-07-13 | Last updated: 2014-07-15

Credits: User Alan Williams

Workflow

Workflow Experiments for gene (2)

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This workflow uses the Allen Brain REST API to fetch the experiements corresponding to a named gene

Created: 2014-07-15 | Last updated: 2014-07-15

Credits: User Alan Williams

Workflow

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

Workflow An iframe test (1)

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But this works

Created: 2014-03-28

Credits: User Alan Williams

Workflow

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

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

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

Workflow BioVeL workshop reduced full workflow (1)

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The workflow is a reduced version of the main workflow. It can be used to call web services to support biodiversity research. It fetches data from GBIF. The occurrences are then used to create a model using OpenModeller, test the model and to project the model. The projection of the model is currently a "native projection" i.e. it uses the same layers as those used to create the model. The services within the workflow will allow non-native projections

Created: 2013-09-04

Credits: User Katy Wolstencroft User Alan Williams

Attributions:

Workflow

Workflow Pathway to Pubmed (1)

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This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2013-09-03

Credits: User Alan Williams User Paul Fisher

Attributions: Workflow Pathway to Pubmed

Workflow

Workflow UnigeneID to KEGG Pathways (1)

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This workflow accepts a list of Unigene gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in (plus pathway image) from the KEGG database. This workflow replaces the earlier SOAP version with the new KEGG REST services

Created: 2013-09-03

Credits: User Katy Wolstencroft User Alan Williams User Paul Fisher

Attributions: Workflow NCBI Gi to Kegg Pathways

Workflow

Workflow Example of interaction via HTML page (1)

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No description

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

Credits: User Alan Williams

Workflow

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Project Biovel

Workflow Data publication example (1)

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This workflow gives an example of an interaction that makes use of published input data. The data is published on the webdav and the URL passed to the HTML page.

Created: 2012-10-11

Credits: User Alan Williams

Workflow

Workflow Blah (1)

No description

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

Credits: User Alan Williams

Workflow

Workflow BiomartAndEMBOSSDisease (4)

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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. 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: 2011-01-27 | Last updated: 2012-09-04

Credits: User Katy Wolstencroft User Alan Williams

Attributions: Workflow BiomartAndEMBOSSAnalysis

Workflow

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: 2012-04-05

Credits: User Alan Williams

Workflow

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: 2012-04-05

Credits: User Alan Williams

Workflow

Workflow Simple Python example (1)

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This workflow generates a random number within the range 0 to 100. The generation is done by a python script. The workflow assumes that python is in the path.

Created: 2012-04-05

Credits: User Alan Williams

Workflow

Workflow Secure Web service call example (2)

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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. You ...

Created: 2012-04-05 | Last updated: 2013-06-11

Credits: User Alan Williams

Workflow

Workflow Secure REST service call example (2)

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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: 2012-04-05 | Last updated: 2014-01-16

Credits: User Alan Williams

Workflow

Workflow Retrieve sequence in EMBL format (1)

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

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow

Workflow Render gene via BioGPS (3)

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This workflow uses the REST API of BioGPS to list the plugins and then allow the user to select which plugin to use to display the input gene id

Created: 2012-04-05 | Last updated: 2012-05-23

Credits: User Alan Williams

Workflow

Workflow Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2012-04-05

Credits: User Alan Williams

Workflow

Workflow 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: 2012-04-05

Credits: User Alan Williams

Workflow

Workflow Multiple choice quiz (1)

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A fun example workflow showing user-interaction and service looping

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow

Workflow Hello World (1)

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One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".

Created: 2012-04-05 | Last updated: 2014-03-03

Credits: User Alan Williams

Workflow

Workflow Hello Anyone (1)

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An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".

