Nl User: Katy Wolstencroft

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Name: Katy Wolstencroft

Joined: Friday 20 July 2007 18:31:02 (UTC)

Last seen: Friday 09 March 2018 10:20:10 (UTC)

Email (public): k.j.wolstencroft [at] liacs.leidenuniv.nl

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

Location: Leiden, Netherlands

Katy Wolstencroft has been credited 99 times

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workflows, ontologies semantic web, bioinformatics

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Blob Annotating Experimental Data

Created: 2015-12-03 08:31:02

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a tutorial about annotating experimental data with RightField

File type: PowerPoint 2007 presentation

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Blob Geo File for Annotation

Created: 2015-12-03 08:23:05

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is an excel file to use in the RightField exercises in the BioSB Data Integration Course 2015

File type: application/excel

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Blob Taverna Tutorial Data Integration NL 2015

Created: 2015-12-02 10:41:00 | Last updated: 2015-12-02 10:43:03

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial introduces you to using the Taverna workbench and shows you how you can use the Open PHACTS REST API to construct workflows over Open PHACTS services

File type: Adobe PDF

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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

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File type: PowerPoint 2007 presentation

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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

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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

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File type: PowerPoint 2007 presentation

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Blob An introduction to designing and executing workflows...

Created: 2014-02-13 08:46:17

Credits: User Norman Morrison User Katy Wolstencroft User Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial uses Bioinformatics exercises as an introduction to designing and executing workflows with Taverna.

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Blob Exploring the Taverna workflow engine

Created: 2014-02-10 14:45:48 | Last updated: 2014-02-10 14:46:54

Credits: User Norman Morrison User Katy Wolstencroft User Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

In this tutorial we will explore the Taverna workflow engine, including: 1) iteration; 2) looping; 3) parallel invocation.

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Blob An introduction to designing and executing workflows...

Created: 2014-02-06 14:52:19 | Last updated: 2014-02-06 16:45:12

Credits: User Norman Morrison User Katy Wolstencroft User Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Part 1 - An introduction to designing and executing workflows with Taverna. Building a simple workflow.

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Blob An introduction to designing and executing workflows...

Created: 2014-02-06 16:42:14 | Last updated: 2014-02-06 16:44:14

Credits: User Norman Morrison User Katy Wolstencroft User Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Part 2 - An introduction to designing and executing workflows with Taverna. Importing and exporting data.

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Blob Introduction to myExperiment

Created: 2014-02-06 14:46:10

Credits: User Norman Morrison User Katy Wolstencroft User Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

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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.

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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.

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Blob XPath service Tutorial

Created: 2013-12-03 22:49:13 | Last updated: 2013-12-03 23:22:57

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

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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

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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

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Blob Shims and Beanshells - tutorial

Created: 2013-09-05 09:49:45

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Shims and Beanshell - introductory tutorial for the workshop at Bonn University 2013

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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

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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

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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 GalaxyGeneList - long : datafile for training

Created: 2013-08-29 10:25:07

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Chip-Seq gene list example used for training purposes. This is the original version of the file  (approx 400 entries). Warning! Running this file in some workflows may  take up to 30 minutes! If you want to use it for training, you may want to reconsider and use the shorter version of the file which is also uploaded.

File type: Excel workbook

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Blob GalaxyGeneList - short : datafile for training

Created: 2013-08-29 10:20:47 | Last updated: 2013-08-29 10:22:02

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Chip-Seq gene list example used for training purposes. This is a shorter version of the file (20 entries) as running the original file (the longer one with approx 400 entries) takes up to 30 minutes.

