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Tag Results (for Workflows only)

Workflows tagged with "cheminformatics" (62)   [See results for all types]

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Manual Web Service

Original Uploader

Workflow Create Ugi Library 001 (v1)

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: 59 times | Downloaded: 35 times

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Taverna 1

Original Uploader

Workflow Download from ChemSpider using Accurate Mass (v2)

Created: 26/11/07 @ 17:16:29 | Last updated: 05/02/08 @ 12:56:12

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Download_from_chemspider_using_accurate_mass_17623_2
No description

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

Viewed: 149 times | Downloaded: 72 times

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Bioclipse Scripting Language

Original Uploader

Workflow /me is having Bioclipse/XMPP/RDF fun.js (v1)

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: 18 times | Downloaded: 4 times

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Bioclipse Scripting Language

Original Uploader

Workflow Visualize Molecules from DBPedia as Molecule Table (v3)

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

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Visualizedbpediahits
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: 62 times | Downloaded: 13 times

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Bioclipse Scripting Language

Original Uploader

Workflow Open PDB entries in Jmol for hits found for HIV in Bio2RDF (v3)

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

Downloadhivprotein
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: 64 times | Downloaded: 11 times

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Bioclipse Scripting Language

Original Uploader

Workflow Download CAS numbers and save as SD file (v1)

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

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Casnumbers2sdf
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: 31 times | Downloaded: 12 times

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Bioclipse Scripting Language

Original Uploader

Workflow Determine the Maximum Common SubStructure (MCSS) (v1)

Created: 23/10/09 @ 12:01:42

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

BSL script to determine the maximum common substructure (MCSS) of a list of molecules and opens this in a JChemPaint editor.

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

Viewed: 39 times | Downloaded: 24 times

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Bioclipse Scripting Language

Original Uploader

Workflow Kabsch Alignment of Small Molecules (v1)

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: 40 times | Downloaded: 22 times

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Bioclipse Scripting Language

Original Uploader

Workflow Convert a SMILES string into a connection table in LaTeX (v1)

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: 3 times | Downloaded: 2 times

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Bioclipse Scripting Language

Original Uploader

Workflow Download all data sets from a OpenTox API capable web resource (v2)

Created: 01/04/10 @ 12:20:18 | Last updated: 01/04/10 @ 12:20:19

Credits: User

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Uses the OpenTox API (REST+RDF) to query all data sets, downloads them as MDL SD file, and opens the results in the Bioclipse molecules table.

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

Viewed: 3 times | Downloaded: 3 times

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Bioclipse Scripting Language

Original Uploader

Workflow Calculate molecular mass for entries in a SD file (v1)

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: 4 times | Downloaded: 9 times

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Bioclipse Scripting Language

Original Uploader

Workflow Download QSAR data sets using the OpenTox API 1.1 (v1)

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: 11 times | Downloaded: 10 times

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Pipeline Pilot

Original Uploader

Workflow C1 Combined Workflow (v1)

Created: 03/06/10 @ 11:26:48 | Last updated: 03/06/10 @ 11:30:10

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithms M1-M5 in one workflow, yielding a sparse matrix of matches annotated by match types.

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

Viewed: 11 times | Downloaded: 10 times

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Pipeline Pilot

Original Uploader

Workflow M1 Exact Matching (v1)

Created: 03/06/10 @ 11:32:02

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M1 which matches fully specified molecules on the basis of their canonical representations.

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

Viewed: 9 times | Downloaded: 4 times

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Pipeline Pilot

Original Uploader

Workflow M2 Similarity Matching (v1)

Created: 03/06/10 @ 11:33:36

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M2 which reads molecules from two sources and produces clusters of highly similar molecules.

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

Viewed: 4 times | Downloaded: 3 times

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Pipeline Pilot

Original Uploader

Workflow M3 Non-stereo Matching (v1)

Created: 03/06/10 @ 11:35:03

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M3 which strips stereochemical information from molecules, performs exact matching, and restores stereochemistry.

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

Viewed: 2 times | Downloaded: 2 times

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Pipeline Pilot

Original Uploader

Workflow M4 Tautomer Matching (v1)

Created: 03/06/10 @ 11:38:27

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M4 which generates canonical tautomers prior to matching, matches, then restores original structures.

