Tag Results

Items tagged with "chemistry" (10)

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Groups (2)

Network-member Cheminformatics

Unique name: cheminformatics
Created: Thursday 04 December 2008 @ 21:18:56 (GMT)

Workflows in the area of cheminformatics, for example, using ChemSpider or PubChem webservices, or using cheminformatics plugins like CDK-Taverna.

7 shared items   |   0 announcements

Members (15):

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Network-member Bioclipse

Unique name: bioclipse
Created: Monday 13 September 2010 @ 10:29:24 (GMT)

 Group around Bioclipse Scripting Language workflows.

2 shared items   |   0 announcements

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Workflows (8)

Workflow Create Ugi Library 001 (1)

Created: 04/12/08 @ 20:34:13

Credits: User Jean-Claude Bradley

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Creates a virtual library of SMILES codes for all possible combinations of Ugi products based on lists of SMILES of starting materials in a Google Spreadsheet.  Uses Rajarshi Guha's web service. Can someone create a Taverna workflow that does this?

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

Viewed: 88 times | Downloaded: 52 times

Tags (6):

Workflow Automatic Protein-Ligand Docking (1)

Created: 15/05/09 @ 03:36:40 | Last updated: 16/05/09 @ 04:36:19

Credits: User Jeffersontan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Nimrod harnesses grid-based high-performance computing resources to evaluate a n umber of protein-ligand interaction algorithms. Different computational chemistry approaches are combined with non-linear optimization algorithms. This work is explained in Abramson, D. A., Amoreira, C., Baldridge, K. K., Berstis, L., Kondrick, C., Peachey, T. C., 2006, "A flexible grid framework for automatic protein-ligand docking", Proceedings of the Second IEEE International Conference on e-Science...

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

Viewed: 148 times | Downloaded: 69 times

Tags (3):

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: 39 times | Downloaded: 18 times

Tags (6):

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: 179 times | Downloaded: 46 times

Tags (7):

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: 76 times | Downloaded: 48 times

Tags (5):

Workflow Convert a SMILES string into a connection ... (1)

Created: 16/12/09 @ 19:52:33

Credits: User

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Bioclipse script that converts a SMILES string into a LaTeX table of the connection table of the molecule.

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

Viewed: 24 times | Downloaded: 26 times

Tags (3):

Workflow Calculate molecular mass for entries in a ... (1)

Created: 08/03/10 @ 09:46:03

Credits: User

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Simple script to demonstrate how to iterate over entries in a MDL SD file and calculate some molecular property.

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

Viewed: 20 times | Downloaded: 20 times

Tags (6):

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

Created: 10/08/10 @ 16:32:51 | Last updated: 10/08/10 @ 16:32:54

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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

Viewed: 35 times | Downloaded: 15 times

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