User: Katy Wolstencroft

View Download

Annotating Experimental Data

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint 2007 presentation

Comments: 0 | Viewed: 52 times | Downloaded: 20 times

This File has no tags!

View Download

Geo File for Annotation

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: application/excel

Comments: 0 | Viewed: 41 times | Downloaded: 22 times

This File has no tags!

View Download

Taverna Tutorial Data Integration NL 2015

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

Comments: 0 | Viewed: 57 times | Downloaded: 22 times

View Download

Importing data from spreadsheets into Taverna workflows

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

Credits: Aleksandra Pawlik Katy Wolstencroft Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint 2007 presentation

Comments: 0 | Viewed: 52 times | Downloaded: 29 times

View Download

Exploring Taverna Engine - managing lists, looping, ...

Created: 2015-01-22 16:01:32

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint 2007 presentation

Comments: 0 | Viewed: 116 times | Downloaded: 30 times

View Download

Using REST services from Biocatalogue

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

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint 2007 presentation

Comments: 0 | Viewed: 55 times | Downloaded: 29 times

View Download

Building simple workflow in Taverna

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

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint 2007 presentation

Comments: 0 | Viewed: 58 times | Downloaded: 31 times

View Download

Short introduction to Taverna 2.5

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

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint 2007 presentation

Comments: 0 | Viewed: 60 times | Downloaded: 42 times

View Download

An introduction to designing and executing workflows...

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

Credits: Norman Morrison Katy Wolstencroft Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 46 times | Downloaded: 33 times

This File has no tags!

View Download

Exploring the Taverna workflow engine

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

Credits: Norman Morrison Katy Wolstencroft Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 60 times | Downloaded: 62 times

This File has no tags!

View Download

An introduction to designing and executing workflows...

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

Credits: Norman Morrison Katy Wolstencroft Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 47 times | Downloaded: 40 times

This File has no tags!

View Download

An introduction to designing and executing workflows...

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

Credits: Norman Morrison Katy Wolstencroft Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 57 times | Downloaded: 43 times

This File has no tags!

View Download

Introduction to myExperiment

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

Credits: Norman Morrison Katy Wolstencroft Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 28 times | Downloaded: 17 times

This File has no tags!

View Download

Introduction to building workflows with Taverna

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

Credits: Aleksandra Pawlik Katy Wolstencroft Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 31 times | Downloaded: 20 times

This File has no tags!

View Download

Cranfield - Introduction to webservices and workflows

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

Credits: Aleksandra Pawlik Katy Wolstencroft Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 31 times | Downloaded: 24 times

This File has no tags!

View Download

XPath service Tutorial

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 25 times | Downloaded: 21 times

This File has no tags!

View Download

XPath service Tutorial

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

Credits: Katy Wolstencroft Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 52 times | Downloaded: 43 times

This File has no tags!

View Download

REST Service Tutorial

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

Credits: Katy Wolstencroft Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 51 times | Downloaded: 40 times

This File has no tags!

View Download

Shims and Beanshells - tutorial

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 40 times | Downloaded: 35 times

This File has no tags!

View Download

Introduction to Taverna -part2 - Bonn 2013

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

Credits: Katy Wolstencroft Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 62 times | Downloaded: 64 times

This File has no tags!

View Download

Introduction to Taverna - Bonn 2013

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

Credits: Katy Wolstencroft Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 57 times | Downloaded: 59 times

This File has no tags!

View Download

Nested UnigeneID_to_KEGG in Import and Convert

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

Credits: Katy Wolstencroft Alan Williams Paul Fisher

Attributions: UnigeneID to KEGG Pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Trident (Package)

Comments: 0 | Viewed: 31 times | Downloaded: 15 times

This File has no tags!

View Download

GalaxyGeneList - long : datafile for training

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

Comments: 0 | Viewed: 29 times | Downloaded: 16 times

This File has no tags!

View Download

GalaxyGeneList - short : datafile for training

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

Comments: 0 | Viewed: 53 times | Downloaded: 95 times

This File has no tags!

View Download

Taverna 2.4 Tutorial

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 20 times | Downloaded: 42 times

This File has no tags!

View Download

Cranfield Msc Intro to Taverna

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 40 times | Downloaded: 47 times

View Download

Agenda of Bonn tutorial

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

Credits: Helen Hulme Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Word document

Comments: 0 | Viewed: 37 times | Downloaded: 15 times

This File has no tags!