Created: 2012-04-05 | Last updated: 2014-03-03

Credits: User Alan Williams

Workflow

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: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow

Workflow Fetch Dragon images from BioMoby (1)

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Fetch images and annotations of snapdragons

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow

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: 2012-04-05

Credits: User Alan Williams

Workflow

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: 2012-04-05

Credits: User Alan Williams

Workflow

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: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow

Workflow Example of explicit looping (1)

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This workflow demonstrates how a nested workflow can be called an explicit number of times. Note that the loop iterator does not need to be used in the logic of the loop contents. It can be used as a sentinel (see the conditional workflow)

Created: 2012-04-05

Credits: User Alan Williams

Workflow

Workflow Example of conditional invocation (1)

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This workflow demonstrates how nested workflows can be conditionally invoked

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow

Workflow Example for external tools with zip and unzip (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: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow

Workflow EBI_InterproScan_NewServices (2)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text and xml. 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: 2012-04-05 | Last updated: 2014-04-09

Credits: User Alan Williams

Workflow

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: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow

Workflow BioMoby tutorial workflow (1)

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A workflow from part of the BioMoby tutorial

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow

Workflow BiomartAndEMBOSSMouseRat (1)

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

Created: 2012-04-05

Credits: User Alan Williams

Workflow

Workflow Render gene via BioGPS (2)

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This workflow uses the REST API of BioGPS to list the plugins and then allow the user to select which plugin to use to display the input gene id

Created: 2012-02-10 | Last updated: 2012-02-15

Credits: User Alan Williams

Workflow

Workflow Example of explicit looping (1)

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This workflow demonstrates how a nested workflow can be called an explicit number of times. Note that the loop iterator does not need to be used in the logic of the loop contents. It can be used as a sentinel (see the conditional workflow)

Created: 2011-11-15 | Last updated: 2011-11-15

Credits: User Alan Williams

Workflow

Workflow Example of conditional invocation (1)

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This workflow demonstrates how nested workflows can be conditionally invoked

Created: 2011-11-15 | Last updated: 2011-11-15

Credits: User Alan Williams

Workflow

Workflow Simple Python example (1)

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This workflow generates a random number within the range 0 to 100. The generation is done by a python script. The workflow assumes that python is in the path.

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: User Alan Williams

Workflow

Uploader

Workflow New York vs. New Jersey Broccoli Production (1)

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Uses the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports two files and generates a single graph comparing the information from the two spreadsheets.

Created: 2011-09-21 | Last updated: 2011-09-21

Credits: User tpacurtis User Alan Williams

Attributions: Workflow Spreadsheet Import Example Blob NY Broccoli Production Blob NJ Broccoli Production

Workflow

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

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

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

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

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

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

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

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

Workflow Example for external tools with gzip and g... (1)

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This workflow is self-contained. It has a fixed URL from which a text file is downloaded (output as Original_file). That file is gzipped (output as Compressed_File) and then gunzipped again (output as Decompressed_File). The workflow wraps external tools from taverna.nordugrid.org and needs a beta version of Taverna 2.3 or later.

Created: 2011-05-18 | Last updated: 2011-05-18

Credits: User Steffen Möller User Alan Williams

Workflow

Workflow R logical vector workflow (1)

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The workflow returns a list containing the logical inversion of the logical vector input

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: User Alan Williams

Workflow

Workflow R string workflow (1)

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This workflow determines the lower case version of the input string.

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: User Alan Williams

Workflow

Workflow R numeric workflow (1)

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This workflow uses an Rshell service to calculate the square of a numeric inputThis workflow uses an

Created: 2010-11-26

Credits: User Alan Williams

Workflow

Workflow String list intersection - yielding empty ... (1)

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The string list intersection service takes in ['a','b','c'] and ['x','y','z'] and returns the empty list [].

