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Showing 39 results. Use the filters on the left and the search box below to refine the results.
Type: Bioclipse Scripting Language

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

Created: 14/03/10 @ 20:57:58

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 293 times | Downloaded: 73 times

Tags (7):

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

Created: 01/04/10 @ 12:25:01 | Last updated: 13/11/10 @ 13:49:17

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 86 times | Downloaded: 45 times

Tags (5):

Workflow Lists all Taverna 2 workflows (1)

Created: 21/08/09 @ 17:09:07 | Last updated: 22/08/09 @ 05:54:06

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Uses Bioclipse and the MyExperiment SPARQL end point.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 105 times | Downloaded: 34 times

Tags (4):

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

Created: 14/03/10 @ 21:26:05 | Last updated: 23/06/10 @ 20:20:41

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 1.0 / 5 (2 ratings) | Versions: 3 | Reviews: 1 | Comments: 0 | Citations: 0

Viewed: 217 times | Downloaded: 56 times

Tags (10):

Workflow NMR Spectrum similarity search witn SWI-Pr... (1)

Created: 13/03/10 @ 02:07:23 | Last updated: 19/03/10 @ 13:15:41

Credits: User Samuel Lampa

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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With the SWI-Prolog (currently in experimental stage, and available from GitHub) plugin Prolog programs can be accessed inside Bioclipse’s scripting environment for querying and other processing of RDF triples. The prolog code in this Bioclipse script performs a simple spectrum similarity search based on a list of peak shift values, for which it tries to find spectra that contain peaks values close to those values, within a certian limit (<0.3 ppm in this case). The data which is u...

Rating: 5.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 116 times | Downloaded: 46 times

Tags (5):

Workflow Kabsch Alignment of Small Molecules (1)

Created: 30/10/09 @ 22:12:57

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Aligns molecules using the Kabsch alignment and visualizes the results in the Jmol viewer.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 90 times | Downloaded: 65 times

Tags (5):

Workflow Extract RDF from HTML+RDFa (2)

Created: 30/09/09 @ 12:18:29 | Last updated: 23/06/10 @ 20:04:25

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 120 times | Downloaded: 94 times

Tags (5):

Workflow Download QSAR data sets using the OpenTox ... (1)

Created: 22/03/10 @ 11:10:25

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Bioclipse script that uses the OpenTox API 1.1 to download all QSAR data sets from a given service.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 62 times | Downloaded: 54 times

Tags (5):

Workflow Download CAS numbers and save as SD file (1)

Created: 15/10/09 @ 09:05:39

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 124 times | Downloaded: 94 times

Tags (5):

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

Created: 21/08/09 @ 15:39:04

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bioclipse script that combines RDF (DBPedia), XMPP cloud services, and local CDK functionality to gain some information on Farnesol in Bioclipse.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 57 times | Downloaded: 34 times

Tags (6):

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