View Download

Workflow Assignment Instructions

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 34 times | Downloaded: 30 times

This File has no tags!

View Download

Bonn Taverna Presentation - Case Studies

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

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint 2007 presentation

Comments: 0 | Viewed: 41 times | Downloaded: 35 times

This File has no tags!

View Download

Bonn Tutorial REST services

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 60 times | Downloaded: 49 times

This File has no tags!

View Download

Bonn Tutorial Different Service Types

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 32 times | Downloaded: 41 times

This File has no tags!

View Download

Bonn Taverna Shims

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 74 times | Downloaded: 61 times

View Download

Bonn Taverna WF Engine

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 64 times | Downloaded: 48 times

View Download

Bonn Taverna Intro Tutorial

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 72 times | Downloaded: 66 times

View Download

Bozeman Advanced

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 18 times | Downloaded: 9 times

This File has no tags!

View Download

Bozeman Tutorial

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 54 times | Downloaded: 65 times

View Download

Getting Started with Taverna - an NGS tutorial

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 79 times | Downloaded: 82 times

View Download

Advanced exercises for Next Gen Taverna tutorial

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 40 times | Downloaded: 50 times

This File has no tags!

View Download

Taverna Tutorial Chip-Seq Downstream analysis

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 50 times | Downloaded: 57 times

This File has no tags!

View Download

Galaxy Chip-Seq Gene List

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

Comments: 0 | Viewed: 42 times | Downloaded: 192 times

This File has no tags!

View Download

BioVel Taverna Tutorial

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

Credits: Katy Wolstencroft Alan Williams Robert Haines Biomobst

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 65 times | Downloaded: 163 times

View Download

Workflow Case Study Portugal

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

Credits: George Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Word document

Comments: 0 | Viewed: 45 times | Downloaded: 35 times

View Download

EraSysBio Summer School Taverna Tutorial

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: application/mspowerpoint

Comments: 0 | Viewed: 76 times | Downloaded: 63 times

View Download

Exploring Taverna 2.1 Beta 1

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: application/mspowerpoint

Comments: 0 | Viewed: 78 times | Downloaded: 93 times

This File has no tags!

View Download

Exploring Taverna 2

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 45 times | Downloaded: 46 times

This File has no tags!

View Download

Introduction to Taverna 1

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 54 times | Downloaded: 53 times

This File has no tags!

View Download

An Introduction to Taverna and myExperiment - Backgr...

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

Credits: Paul Fisher Franck Tanoh Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 131 times | Downloaded: 187 times

View Download

A Taverna Users Guide

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

Credits: Paul Fisher Katy Wolstencroft Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 152 times | Downloaded: 166 times

View Download

An Introduction to Taverna Tutorial

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

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 114 times | Downloaded: 215 times

View Download

The Data Playground: An Intuitive Workflow Specifica...

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

Credits: Katy Wolstencroft Andrew Gibson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

Comments: 0 | Viewed: 214 times | Downloaded: 228 times

View Download

Taverna tutorial

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

Credits: Franck Tanoh Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 4 | Viewed: 472 times | Downloaded: 664 times

View Download

Taverna tutorial

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

Credits: Franck Tanoh Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 205 times | Downloaded: 282 times

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

• Download

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: Nikolaos Bismpikos Katy Wolstencroft

Attributions: FunctionalClusterDavid

entreztoKeggImage (1)

• Download

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: Katy Wolstencroft

ImportConvertEnsembl (1)

• Download

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: Katy Wolstencroft

FunctionalClusterDavid (1)

• Download

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: Katy Wolstencroft

Example dbfetch (2)

• Download

Run EBI's dbfetch

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

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions:

Usability Test 3 (1)

Created: 2014-08-12

Credits: Katy Wolstencroft

EBI_InterproScan_broken (1)

• Download

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: Alan Williams Katy Wolstencroft Hamish McWilliam

Attributions: EBI_InterproScan_NewServices

Simple FASTA workflow (1)

• Download

A simple Taverna workflo

Created: 2014-01-22

Credits: Aleksandra Pawlik Katy Wolstencroft Alan Williams

Visualize PAV provenance as SVG (1)

• Download

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: Katy Wolstencroft Aleksandra Pawlik

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

• Download

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: Stian Soiland-Reyes Katy Wolstencroft

Attributions: Blast_Align_and_Tree

BioVeL workshop reduced full workflow (1)

• Download

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: Katy Wolstencroft Alan Williams