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Pad numeral with leading 0s - too short ta... (1)

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The pad numeral with leading 0s takes the input '12' and because the specified target length of 1 is too short, yields the output '12'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow FIlter list of strings by regex extracting... (1)

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The workflow examines the five element list split from the first service. For each element, if it contains an 'a' followed by two characters, then the two characters after the 'a' are included in the output. Thus, for the input ['a','b','abcde','cdef','axy'], only 'abcde' and 'axy' contain a match and so ['bc', 'xy'] is output.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Ask - just title parameter (1)

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The ask service displays a prompt with the title 'Some title' but no prompt message. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Warn - title and message parameters (1)

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The warn service displays a warning dialog with 'Some title' and message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Select - title and message parameters (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The select service displays a dialog with ''Some title' and 'Some message'. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow List files by regex - single answer (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_regex service and the file path to the one file matching 'c.*' i.e. starting with 'c' is output.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Choose - single element list (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a' and outputs the list ['a']. The choose service displays a dialog with 'Some title' and 'Some message'. The user is only able to choose the value 'a'. When the user presses OK 'a' is passed to the answer port of the choose service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

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: 2009-12-15

Credits: User Alan Williams

Workflow

Workflow Warn - no parameters (1)

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The warn service displays a prompt with no title or message. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Select - no title or message parameters (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The select service displays a dialog with no title or message. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Choose - no title or message parameters (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The choose service displays a dialog with no title or message. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow EBI_InterProScan for Taverna 2 (1)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: User Alan Williams

Workflow

Workflow Tell - no parameters (1)

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The tell service displays an informative dialog with no title or message. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow String list intersection - yielding non em... (1)

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The string list intersection service takes in ['a','b','c'] and ['a','e','c] and returns the list ['a','c'].

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Pad numeral with leading 0s - specified ta... (1)

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The pad numeral with leading 0s takes the input '12' and pads it to the specified target length of 4, yielding the output '0012'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Ask - no parameters (1)

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The ask service displays a prompt with no title and no prompt message. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow BiomartAndEMBOSSAnalysis (1)

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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: 2010-07-04 | Last updated: 2010-07-04

Credits: User Alan Williams

Workflow

Workflow Warn - message parameter (1)

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The warn service displays a warning dialog with no title but message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Select - message parameter (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The select service displays a dialog with no title but with 'Some message'. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow List files by extension - no answer (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_extension service. Since no files end in ".fred", an empty list is output.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Choose - title and message parameters (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The choose service displays a dialog with 'Some title' and with 'Some message'. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Tell - message parameter (1)

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The tell service displays an informative dialog with no title but with message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Remove duplicate strings - empty list (1)

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The remove duplicate strings service takes the empty list [] and outputs the result [].

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow FIlter list of strings by regex extracting... (1)

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The workflow examines the five element list split from the first service. For each element, if it contains an 'a' followed by two characters, the second character after the 'a' is included in the output. Thus, for the input ['a','b','abcde','cdef','axy'], only 'abcde' and 'axy' contain a match and so ['c', 'y'] is output.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Byte[] to string - non empty value (1)

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The beanshell converts the string 'hello' to a byte array which is then converted back to the string 'hello' by the Byte[]_to_string service.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Echo_with_occasional_failure-1 (1)

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The echo_with_occasional_failure service mostly echoes the string 'hello' to the out port. Sometimes, it throws a service failure.

Created: 2008-09-29

Credits: User Alan Williams

Workflow

Workflow String list union - yielding empty list (1)

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The string list union service takes in two empty lists [] and [] and returns an empty list [].

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow String list difference - yielding non-empt... (1)

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The string list difference service takes in ['a','b','c'] and ['a','e','c'] and returns the list ['b','e'].

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow List files by regex - no answer (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_regex service. Since no files match the regular expression 'x.*' i.e. no files have a name that starts with 'x', an empty list is output.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow EBI_InterProScan_T2 (1)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2009-12-15

Credits: User Alan Williams

Workflow

Workflow Warn - title parameter (1)

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The warn service displays a warning dialog with 'Some title' but no message. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Select - title parameter (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The select service displays a dialog with 'Some title' but no message. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow List files by extension - single answer (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_extension service and the file path to the one file ending in ".bin" is output.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Choose - title parameter (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The choose service displays a dialog with 'Some title' but no message. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Tell - title parameter (1)

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The tell service displays an informative dialog with 'Some title' but no message. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Get image URLs from HTTP document (1)

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Retrieve the web page at http://www.mygrid.org.uk/usermanual1.7/user_gettings_started.html and examine it for images. The workflow should return an empty list.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Flatten list - two depth (1)

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The flatten_list service takes the list [[['a']], [['b']], [['c']], [['d']]] and, using the default flatten depth of 2, outputs the list [['a'], ['b'], ['c'], ['d'], ['e']].

