Workflows

Load affymetrix experiments results into S... (1)

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The affymetrix data source is not public.

Created: 2009-02-17

Credits: Francois Belleau

Sesame triplestore loader from a dereferen... (2)

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Load triples obtained from an URL in N3 or XML format and load them into your local Sesame Triplestore locally installed and available at http://localhost/sesame. The http://localhost/sesame/servlets/uploadURL service of Sesame is used in HTTP POST mode.

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

Bio2RDF: Sesame triplestore loader from tr... (2)

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INSERT IN GRAPH

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

Bio2rdf: Bind search, rdfise and load demo (1)

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INSERT IN GRAPH <http://localhost/sesame/mem_rdf_db> {     CONSTRUCT { ?s, ?p, ?o . }     FROM <http://soap.bind.ca/wsdl/bind.wsdl>     WHERE {         SELECT ?s         FROM <http://soap.bind.ca/wsdl/bind.wsdl>         WHERE {              ?s, ?p, ?o .        ...

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

Bio2RDF: Rdfiser for Bind protein interact... (1)

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CONSTRUCT{ <bmuri>, ?p, ?o . } FROM <http://soap.bind.ca/wsdl/bind.wsdl> WHERE { <bmuri>, ?p, ?o . }

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

Bio2RDF: Bind fulltext search service retu... (1)

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SELECT ?s FROM <http://soap.bind.ca/wsdl/bind.wsdl> WHERE {   ?s, ?p, ?o .   FILTER ( regex(?o, "query")) . }

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

Bio2RDF: CPath search, rdfise and load dem... (1)

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Search for a list of genes into the Pathway Commons interaction database and load the fetched triples into a triplestore. INSERT IN GRAPH < http://localhost/sesame/mem_rdf_db> {     CONSTRUCT{ ?s, ?p, ?o . }     FROM < http://www.pathwaycommons.org/pc/webservice.do>     WHERE {         SELECT ?s         FROM <http://www.pathwaycommons.org/pc/webservice.do>  ...

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

Bio2RDF: CPath search, rdfise and load dem... (1)

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No description

Created: 2009-02-19

Credits: Francois Belleau

Bio2RDF: CPath describe interaction (1)

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No description

Created: 2009-02-19

Credits: Francois Belleau

Bio2RDF: CPath reverse links (1)

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No description

Created: 2009-02-19

Credits: Francois Belleau

Bio2RDF: CPath search in taxon (1)

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No description

Created: 2009-02-19

Credits: Francois Belleau

Lymphoma type prediction based on microar... (7)

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Scientific value Using gene-expression patterns associated with DLBCL and FL to predict the lymphoma type of an unknown sample. Using SVM (Support Vector Machine) to classify data, and predicting the tumor types of unknown examples. Steps Querying training data from experiments stored in caArray. Preprocessing, or normalize the microarray data. Adding training and testing data into SVM service to get classification result.

Created: 2010-05-11 | Last updated: 2010-05-11

Credits: Wei Tan Ravi Stian Soiland-Reyes

Get the list of GeneID for all pathways of... (1)

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No description

Created: 2009-04-28

Credits: Francois Belleau

Insert in local triplestore GeneID and KEG... (1)

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No description

Created: 2009-04-28

Credits: Francois Belleau

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: Katy Wolstencroft Hamish McWilliam Stian Soiland-Reyes

Attributions: EBI_InterProScan for Taverna 2 EBI_InterProScan for Taverna 2 EBI_InterProScan

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

QSPR Model Discovery -- workflow structure... (2)

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replicates the structure of the QSPR model discovery workflow. Ref.: replicates the structure of the QSPR model discovery workflow. Ref.: http://www.openqsar.com/

Created: 2011-01-18 | Last updated: 2011-01-18

PRM With External Data (1)

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IN PROGRESS! Runs the PRM using data from an external on-line source.

Created: 2011-01-19 | Last updated: 2011-01-19

Credits: Nick Malleson

Pathways and Gene annotations forQTL region (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Cow, Bos taurus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway data...

Created: 2011-01-21 | Last updated: 2011-01-21

Credits: Paul Fisher

SELECT3 (2)

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Select3 decides if a particular transition matches the selection criteria based on the line strength and line opacity in a given medium. To do that select3 requires a model of the medium (temperature, pressure, node spacing), chemical composition and boundary conditions. Only 1D models are supported at the moment. Select3 processes one transition at a time working in two modes: opacity and synthesis. In the first mode it computes line opacity, compares it to the reference (e.g. bf and ff opa...

Created: 2011-01-22 | Last updated: 2011-02-27

A workflow version of the EMBOSS tutorial (1)

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Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.

Created: 2011-01-27 | Last updated: 2011-01-27

Credits: Maninder

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

Define one query and retrieve Molecular In... (3)

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Define one query and retrieve Molecular Interactions from PSICQUIC Services registered in the PSICQUIC registry.

Created: 2011-01-31 | Last updated: 2013-07-10

Credits: Rafael C. Jimenez

Select redundant accessions (1)

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Simple workflows to select accessions which appear more than once. Chose threshold to specify how many times an accession has to appear to be selected. This workflow uses a list of Comma-separated values as input. The accessions selected is the result which is presented in a String of Comma-separated values.

Created: 2011-01-31 | Last updated: 2011-01-31

Credits: Rafael C. Jimenez