File type: Excel workbook

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Blob Taverna 2.4 Tutorial

Created: 2013-07-17 11:02:49

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A tutorial for designing and executing workflows in Taverna

File type: PowerPoint presentation

Comments: 0 | Viewed: 17 times | Downloaded: 39 times

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Blob Cranfield Msc Intro to Taverna

Created: 2013-01-09 16:43:00

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial give a brief introduction to designing and running workflows in Taverna, using a variety of different types of services and reusing workflows from myExperiment

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Blob Agenda of Bonn tutorial

Created: 2012-09-14 09:51:22

Credits: User Helen Hulme User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is the list of presentations and workshop items from the Bonn tutorial 2012. The presentations (and many of the workflows and datafiles) for this are in the pack: "Pack for Bonn2012" http://www.myexperiment.org/packs/330

File type: Word document

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Blob Workflow Assignment Instructions

Created: 2012-09-05 08:20:34

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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File type: PowerPoint presentation

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Blob Bonn Taverna Presentation - Case Studies

Created: 2012-09-04 10:17:41 | Last updated: 2012-09-04 13:45:55

Credits: User Helen Hulme User Katy Wolstencroft User Paul Fisher User Shoaib Sufi User Mcornell User Robert Haines

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Presentation comparing and contrasting Taverna workbench use on two case studies: 1. African Sleeping Sickness (Trypanosomiasis) Wellcome Trust Project 2. NHS / TSB SNP annotation pipeline

File type: PowerPoint 2007 presentation

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Blob Bonn Tutorial REST services

Created: 2012-09-03 19:34:12

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a brief introduction to using REST servicces through Taverna

File type: PowerPoint presentation

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Blob Bonn Tutorial Different Service Types

Created: 2012-09-03 19:32:32

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Thie tutorial introduces you to using different types of services with Taverna - e.g. asynchronous, biomart and soaplab

File type: PowerPoint presentation

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Blob Bonn Taverna Shims

Created: 2012-08-30 14:18:06

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial provides an introduction to finding, using and designing Shim services for Taverna workflows

File type: PowerPoint presentation

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Blob Bonn Taverna WF Engine

Created: 2012-08-30 14:15:51

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial provides an introduction to using the advanced features of the Taverna workflow engine, such as iterations, looping etc

File type: PowerPoint presentation

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Blob Bonn Taverna Intro Tutorial

Created: 2012-08-30 14:11:55

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial provides an introduction to designing, combining and sharing workflows with Taverna and myExperiment

File type: PowerPoint presentation

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Blob Bozeman Advanced

Created: 2012-08-23 20:29:25

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: PowerPoint presentation

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

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Blob Bozeman Tutorial

Created: 2012-08-22 09:59:37

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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Blob Getting Started with Taverna - an NGS tutorial

Created: 2012-05-23 14:53:24 | Last updated: 2012-05-30 08:48:19

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial is an introduction to using Taverna, using an example from Chip-Seq analysis

File type: PowerPoint presentation

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Blob Advanced exercises for Next Gen Taverna tutorial

Created: 2012-01-16 16:56:02 | Last updated: 2012-01-17 16:00:23

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

These exercises highlight some of the more advanced features of the Taverna engine, for example, looping, iteration and retries

File type: PowerPoint presentation

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Blob Taverna Tutorial Chip-Seq Downstream analysis

Created: 2012-01-17 13:26:09

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a tutorial to introduce the use of Taverna for Next Gen sequence analysis

File type: PowerPoint presentation

Comments: 0 | Viewed: 48 times | Downloaded: 55 times

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Blob Galaxy Chip-Seq Gene List

Created: 2012-01-12 12:50:30 | Last updated: 2012-01-12 12:50:31

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of genes associated with Chip-Seq peaks. It is part of a Galaxy-Taverna Next Gen Sequencing tutorial

File type: Excel workbook

Comments: 0 | Viewed: 40 times | Downloaded: 190 times

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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 Workflow Case Study Portugal

Created: 2009-11-16 14:58:41

Credits: User George User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: Word document

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Blob EraSysBio Summer School Taverna Tutorial

Created: 2009-07-24 21:54:27

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial is an introduction to Taverna and myExperiment

File type: application/mspowerpoint

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Blob Exploring Taverna 2.1 Beta 1

Created: 2009-06-08 19:29:23 | Last updated: 2009-06-08 19:29:52

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Blob Exploring Taverna 2

Created: 2009-05-28 09:08:37

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

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Comments: 0 | Viewed: 41 times | Downloaded: 44 times

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Blob Introduction to Taverna 1

Created: 2009-05-28 09:07:45

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Blob An Introduction to Taverna and myExperiment - Backgr...