Created: 2008-09-29

Credits: User Alan Williams

Workflow

Workflow Fail if false - non false value (1)

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The fail if true service executes without an exception if given a non-false value such as 'fred'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

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: 2009-12-15

Credits: User Alan Williams

Workflow

Workflow BiomartAndEMBOSSAnalysis (1)

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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: 2009-12-15

Credits: User Alan Williams

Workflow

Workflow Concatenate two strings - empty strings (1)

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The concatenate two strings service takes two empty strings and returns an empty string.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Write text file - empty string value (1)

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file service which writes the empty string '' into the file. '' is also output by the service.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Transform XML - no output file (1)

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The get_xml_file_from_web service downloads an example xml from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xml_file. The path to the temporary file is passed to the inFileURL port of Transform_XML. The get_xslt_file_from_web service downloads an example xslt file from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xslt_file. The path to the temporary file is passed to the xslFileURL port...

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Remove duplicate strings (1)

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The remove duplicate strings service takes the list ['a','b','c','b','a','d'], strips out duplicate strings and outputs the result ['a','b','c','d'].

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow FIlter list of strings by regex with a sui... (1)

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The workflow filters the five element list split from the first service and returns the three elements that match the regular expression.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Concatenate files - echo results and multi... (1)

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The workflow splits the string 'a,b,c,d,e' into its five elements and saves the individual strings to five temporary files. The file paths to those files are then output by the create_and_populate_temporary_file beanshell. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service concatenates the five files and writes the result to the temporary output file. Because the displayresults port has been given a default value of...

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Ask - title and message parameters (1)

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The ask service displays a prompt with 'Some title' and the prompt message 'Some message'. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2009-12-15

Credits: User Alan Williams

Workflow

Workflow Extract elements from a list - extraction ... (1)

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The extract_elements_from_a_list is passed the list [['a','b','c', 'd'], ['e','f','g','h'],['i','j','k','l'],['m','n','o','p']] with fromIndex of 1 and toIndex of 3 and the default depth of 1, will output the list [['b','c'], ['f','g'],['j','k'],['n','o'']] as it is the list with depth 1 e.g. ['e','f','g','h'] that are considered.

Created: 2008-09-29

Credits: User Alan Williams

Workflow

Workflow Read text file (1)

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The beanshell write the string 'hello' to a temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the string 'hello'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Get image from URL - url and base specified (1)

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Retrieve the image at http://www.mygrid.org.uk/files/2008/09/dragon-workflow.png using both the url and base parameters

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Fail if false - true value (1)

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The fail if true service executes without an exception if given the value 'true'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Transform XML - output file by extension (1)

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The get_xml_file_from_web service downloads an example xml from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xml_file. The path to the temporary file is passed to the inFileURL port of Transform_XML. The get_xslt_file_from_web service downloads an example xslt file from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xslt_file. The path to the temporary file is passed to the xslFileURL port...

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Merge string list to string - default sepa... (1)

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The merge string list to string service takes the list ['a','b','c'] and outputs the string 'a b c'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow FIlter list of strings by regex extracting... (1)

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The workflow examines the five element list split from the first service. For each element, if it contains an 'a' followed by two characters, then that triple is included in the output. Thus, for the input ['a','b','abcde','cdef','axy'], only 'abcde' and 'axy' contain a match and so ['abc', 'axy'] is output.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Concatenate two strings (1)

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The concatenate two strings service takes the strings 'good' and 'bye' and returns the result 'goodbye'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Byte[] to string - empty value (1)

