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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: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: Fetch today's xkcd comic

Biomart and EMBOSS analysis (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: 2009-07-03 | Last updated: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: BiomartAndEMBOSSAnalysis

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: Stian Soiland-Reyes Katy Wolstencroft

Attributions:

DOI Files (1)

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This workflow generates additional files required for handling DOI creation: the DOI URL mapping required for the DOI deposit, and a set of sql update statements to insert the DOIs into an eprints database. Note that it is extremely important for this workflow to use the same CSV file as was used with the DOI record generator, as well as the same seed number.

Created: 2009-06-05

Credits: Andrea Wiggins

Attributions: DOI Record Generator

KEGG Gene IDs to KEGG Pathways (1)

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this is a simplified version of Paul's workflow (linked?) that is designed to be provenance-friendly

Created: 2009-06-04 | Last updated: 2010-01-07

Credits: Paolo

Attributions: Pathways and Gene annotations for QTL region

Test SOAP/WSDL Service Availability (1)

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This workflow tests for all Taverna workflows stored at myExperiment wether the SOAP/WSDL services used still exists. For each SOAP/WSDL service it checks wether the WSDL file is still accessible and whether the operation is still exists. The output is among others a report of accessible services and operation, operations which WSDL file is not accessible, operations which WSDL file still exists, but the operation is not defined anymore. The last set needs to be checked by hand, because...

Created: 2009-05-29

Credits: Wassinki

Index MyExperiment Workflow (2)

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This workflow uses AIDA components to index all of the workflows on MyExperiment. First, it lists and downloads each workflow's xml file. Then, the titles and descriptions are parsed and submitted to an Indexer webservice. After it's finished, your index will be searchable by visiting http://aida.science.uva.nl:9999/search.

Created: 2009-05-26 | Last updated: 2009-05-27

Credits: Edgar

GATE Monte-Carlo simulations (3)

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Application description is found in the following papers: Jan S et al, GATE: a simulation toolkit for PET and SPECT. Phys. Med. Biol. 49 (2004) 4543-4561 Sarrut D. and Guigues L. Region-oriented CT image representation for reducing computing time of Monte Carlo simulations. Med Phys. 35(4):1452-1463. 2008 Two components (fgate and merge, merge being disabled in experiments conducted for the heteropar and JGC papers) are run on the EGEE grid. A quite elaborated workflow is ma...

Created: 2009-05-23 | Last updated: 2009-08-13

Credits: Glatard

MassBank to KEGG (1)

Workflow that queries MassBank DB to retrieve database identifiers (KEGG, PubChem, InChI) and continue search with them to retrieve pathways from KEGG for given compound identifier,searches PubChem via eutils and PUG, queries ChemSpider for compound information and image. Note: Usage of ChemSpider web services requires a valid security token - receive one by registering at ChemSpider (look at your profile to see your token)

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

Download pathways for external references ... (2)

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Takes a list of external references to genes/proteins/metabolites, finds all pathways on WikiPathways that contain one of the given genes/proteins/metabolites and downloads them in a given file format.

Created: 2009-02-03

Credits: Thomaskelder