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Taverna rendering of the PAN-STARRS workfl... (1)

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Example inputs: CSVRootPath = /Users/paolo/Documents/myGRID/OPM/PC3/SampleData/J062941 JobID:J062941  

Created: 2009-04-30

Credits: Paolo

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myExperiment paper for Concurrency Practice and Expe...

Created: 2009-04-10 13:41:56 | Last updated: 2009-04-14 08:38:09

8 items in this pack

Comments: 1 | Viewed: 228 times | Downloaded: 40 times

Search InChI in ChemSpider (1)

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This workflows queries ChemSpider for compound information and compound images. Note that a Chemspider security token is needed in order to access some of the ChemSpider services (receive one by registering at ChemSpider). Possible search terms might be InChI codes, ChemSpider identifiers or names.

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

Credits: Michael Gerlich

Retrieve Pathways and Compound information... (1)

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Given a KEGG compound identifier (e.g. cpd:C00905), this workflow queries KEGG DB for pathways and compound information for each of these compounds. As the KEGG pathway service tries to find pathways which contain all input compounds, the input list is split up to circumvent this behaviour and to search for only one compound in a pathway at a time. Compounds identified in pathways are marked as red in the resulting pathway image.

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

Credits: Michael Gerlich

MiscanMod (1)

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Created: 2009-03-27 | Last updated: 2009-04-23

Credits: Robert Muetzelfeldt

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Experiment One: Vapor Pressure of Liquids [Lab Report]

Created: 2009-03-23 22:50:57

Credits: Lance A. Schell

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Word 2007 document

Comments: 0 | Viewed: 112 times | Downloaded: 595 times

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Kegg_DrugID (1)

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 This workflow accepts looks up drug identifiers from KEGG given a pathway identifier. You can enter a pathway ID in the form path:map07026

Created: 2009-03-18 | Last updated: 2009-03-18

Credits: Rory

Get Graphs of Name (1)

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This workflow gets the Ondex graphs relating to a specified name

Created: 2009-02-27

Credits: Paul Fisher

Get Concepts (1)

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This workflow gets all the concepts in an Ondex graph, using a given graph id

Created: 2009-02-27

Credits: Paul Fisher

CDK Example (1)

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This workflow reads a library from an SD file (change the default value of Read_MDL_SD_File) and identifies those structures that conform to Lipinski's Rule of Five. It then performs a substructure query, represented as SMILES (change the default value on Parse_SMILES), on the structures that pass Lipinski, and creates PNG images of those structures that contain the substructure. The image results will be found in your Taverna Data folder.

Created: 2009-02-26

Credits: Paul Dobson

SH2 domain screen in homo (1)

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You can now Download this Workflow and import it into BioExtract Server at bioextract.org. This workflow retrieves a set of protein sequences containing SH2 domain in homo sapiens from NCBI GenBank Protein, then extracts the sequences of SH2 regions and performs a multiple alignment using EMMA and ClustalW. The alignment by EMMA is then plotted to PNG images, simultaneously creating a frequency matrix by prophecy. Finally scan a protein sequence queried with the frequency matrix using prophet.

Created: 2009-02-19 | Last updated: 2009-06-08

Credits: Youguruozhu

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: 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: 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 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

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

Initialize triplestore with Murin's protoc... (1)

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This workflow initialize the Sesame triplestore with initial data.  The 5 rdfiser in JSP are needed, they are executed on localhost.

Created: 2009-02-17 | Last updated: 2009-02-17

Credits: Francois Belleau

Pubmed mashup demo in a Virtuoso triplestore (1)

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This workflow build a mashup in your local virtuoso server (available at http://localhost:8890/sparql) by downloading the needed pubmed documents from NCBI and by converting them into N3 format.  Once all documents loaded into the triplestore you can query them with SPARQL. For example try those queries : SELECT count(*) WHERE {?s ?p ?o} SELECT ?o, count(*) WHERE {?s <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?o} Dr Labrie's MeSH subject of interest : SELECT ?o, count...

Created: 2009-02-11

Credits: Francois Belleau

Rich Get Richer (1)

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This workflow is a replication of the analysis from an OSCon 2004 presentation by Megan Conklin, entitled "Do the Rich Get Richer?" to demonstrate scale-free distribution of FLOSS developers among projects. The workflow retrieves the current number of active developers (for the most recent calculation of said statistic) from the FLOSSmole database. It summarizes and plots the distribution of developers to projects, on both a straight and log-log scale. It also generates a flat list of the de...

Created: 2009-02-05

Credits: Andrea Wiggins

Workflow Pattern - Cancelling Discriminator (1)

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This workflow is a GWorkflowDL representation of a cancelling discriminator that cancels the invocation of B if A has been executed and vice versa. This is only one out of various possibilities to model this workflow pattern. Please regard that this workflow example uses a separate method for cancelling the invocation of the activity. This is very useful if the invocation of the activity is done asynchronously as it is often implemented for long running methods. It may be necessary to propag...

Created: 2009-01-06

Credits: Andreas Hoheisel

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Test Input for Mapping oligonucleotides to an assembly

Created: 2008-12-11 12:06:36 | Last updated: 2008-12-11 12:21:53

Credits: Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

Comments: 0 | Viewed: 817 times | Downloaded: 53 times

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Input for Mapping oligonucleotides to an assembly

Created: 2008-12-11 12:04:22 | Last updated: 2008-12-11 12:21:40

Credits: Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

Comments: 0 | Viewed: 101 times | Downloaded: 35 times

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caDSR metadata query in caGrid (1)

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This workflow shows the coordinated use of two services in CaGrid, i.e., the caDSR (Cancer Data Standards Repository) and EVS (Enterprise Vocabulary Services) services. caDSR is to define a comprehensive set of standardized metadata descriptors for cancer research terminology used in information collection and analysis. EVS provides resources and services to meet NCI needs for controlled terminology, and to facilitate the standardization of terminology and information systems across the Insti...

Created: 2008-12-05 | Last updated: 2008-12-05

Credits: Wei Tan

Affimetrix microarray: part three (concat) (1)

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Collecting the results from the perumtation.

Created: 2008-12-05

Credits: Zhiming Zhao

Affimetrix microarray: part one (obs) (1)

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The R/MAANOVA package [1] is being adapted to carry out our computations. To enable R/MAANOVA to handle probe-sets with different probe numbers, which is necessary when using probe-set definitions other than the original one provided by Affimetrix, we will pre-process the input data by dividing it into groups, each group formed by genes reported by the same number of probes.

Created: 2008-12-05

Credits: Zhiming Zhao