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The beanshell converts the empty string '' to a byte array which is then converted back to the empty string '' by the Byte[]_to_string service.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

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: 2009-12-15

Credits: User Alan Williams

Workflow

Workflow Write text file - specified value (1)

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file service which writes 'hello' into the file. 'hello' is also output by the service.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Transcribe DNA (1)

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The Transcribe DNA service takes the DNA sequence, here defaulted to 'gatcctccat' and outputs the corresponding transcribed RNA sequence, in this example, 'gauccuccau'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Split string into string list by regular e... (1)

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The split string into string list by regular expression takes the string 'a,b,c' and using the default regular expression ',' splits it into the list ['a','b','c']

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Read text file - empty file (1)

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the empty string ''.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Fail if true - false value (1)

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The fail if true service executes without an exception if given the value 'false'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Ask - just message parameter (1)

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The ask service displays a prompt with no title but with the prompt message 'Some message'. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

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: 2009-12-15

Credits: User Alan Williams

Workflow

Workflow Flatten list - three depth (2)

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The flatten_list service takes the list [[['a']], [['b']], [['c']], [['d']],[['e']]] and, using a flatten depth of 3, outputs the list ['a', 'b', 'c', 'd','e'].

Created: 2008-09-29 | Last updated: 2008-09-30

Credits: User Alan Williams

Workflow

Workflow Create lots of strings (1)

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The create lots of strings service returns a list containing a large number of strings.

Created: 2008-09-27 | Last updated: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Write text file - overwriting content (1)

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file A service which writes the string 'hello' into the file. After service A has run, service B writes 'goodbye' into the file. The file is then read by the Read_Text_File service and its content, 'goodbye', output by the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Transform XML - explicit output file (1)

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The get_xml_file_from_web service downloads an example xml from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xml_file. The path to the temporary file is passed to the inFileURL port of Transform_XML. The get_xslt_file_from_web service downloads an example xslt file from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xslt_file. The path to the temporary file is passed to the xslFileURL port...

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow List files by regex - empty directory (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The empty directory is examined by the List_files_by_regex service. Since there are no files, an empty list is output.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow FIlter list of strings by regex with an un... (1)

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The workflow filters the five element list split from the first service and returns an empty list as no elements match.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Concatenate files - multiple files (1)

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The workflow splits the string 'a,b,c,d,e' into its five elements and saves the individual strings to five temporary files. The file paths to those files are then output by the create_and_populate_temporary_file beanshell. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service concatenates the five files and writes the result to the temporary output file. Because the displayresults port has no value, the results are not...

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Retrieve sequence in EMBL format (1)

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

Created: 2009-12-15

Credits: User Alan Williams

Workflow

Workflow Select - single element list (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a' and outputs the list ['a']. The select service displays a dialog with 'Some title' and 'Some message'. The user is only able to select the value 'a'. When the user presses OK 'a' is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Read text file - several lines (1)

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The beanshell write the string 'hello' four times separated by a new lineto a temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the string 'hello hello hello hello'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow List files by extension - empty directory (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The empty directory is examined by the List_files_by_extension service. Since no files end in ".png", an empty list is output.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow String list union - yielding non-empty list (1)

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The string list union service takes in ['a','b','c'] and ['a','e','c'] and returns a list equivalent to ['a','b','c','e'].

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Read SwissProt file (1)

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The Get_web_page_from_URL downloads a file from myExperiment that contains SwissProt data. That data is then saved to a temporary file generated by the create_and_populate_temporary_file beanshell. The path to the temporary file is then passed to the Read_SwissProt_file service. That service reads the file and converts the SwissProt data into Agave format. The result is then sent to the workflow's out port.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow List files by regex - several answers (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_regex service and the file paths matching the regular expression '.*i.*', i.e. those containing an 'i', are output.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Fail if true - non true value (1)

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The fail if true service executes without an exception if given a value that is not true e.g. 'fred'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Concatenate files - echo results but no files (1)

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The split_string_into_string_list_by_regular_expresson outputs an empty list since the string to be split is defaulted to ''. As there are no input values, the create_and_populate_temporary_file generates an empty list. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service does not write anything to the temporary output file. Because the displayresults port has been given a default value of 'true', the empty string is ...

