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Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.

Created: 2009-07-03 | Last updated: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: Fetch PDB flatfile from RCSB server Fetch PDB flatfile from RCSB server

Analysing workflows (3)

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This workflows analyses workflows stored at the myExperiment site. It is used in the paper submitted to the Workshop on Scientific Workflow 2009. The workflow shows the task usage in the Taverna workflows stored at the myExperiment site The amount of services used The amount of local processors used The amount of scripting tasks The amount of sub workflows Furthermore it classifies the local services based on their intended function. The workflow has two inputs: ...

Created: 2009-05-06 | Last updated: 2009-05-06

Credits: Wassinki Pieter Neerincx Katy Wolstencroft Marco Roos

AffyArrayNormalization (2)

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The AffyArrayNormalization web services normalise raw Affymetrix GeneChip data. They are wrappers around Philip de Groot's normalization R script to provide remote programmatic access. This example workflow demonstrates the use of the AffyArrayNormalization services. The flow is as follows: A client executes the AffyArrayNormalization_submit service with two inputs: a User object and a collection of URLs linking to CEL files. The User object contains a user ID, a password and an ...

Created: 2009-02-16 | Last updated: 2009-02-16

Credits: Pieter Neerincx Philipg

MediGRID FEAT Workflow (1)

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This workflow is a translation of the VLeMed workflow to the GWorkflowDL format, which is used in MediGRID. The translation of the "cross product" iteration strategy is currrently under work and not yet finished. So this workflow only varies the parameters p1, p2, and p3.

Created: 2009-02-13

Credits: Andreas Hoheisel

Attributions: feat_workflow

FLOSS Communication Centralization Plot, U... (2)

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The analysis in this workflow represents the basis of the analysis in our paper, Social dynamics of FLOSS team communication across channels. This workflow uses WSDL components to select periodized data from the FLOSSmole database and generate sociomatrices. The workflow parses the threaded list structure into a communication network based on reply-to relationships. In the analysis process, an unit weighting is applied to the edges. The weighted sociomatrices are then dichotomized according ...

Created: 2009-02-07

Credits: Andrea Wiggins Crowston James Howison

What is known about HIV using Bio2RDF's SP... (2)

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To answer this question Bio2RDF Atlas about mouse and human genome sparql endpoint available at http://atlas.bio2rdf.org/sparql is searched.  The selected URIs are then loaded into your local Virtuoso triplestore at http://localhost:8890/sparql. You must enable insert mode into the graph. Once the mashup is built, two SPARQL queries analyze the obtained graph.  Finally you can submit queries to the RDF mashup about HIV as you like.  Enjoy. This is the queries present in t...

Created: 2009-02-05 | Last updated: 2009-02-05

Credits: Francois Belleau

BlatBlastCombi (2)

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This workflow combines the blat and blast workflows. It takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and and a set of Fasta sequences. It first tries to perform a blat (at www.bioinformatics.nl). When this service returns nothing, a blast is done (also at www.bioinformatics.nl). The resulting reports are combined.   To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the ...

Created: 2009-02-03 | Last updated: 2009-02-03

Credits: Wassinki

Workflow Pattern - Structured Discriminator (2)

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This workflow is a GWorkflowDL representation of a structured discriminator (1-out-of-M Join) that invokes C after the first invocation of A or B (M=2). All next (M-1) invocations of A or B are ignored. This is only one out of various possibilities to model this workflow pattern. Notice alternative representation of this pattern at http://www.myexperiment.org/workflows/632

Created: 2009-01-19 | Last updated: 2009-01-19

Credits: Andreas Hoheisel

REST access of xml.nig.ac.jp (WABI) (1)

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This workflow has a beanshell script for composing the REST URL for the services at xml.nig.ac.jp  (WABI) This URL is passed to the local worker Get_web_page_from_URL that fetches the requested data. Note: This is a proof of concept of accessing REST services through Taverna. All of WABI's services can more easily be browsed and used in Taverna by adding their WSDL, for instance http://xml.nig.ac.jp/wsdl/GetEntry.wsdl The example invokes the getDDBJEntry(accession) method of the getE...

Created: 2008-10-14 | Last updated: 2008-10-14

Credits: Stian Soiland-Reyes

color_pathway_by_objects (1)

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Color given objects on a pathway map with specified colors and return the URL of the colored image. In the KEGG pathway maps, a gene or enzyme is represented by a rectangle and a compound is shown as a small circle. Example of input: pathway_id: path:eco00260 object_list: (to add as list) eco:b0514 eco:b2913 fg_color: (to add as list) blue orange bg_color: (to add as list) red orange

Created: 2008-10-01 | Last updated: 2008-10-01

Credits: Franck Tanoh