Content from the Bonn eScience Workshop group

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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 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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Blob Human Gene expression data -

Created: 2011-04-01 09:12:28 | Last updated: 2011-04-01 09:12:40

Credits: User Saeedeh

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list processed  for Human gene expression CEL files relating to the: Impact of NRSF variant over-expression in SK-N-AS human neuroblastoma cells (http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-GEOD-22467&expandefo=on). The CEL files were analysed using the MADAT Taverna workflow available on myExperiment: http://www.myexperiment.org/workflows/2002.html

File type: ZIP archive

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Blob Human Probeset data from Affymetrix

Created: 2011-04-01 09:08:45 | Last updated: 2011-04-01 09:08:51

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list or affymetrix probest identifiers for Human gene expression data relating to the: Impact of NRSF variant over-expression in SK-N-AS human neuroblastoma cells (http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-GEOD-22467&expandefo=on)

File type: Plain text

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Blob Taverna XPath practical slides .

Created: 2011-03-30 09:17:52 | Last updated: 2011-03-30 09:17:55

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Taverna training material for using and configuring XPath queries using native XPath Java methods, and XPath Service templates.

File type: PowerPoint presentation

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Blob Taverna Iteration training slides

Created: 2011-03-28 11:44:06 | Last updated: 2011-03-28 11:44:08

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Training slides to outline how to use iterations and iteration strategies in Taverna

File type: PowerPoint presentation

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Blob Bonn Taverna Training agenda March/April 2011

Created: 2011-03-28 11:31:38 | Last updated: 2011-03-28 11:31:39

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Agenda of Taverna training

File type: Word document

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Blob Taverna Introduction

Created: 2011-03-28 11:29:08 | Last updated: 2011-03-28 11:29:10

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This powerpoint presentation contains a set of starting exercises for begining your Taverna training.

File type: PowerPoint presentation

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Blob Example XML

Created: 2011-03-23 17:25:09 | Last updated: 2011-03-23 17:25:11

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains some example XML to be used for teaching material and XPath queries

File type: XML

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Workflow XPath Pubmed Ids (2)

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This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml. The xml is then parsed to retrieve a list of PubMed ids

Created: 2011-03-23 | Last updated: 2011-03-30

Credits: User Paul Fisher

Attributions: Workflow XPath Pubmed Ids

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