Created: 2008-09-27

Credits: User Alan Williams

Workflow

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: 2009-12-15

Credits: User Alan Williams

Workflow

Workflow Extract elements from a list - extraction ... (1)

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The extract_elements_from_a_list is passed the list [['a','b','c', 'd'], ['e','f','g','h'],['i','j','k','l'],['m','n','o','p']] with fromIndex of 1 and toIndex of 3 and depth 2, will output the list [['e','f','g','h'],['i','j','k','l']] as it is the outermost list i.e. that with depth 2 that is considered.

Created: 2008-09-29

Credits: User Alan Williams

Workflow

Workflow Tell - title and message parameters (1)

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The tell service displays an informative dialog with no title but with message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow String list difference - yielding empty list (1)

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The string list difference service takes in ['a','b','c'] and ['a','c','b'] and returns the empty list [].

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Pad numeral with leading 0s - default targ... (1)

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The pad numeral with leading 0s takes the input '12' and pads it to the default target length of 7, yielding the output '0000012'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Merge string list to string - empty list (1)

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The merge string list to string service takes an empty list [] and outputs an empty string ''.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow List files by extension - several answers (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_extension service and the file paths to the three files ending in ".png" are output.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Get web page from URL - url and base (1)

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Fetches a web page from http://www.mygrid.org.uk/tools with the base parameter as "http://www.mygrid.org.uk" and the url as "/tools". Note that when viewed, the HTML may not be rendered correctly. However, the HTML may be viewed by rendering the result as plain text.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Get web page from URL - just url (1)

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Fetches a web page from http://www.mygrid.org.uk/tools using just the url parameter of the service. Note that when viewed, the HTML may not be rendered correctly. However, the HTML may be viewed by rendering the result as plain text.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Get image URLs from HTML document and outp... (1)

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Retrieve the web page at http://www.mygrid.org.uk, examine it for images and output the images.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Decode base64 to byte[] (1)

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The decode base64 to byte[] service decodes the base64 string. The byte array is then converted into the string 'Hello world'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Fail if true - true value (1)

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The fail if true service throws an exception when passed the value true.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Test always fails - one parameter (1)

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The test always fails service generates a service failure when one parameter value is supplied.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Reverse complement DNA (1)

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The Reverse Complement DNA service takes the DNA sequence, here defaulted to 'gatcctccat' and outputs the corresponding reverse complement sequence, in this example, 'atggaggatc'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Get image from URL - only url specified (1)

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Retrieve the image at http://www.mygrid.org.uk/files/2008/09/dragon-workflow.png using just the url parameter

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Merge string list to string - colon separator (1)

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The merge string list to string service takes the list ['a','b','c'] and using the separator ':' outputs the string 'a:b:c'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Test always fails - two parameters (1)

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The test always fails service generates a service failure when two parameter values are supplied.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Split string into string list by regular e... (1)

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The split string into string list by regular expression takes the string 'boo:and:foo' and using the specified regular expression 'o' splits it into the list ['b','',':and:f']

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Extract elements from a list - single elem... (1)

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The extract_elements_from_a_list is passed the list ['a','b','c','d','e']. The fromIndex is 2 and the toIndex is 3, so the service outputs the single element list ['c'].

Created: 2008-09-29

Credits: User Alan Williams

Workflow

Workflow Test always fails - no parameters (1)

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The test always fails service generates a service failure when no parameter values are supplied.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Split string into string list by regular e... (1)

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The split string into string list by regular expression takes the string 'boo:and:foo' and using the specified regular expression ':' splits it into the list ['boo','and','foo']

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Encode byte[] to base64 (1)

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The encode byte[] to base 64 service encodes the bytes representing (in the local character set) 'hello'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Extract elements from a list - full extrac... (1)

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The extract_elements_from_a_list is passed the list ['a','b','c','d','e']. The fromIndex is 0 and the toIndex is 5, so the service outputs an identical list.