Created: 2008-08-04 17:49:10

Credits: User Paul Fisher User Franck Tanoh User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

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Comments: 0 | Viewed: 100 times | Downloaded: 164 times

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Blob A Taverna Users Guide

Created: 2008-08-04 17:40:21

Credits: User Paul Fisher User Katy Wolstencroft User Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

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Comments: 0 | Viewed: 120 times | Downloaded: 139 times

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Blob An Introduction to Taverna Tutorial

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

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

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

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

Created: 2008-06-02 14:46:40

Credits: User Katy Wolstencroft User Andrew Gibson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

File type: Adobe PDF

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Blob Taverna tutorial

Created: 2008-03-03 11:05:24 | Last updated: 2008-03-03 11:20:45

Credits: User Franck Tanoh User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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Blob Taverna tutorial

Created: 2008-03-03 11:15:00 | Last updated: 2008-03-03 11:16:11

Credits: User Franck Tanoh User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

File type: PowerPoint presentation

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Workflow

Workflow SNP identification and evaluation for Diab... (1)

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This workflow gathers SNP information for a gene set of Diabetes Type II phenotype using BioMart queries. Furthermore, GO Terms and functional annotation clustering are defined for this gene set using FunctionalClusterDavid workflow. 

Created: 2015-06-23

Credits: User Nikolaos Bismpikos User Katy Wolstencroft

Attributions: Workflow FunctionalClusterDavid

Workflow

Workflow entreztoKeggImage (1)

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This workflow accepts a list of Entrez Gene IDs. It dentifies which KEGG pathway each gene is involved with and displays the pathway diagrams

Created: 2014-09-05

Credits: User Katy Wolstencroft

Workflow

Workflow ImportConvertEnsembl (1)

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This workflow accepts a spreadsheet file as input and extracts a list of ENSEMBL Gene IDs from column A. The hsapiens_gene_ensembl service converts these IDs to Entrez_geneIds

Created: 2014-09-05

Credits: User Katy Wolstencroft

Workflow

Workflow FunctionalClusterDavid (1)

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This workflow takes a list of Entrez Gene IDs as input and submits them to the DAVID REST API for functional clustering using OG annotaiton, biological pathways and disease associations. Used for analysing a set of genes (i.e. those differentially expressed for a particular disease condition).

Created: 2014-09-05

Credits: User Katy Wolstencroft

Workflow

Workflow Example dbfetch (2)

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Run EBI's dbfetch

Created: 2014-09-03 | Last updated: 2014-09-03

Credits: User Stian Soiland-Reyes User Katy Wolstencroft

Attributions:

Workflow

Workflow Usability Test 3 (1)

No description

Created: 2014-08-12

Credits: User Katy Wolstencroft

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 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 Visualize PAV provenance as SVG (1)

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

Created: 2014-05-08

Credits: User Katy Wolstencroft User Aleksandra Pawlik

Workflow

Workflow Find compounds pharmacology and align agai... (1)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTs API https://dev.openphacts.org/docs/alpha and the myExperiment workflow 3369 "Blast_Align_and_Tree" http://www.myexperiment.org/workflows/3369. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this mean...

Created: 2013-10-16

Credits: User Stian Soiland-Reyes User Katy Wolstencroft

Attributions: Workflow Blast_Align_and_Tree

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 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 OPS_FreetextToTargetInfo (1)

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Workflow to retrieve target information for the concepts as refered to by humans (the input). Known issues: It produces error values for the concepts returned by ConceptWiki that are apparently not present in OPS (e.g. for "ezh2" and limit=10, it gives 7/10 error values vs "ezh2 (homo sapiens)" giving 2 valid values).

Created: 2013-06-18

Credits: User Marco Roos User Katy Wolstencroft User paul groth

Workflow

Workflow Free text search to Concept Wiki URI (4)

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Free text search of concept wiki using the Openphacts "Map free text to a concept url based on semantic tag" ie /search/byTag. Search for either compounds or targets depending on the input uuid for "searchType" and filter by source authority with the "branch" input

Created: 2013-06-24 | Last updated: 2013-06-24

Credits: User Ian Dunlop User Katy Wolstencroft User Marco Roos User paul groth

Workflow

Workflow Blast_Align_and_Tree (2)

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This workflow accepts a protein sequence as input. This sequence is compared to others in the Uniprot database, using the NCBI BLAST Web Service from the EBI (WSDL), and the top 10 hits are returned (Nested workflow:EBI_NCBI_BLast). For each extracted hit, the Uniprot REST service returns the protein sequence in FASTA format. The workflow concatenates the 10 protein sequences and submits them as input to the EBI CLustalw service (Nested workflow EMBL_EBI_clustalw2_SOAP). These sequences are ...

