Workflows

List all algorithms and descriptors an Ope... (2)

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 Uses the OpenTox API 1.1 to discover all the available algorithms and descriptors for a given service.

Created: 2010-04-01 | Last updated: 2010-11-13

Credits: Egon Willighagen

Create an OpenTox API dataset and add mole... (2)

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 Bioclipse script that creates a data set  at an OpenTox API capable server, and adds molecules to it.

Created: 2010-08-04 | Last updated: 2010-11-13

Credits: Egon Willighagen

Count the number of MetaPrint2D predicted ... (1)

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 MetaPrint2D (doi: 10.1186/1471-2105-11-362) is used to calculate the number of red, orange, and green markers that indicate how likely an atom in the drug is metabolized (read the paper for the fine prints). It counts them for each molecule and reports them, as a set of three molecular descriptors that could potentially correlate with how well the molecule is metabolized (hypothesis).

Created: 2010-08-04 | Last updated: 2010-08-04

Credits: Egon Willighagen

Visualize the boiling point data from the ... (1)

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 Downloads the RDF data from a HTML page, extracts the boiling point data, calculates atom counts from SMILES representations, and opens the data in a matrix editor, ready to be visualized in a scatter plot.

Created: 2010-08-10 | Last updated: 2010-08-10

Credits: Egon Willighagen

/me is having Bioclipse/XMPP/RDF fun.js (1)

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Created: 2009-08-21

Credits: Egon Willighagen

Lists all Taverna 2 workflows (1)

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Uses Bioclipse and the MyExperiment SPARQL end point.

Created: 2009-08-21 | Last updated: 2009-08-22

Credits: Egon Willighagen

Extract RDF from HTML+RDFa (2)

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Small script for Bioclipse that extracts RDF from HTML+RDFa webpages.

Created: 2009-09-30 | Last updated: 2010-06-23

Credits: Egon Willighagen

Visualize Molecules from DBPedia as Molecu... (3)

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Downloads entries from DBPedia which have a SMILES and creates a molecule table with 2D structures of the hits found with SPARQL.

Created: 2010-03-14

Credits: Egon Willighagen

Open PDB entries in Jmol for hits found fo... (3)

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Queries Bio2RDF for proteins of which the title contains 'HIV', downloads them using the EMBL webservices and opens them in Bioclipse for visualization with Jmol.

Created: 2010-03-14 | Last updated: 2010-06-23

Credits: Egon Willighagen

Download CAS numbers and save as SD file (1)

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Download molecules from a REST services using the CAS registry number, create 3D coordinates and save the results as a MDL SD file.

Created: 2009-10-15

Credits: Egon Willighagen