Created: 2008-09-29

Credits: User Alan Williams

Workflow

Workflow Read GenBank file (1)

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The Get_web_page_from_URL downloads a file from myExperiment that contains GenBank data. That data is then saved to a temporary file generated by the create_and_populate_temporary_file beanshell. The path to the temporary file is then passed to the Read_GenBank_file service. That service reads the file and converts the GenBank data into Agave format. The result is then sent to the workflow's out port.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Fail if false - false value (1)

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The fail if true service throws an exception if given the value 'false'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Execute cmd line app - unix - /bin/ls -R o... (1)

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Note that this workflow only works on Unix systems. The get_temporary_directory beanshell returns the path to the directory in which temporary files are held. This value is passed to the create_and_populate_list beanshell which creates a list of '-R' and the path. The resultant list is passed to the args port of the Execute_cmd_line_app service. The command port of that service has been defaulted to '/bin/ls'. The execute_cmd_line_app service runs the /bin/ls -R command on the temporary ...

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow Execute cmd line app - unix - /bin/ls of t... (1)

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Note that this workflow only works on Unix systems. The get_temporary_directory beanshell returns the path to the directory in which temporary files are held. This value is passed to the args port of the execute_cmd_line_app service. The command port of that service has been defaulted to '/bin/ls'. The execute_cmd_line_app service runs the /bin/ls command on the temporary directory. The result is passed to its result port and then to the out port of the workflow.

Created: 2008-09-27

Credits: User Alan Williams

Workflow

Workflow R integer vector example (1)

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This workflow takes a list of integer values and returns a list containing the square of the input list's elements, and the sum of the input list's elements.

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: User Alan Williams

Workflow

Workflow R string vector example (1)

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The workflow takes a list of strings and outputs a list contains the lower-cased versions of the input elements, and also a concatenation of the input elements

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: User Alan Williams

Workflow

Workflow R integer workflow (1)

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This workflow uses an Rshell service to calculate 100 modulus the integer input

Created: 2010-11-29

Credits: User Alan Williams

Workflow

Workflow R integer vector example (1)

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This workflow takes a list of integer values and returns a list containing 100 modulus the list's elements, and the sum of the input list's elements.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: User Alan Williams

Workflow

Workflow R PNG-value example (2)

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This workflow produces a PNG plot on the figure port.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: User Alan Williams

Workflow

Workflow R Text-file example (1)

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This workflow contains two services. The file_writer uses a File in R to output a string. The file_reader uses a File in R to input a string, the contents of which are output.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: User Alan Williams

Workflow

Workflow R generic example (1)

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This workflow shows how string vectors can be used to transfer a complex R object (in this case a matrix) between Rshell services

Created: 2010-11-29

Credits: User Alan Williams

Workflow

Workflow R logical workflow (1)

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Checks what the logical_input is in R. For an logical_input of TRUE - is_false should be FALSE and is_true TRUE FALSE - is_false should be TRUE and is_true FALSE For any other input values, is_false and is_true should both be NA

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: User Alan Williams

Workflow

Workflow retry-example (1)

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This workflow executes a local beanshell script that has been programmed to fail on some iterations. It demonstrates the advantages of setting retries in your workflows to make them more robust

Created: 2010-11-08 | Last updated: 2010-11-08

Credits: User Alan Williams

Workflow

Workflow BioMart and Emboss Analysis (T2) (1)

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This is the Taverna 2 version of the Biomart and Emboss Analysis workflow http://www.myexperiment.org/workflows/158   Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned. Previous versions of this workflow only returned sequences with an ID mapped to a MIM_morbid_accession. This was primarily to reduce the numbe...

Created: 2009-09-15

Credits: User Katy Wolstencroft User Alan Williams

Attributions: Workflow BiomartAndEMBOSSAnalysis

Workflow

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.  I just uploaded this example so I can play around with the myexperiment api.

