Content from the Bonn eScience Workshop group

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: Katy Wolstencroft Alan Williams

Attributions: BiomartAndEMBOSSAnalysis

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: Katy Wolstencroft Hamish McWilliam

Attributions: EMBL-EBI ClustalW2 (SOAP) EBI_ClustalW2

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Human Gene expression data -

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

Credits: Saeedeh

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

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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

File type: Plain text

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Taverna XPath practical slides .

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

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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Taverna Iteration training slides

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

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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Bonn Taverna Training agenda March/April 2011

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

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Word document

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Taverna Introduction

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

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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Example XML

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

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

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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: Paul Fisher

Attributions: XPath Pubmed Ids