Attributions:

UnigeneID to KEGG Pathways (1)

• Download

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: Katy Wolstencroft Alan Williams Paul Fisher

Attributions: NCBI Gi to Kegg Pathways

OPS_FreetextToTargetInfo (1)

• Download

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: Marco Roos Katy Wolstencroft paul groth

Free text search to Concept Wiki URI (4)

• Download

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: Ian Dunlop Katy Wolstencroft Marco Roos paul groth

Blast_Align_and_Tree (2)

• Download

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: Katy Wolstencroft Hamish McWilliam

Attributions: Protein_search_fetch_align_tree

clustal_phylogeny (3)

• Download

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: Katy Wolstencroft

Blast_and_Interproscan (5)

• Download

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: Katy Wolstencroft

InterproScan_Example (3)

• Download

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: Katy Wolstencroft

ImportRefSeqtoKegg (3)

• Download

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: Katy Wolstencroft

BiomartAndEMBOSSDisease (4)

• Download

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: Katy Wolstencroft Alan Williams

Attributions: BiomartAndEMBOSSAnalysis

SNP Position Information (1)

• Download

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: Katy Wolstencroft

InterproScan without Looping (1)

• Download

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: Katy Wolstencroft

BiomartAndEMBOSSMouseRat (1)

• Download

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: Katy Wolstencroft

Reactome pathways (1)

• Download

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: Katy Wolstencroft

UnigeneID to KEGG Pathways (3)

• Download

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: Katy Wolstencroft Paul Fisher

Attributions: NCBI Gi to Kegg Pathways

Import and convert gene list (1)

• Download

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: Katy Wolstencroft

NCBI Gi to Kegg Pathway Descriptions (5)

• Download

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: Katy Wolstencroft

Attributions: NCBI Gi to Kegg Pathways

EBI_InterproScan_NewServices (1)

• Download

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: Alan Williams Katy Wolstencroft

Attributions: EBI_InterproScan_NewServices

BiomartAndEMBOSSDisease (2)

• Download

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: Katy Wolstencroft

Attributions: BiomartAndEMBOSSDisease

EBI_InterproScan_NewServices (2)

• Download

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: Katy Wolstencroft Hamish McWilliam Stian Soiland-Reyes

Attributions: EBI_InterProScan for Taverna 2 EBI_InterProScan for Taverna 2 EBI_InterProScan

EBI_NCBI_BLAST (4)

• Download

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: Katy Wolstencroft Hamish McWilliam

Attributions: EBI_NCBI_BLAST

omim and pathways (2)

• Download

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: Katy Wolstencroft Paul Fisher

Attributions: Get Kegg Gene information

BioMart and Emboss Analysis (T2) (1)

• Download

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: Katy Wolstencroft Alan Williams

Attributions: BiomartAndEMBOSSAnalysis

EBI_InterProScan for Taverna 2 (2)

• Download

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: Stian Soiland-Reyes Paolo Katy Wolstencroft Hamish McWilliam

Attributions: EBI InterproScan T2 EBI_InterProScan

EBI InterproScan T2 (1)

• Download

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: Stian Soiland-Reyes Katy Wolstencroft

Attributions:

Analysing workflows (3)

• Download

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: Wassinki Pieter Neerincx Katy Wolstencroft Marco Roos

Retrieve Protein Sequence (1)

• Download

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: Katy Wolstencroft

genscan_shim_example2.xml (1)

• Download

No description

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

Credits: Katy Wolstencroft

genscan_shim_example.xml (1)

• Download

No description

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

Credits: Katy Wolstencroft

countryExample_working (1)

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: Katy Wolstencroft

countryExammple_unfinished (1)

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: Katy Wolstencroft

Retrieve Protein Sequence and BLAST (1)

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: Katy Wolstencroft

Fetch PDB flatfile from RCSB server (1)

• Download

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: Katy Wolstencroft

ExampleWorkflow1 (2)

• Download

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: Katy Wolstencroft

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

• Download

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: Katy Wolstencroft Peter Li

EBI_InterProScan for Taverna 2 (2)

• Download

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: Stian Soiland-Reyes Katy Wolstencroft Paolo Hamish McWilliam

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

EMBL-EBI ClustalW2_SOAP (2)

• Download

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: Katy Wolstencroft Hamish McWilliam

Attributions: EMBL-EBI ClustalW2 (SOAP) EBI_ClustalW2