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

Credits: User Alan Williams

Attributions: Workflow Fetch today's xkcd comic

Workflow

Workflow Multiple Protein Alignment Profiling(1) (4)

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Designed from an example workflow at Traverna, this workflow retrieves a set of sequences from UniProt, then simultaneously scans for transmembrane regions and performs a multiple alignment using EMMA. The alignment is then plotted to a set of PNG images, followed by a profile analysis using prophecy and prophet tools.

Created: 2010-01-13 | Last updated: 2010-11-17

Credits: User Carol Lushbough User Alan Williams

Attributions: Workflow A workflow version of the EMBOSS tutorial

Workflow

Uploader

Workflow Population histogram in R (with Ask Box!) (1)

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This workflow fetches the details of the countries in the world and then uses R to produce a histogram of the log of their population. Prompts the user to enter a title for the histogram.

Created: 2011-09-21 | Last updated: 2011-09-21

Credits: User tpacurtis User Alan Williams

Attributions:

Workflow

Uploader

Workflow Spreadsheet Import Fertilizer Use (1)

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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file FertilizerUse.xlsx and generates a graph from the date. The source data is from http://www.myexperiment. org/files/568/download/FertilizerUse.xls and ERS, TVA (Tennessee Valley Authority), AAPFCO (Association of American Plant Food Control Officials), TFI (The Fertilizer Institute).

Created: 2011-09-21 | Last updated: 2011-09-21

Credits: User tpacurtis User Alan Williams

Attributions: Workflow Spreadsheet Import Example Blob US Fertilizer Use

Workflow

Workflow Ag Spreadsheet Import (1)

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Based on Spreadsheet Import Example by David WithersSusan 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: 2011-09-21 | Last updated: 2011-09-21

Credits: User Mutanthumb User Alan Williams

Workflow

Workflow Failed 2 Chart Attempt (1)

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Tried to show 2 charts simulatneously.

Created: 2011-09-21 | Last updated: 2011-09-21

Credits: User Mutanthumb User Alan Williams

Workflow

Workflow Time Series Data Graphed and Cited (1)

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This workflow uses time series data from Rob Hyndman's Time Series Data Library (TSDL) and graphs it with Google charts. It also provides the citation information with the current date. The outputs are a Google Chart and the corresponding citation information. The inputs are URL strings for two datasets provided by Rob Hyndman under the subject of Ecology. These datasets include the annual number of lynx pelts and the annual unit price of lynx pelts during the year range 1857 -1911. This...

Created: 2011-10-05 | Last updated: 2011-10-05

Credits: User Trisha Adamus User Alan Williams User Jeff adamus

Attributions: Workflow Fetch today's xkcd comic Workflow Spreadsheed Data Import Example Workflow HTML Citation Extraction Workflow Current Date Output

Workflow

Workflow Get Element ID from Gzipped GenBank file (1)

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This workflow gunzips a *.gbk.gz file, converts it to XML (via agavewriter) and finds the Element ID. Does not work on *.gz files larger than 10MB. I upped the JVM settings on Taverna to:         <key>VMOptions</key>         <string>-Xmx4096m -XX:MaxPermSize=1024m</string> Created my own agave.dtd to get the XPath service to work the XML file generated from the Read_GenBank_File service. You will need to ...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: User Mutanthumb User Alan Williams

Workflow

Uploader

Workflow Broccoli Production New York State, 1960-1965 (1)

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This workflow takes data about agricultural production in New Jersey and New York from 1960 -1965, to compare productivity in broccoli growing.

Created: 2011-10-09 | Last updated: 2011-10-09

Credits: User Atminer User Alan Williams

Attributions: Workflow Spreadsheet Import Example

Workflow

Workflow FetchandDisplaySpecies (3)

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This workflow uses GBIF to search and report species occurrence data and then displays them on Google Earth. An interactive step then allows you to alter the co-ordinates of data displayed.

Created: 2011-11-27 | Last updated: 2011-11-29

Credits: User Alan Williams

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