Created: 2013-01-28 | Last updated: 2013-01-30

Credits: User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow Protein_search_fetch_align_tree

Workflow

Workflow clustal_phylogeny (3)

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This workflow accepts a ClustalW protein sequence alignment and produces a phylogenetic tree, using the EBI clustalw_phylogeny web service, which implements phylip.

Created: 2013-01-28 | Last updated: 2013-03-11

Credits: User Katy Wolstencroft

Workflow

Workflow Blast_and_Interproscan (5)

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This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hits to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required. The sequences for the top 10 hits are retrieved from the UniProt database and analysed using InterproScan (also from the EBI) to determine functional domains and motifs in each sequenc...

Created: 2013-01-28 | Last updated: 2013-01-30

Credits: User Katy Wolstencroft

Workflow

Workflow InterproScan_Example (3)

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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.

Created: 2013-01-28 | Last updated: 2013-01-30

Credits: User Katy Wolstencroft

Workflow

Workflow ImportRefSeqtoKegg (3)

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This workflow extracts a column of RefSeq gene IDs from a CSV file and then converts them to Kegg gene identifiers. This workflow uses the new KEGG REST service, which replaces the old SOAP interface from 31st December 2012

Created: 2012-11-12 | Last updated: 2013-01-08

Credits: User Katy Wolstencroft

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 SNP Position Information (1)

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This workflow extracts information about the position of SNPs and the genes they are associated with, using BioMart (ENSEMBL Variation 66).

Created: 2012-04-17 | Last updated: 2012-04-17

Credits: User Katy Wolstencroft

Workflow

Workflow InterproScan without Looping (1)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text 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. This workflow will not work properly until we add looping.

Created: 2011-03-16 | Last updated: 2012-08-29

Credits: User Katy Wolstencroft

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 Katy Wolstencroft

Workflow

Workflow Reactome pathways (1)

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This workflow returns a list of pathways gene products are involved in, along with their descriptions and Gene Ontology annotations

Created: 2012-01-16

Credits: User Katy Wolstencroft

Workflow

Workflow UnigeneID to KEGG Pathways (3)

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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: 2012-01-16 | Last updated: 2012-12-17

Credits: User Katy Wolstencroft User Paul Fisher

Attributions: Workflow NCBI Gi to Kegg Pathways

Workflow

Workflow Import and convert gene list (1)

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This workflow extracts a column of RefSeq gene IDs from a CSV file and then converts them to Unigene identifiers

Created: 2012-01-15 | Last updated: 2012-03-12

Credits: User Katy Wolstencroft

Workflow

Workflow NCBI Gi to Kegg Pathway Descriptions (5)

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This workflow accepts a list of NCBI 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: 2012-01-12 | Last updated: 2013-01-30

Credits: User Katy Wolstencroft

Attributions: Workflow NCBI Gi to Kegg Pathways

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 BiomartAndEMBOSSDisease (2)

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

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

Credits: User Katy Wolstencroft

Attributions: Workflow BiomartAndEMBOSSDisease

Workflow

Workflow EBI_InterproScan_NewServices (2)

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This workflow performs an interproscan on provided sequencesThis 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: 2011-01-17 | Last updated: 2011-01-17

Credits: User Katy Wolstencroft User Hamish McWilliam User Stian Soiland-Reyes

Attributions: Workflow EBI_InterProScan for Taverna 2 Workflow EBI_InterProScan for Taverna 2 Workflow EBI_InterProScan

Workflow

Workflow EBI_NCBI_BLAST (4)

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This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hits to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required. This workflow uses the new EBI services. They are asynchronous and so require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now wo...

Created: 2011-01-17 | Last updated: 2013-05-30

Credits: User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST

Workflow

Workflow omim and pathways (2)

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This workflow searches OMIM for entries associated with a particular disease in OMIM, returns the IDs and maps them to Kegg Gene IDs. For each gene, it then gets the description and any corresponding pathways those genes are involved with

Created: 2009-03-03 | Last updated: 2009-11-02

Credits: User Katy Wolstencroft User Paul Fisher

Attributions: Workflow Get Kegg Gene information

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 EBI_InterProScan for Taverna 2 (2)

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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: 2010-01-26 | Last updated: 2010-01-26

Credits: User Stian Soiland-Reyes User Paolo User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EBI InterproScan T2 Workflow EBI_InterProScan

Workflow

Uploader

Workflow EBI InterproScan T2 (1)

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This T2 version of the Interpro scan workflow is an example of the while loop in action. This is used to poll the async EBI service for the result (busy waiting)

Created: 2009-06-30 | Last updated: 2009-06-30

Credits: User Stian Soiland-Reyes User Katy Wolstencroft

Attributions:

Workflow

Uploader

Workflow Analysing workflows (3)

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

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

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

Workflow

Workflow Retrieve Protein Sequence (1)

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Retrieves a protein sequence in Fasta format from GenBank, given a GenBank identifier. Example input for this workflow is: EDL10223.1

Created: 2008-07-30 | Last updated: 2009-12-03

Credits: User Katy Wolstencroft

Workflow

Workflow genscan_shim_example2.xml (1)

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No description

Created: 2008-07-30 | Last updated: 2008-07-30

Credits: User Katy Wolstencroft

Workflow

Workflow genscan_shim_example.xml (1)

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No description

Created: 2008-07-30 | Last updated: 2008-07-30

Credits: User Katy Wolstencroft

Workflow

Workflow countryExample_working (1)

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This Workflow allows you to find a list of the cities in a particular country, the time zone that country is in, the conversion rate of the currency in that country and yours and the international dialling code for that country

Created: 2008-06-16

Credits: User Katy Wolstencroft

Workflow

Workflow countryExammple_unfinished (1)

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This Workflow is unfinished, but when connected up, it will allow you to find a list of the cities in a particular country, the time zone that country is in, the conversion rate of that country and yours and the international dialling code for that country

Created: 2008-06-16

Credits: User Katy Wolstencroft

Workflow

Workflow Retrieve Protein Sequence and BLAST (1)

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Retrieves a protein sequence in Fasta format from Genbank and then performs a BLAST on that sequence

Created: 2007-11-09 | Last updated: 2008-06-05

Credits: User Katy Wolstencroft

Workflow

Workflow Fetch PDB flatfile from RCSB server (1)

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Given aPDB identifier such as '1crn', this workflow fetches the PDB format flatfile from the RCSB

Created: 2008-01-25 | Last updated: 2008-03-05

Credits: User Katy Wolstencroft

Workflow

Workflow ExampleWorkflow1 (2)

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This workflow was created based on the Leeds Taverna Workshop 2008-02-04 material developed by Katy.

Created: 2008-02-04 | Last updated: 2008-02-04

Credits: User Katy Wolstencroft

Workflow

Workflow Gene annotation pipeline for the Graves di... (2)

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This is a revised workflow for the Graves disease scenario gene annotation pipeline used in the myGrid project. The workflow had to be re-written due to the loss of the services invoked in the original workflow.

Created: 2007-10-03 | Last updated: 2007-11-22

Credits: User Katy Wolstencroft User Peter Li

Workflow

Workflow EBI_InterProScan for Taverna 2 (2)

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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 t...

Created: 2010-01-26 | Last updated: 2010-11-24

Credits: User Stian Soiland-Reyes User Katy Wolstencroft User Paolo User Hamish McWilliam

Attributions: Workflow EBI_InterProScan for Taverna 2 Workflow EBI InterproScan T2 Workflow EBI_InterProScan Workflow EBI InterProScan

Workflow

Workflow EMBL-EBI ClustalW2_SOAP (2)

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Perform a ClustalW2 alignment of protein sequences using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap). 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: 2011-01-17 | Last updated: 2013-01-30

Credits: User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EMBL-EBI ClustalW2 (SOAP) Workflow EBI_ClustalW2

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