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

Viewed: 4 times | Downloaded: 2 times

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Pipeline Pilot

Original Uploader

Workflow M5 Charge Matching (v1)

Created: 03/06/10 @ 11:39:28

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M5 which ionises molecules at pH 7 prior to matching, restores original structures.

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

Viewed: 7 times | Downloaded: 3 times

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Taverna 2

Original Uploader

Workflow Generate inChi (v1)

Created: 09/07/10 @ 10:06:35 | Last updated: 09/07/10 @ 10:08:37

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Generate_inchi
Generates an inChi string for a given chemical represented by its SMILES string, SDF or MOL file using the inchi web service provided by ChemSpider

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

Viewed: 1 time | Downloaded: 1 time

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Taverna 2

Original Uploader

Workflow Generate inChi information (v1)

Created: 09/07/10 @ 10:22:29 | Last updated: 09/07/10 @ 10:23:47

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Generrate_inchi_information
Uses the GenerateInchiInfo web service operation from ChemSpider to generate information relating to the InChi string for a given chemical compound

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

Viewed: 1 time | Downloaded: 2 times

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Taverna 2

Original Uploader

Workflow Generate InChi key (v1)

Created: 09/07/10 @ 10:45:09 | Last updated: 09/07/10 @ 10:45:11

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Generate_inchi_key
Generates an inchi key for a given compound using the inchi web service provided by ChemSpider

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

Viewed: 2 times | Downloaded: 2 times

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Taverna 2

Original Uploader

Workflow InChi key to ChemSpider identifier (v1)

Created: 09/07/10 @ 10:54:07 | Last updated: 09/07/10 @ 10:54:08

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Inchi_key_to_chemspider_identifier
Returns Converts an InChIKey to a ChemSpider ID

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

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Taverna 2

Original Uploader

Workflow InChi key to Inchi string (v1)

Created: 09/07/10 @ 10:58:54 | Last updated: 09/07/10 @ 11:00:16

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

_untitled_
Converts an InChI key to an InChI string using the ChemSpider Inchi web service.

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

Viewed: 2 times | Downloaded: 0 times

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Taverna 2

Original Uploader

Workflow InChi key to MOL file (v1)

Created: 09/07/10 @ 11:05:11 | Last updated: 09/07/10 @ 11:05:13

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Inchi_key_to_mol_file
Returns a MOL file for a given InChi key

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

Viewed: 4 times | Downloaded: 4 times

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Taverna 2

Original Uploader

Workflow InChIToCSID (v1)

Created: 09/07/10 @ 11:09:29 | Last updated: 09/07/10 @ 11:09:31

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Inchitocsid
Convert InChI to ChemSpider ID

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Taverna 2

Original Uploader

Workflow InChIStringToInChiKey (v1)

Created: 09/07/10 @ 11:12:58 | Last updated: 09/07/10 @ 11:23:55

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Inchitoinchikey
Converts an InChI string to an InChi key

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

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Taverna 2

Original Uploader

Workflow InChIStringToMolFile (v1)

Created: 09/07/10 @ 11:21:23 | Last updated: 09/07/10 @ 11:23:05

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Inchitomolfile
Converts an InChI string into a MOL file using the Inchi ChemSpider web service

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

Viewed: 1 time | Downloaded: 0 times

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Taverna 2

Original Uploader

Workflow InchiStringToSmiles (v1)

Created: 09/07/10 @ 11:38:59 | Last updated: 09/07/10 @ 11:39:01

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Inchistringtosmiles
Converts an inchi string into SMILES format

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

Viewed: 1 time | Downloaded: 0 times

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Taverna 2

Original Uploader

Workflow isValidInChiKey (v1)

Created: 09/07/10 @ 11:55:56 | Last updated: 09/07/10 @ 11:55:58

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Isvalidinchikey
Checks that specified argument is valid InChIKey. Works for v1.02b InChIKey only.

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

Viewed: 1 time | Downloaded: 0 times

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Taverna 2

Original Uploader

Workflow MolToInchiString (v1)

Created: 09/07/10 @ 12:01:45 | Last updated: 09/07/10 @ 12:01:47

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Moltoinchistring
Converts a MOL file to InChI. Result is v1.02s InChI.

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

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Taverna 2

Original Uploader

Workflow MolToInchiKey (v1)

Created: 09/07/10 @ 12:10:00 | Last updated: 09/07/10 @ 12:10:02

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Moltoinchikey
Converts a MOL file to an InChIKey. Result is v1.02s InChIKey.

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

Viewed: 0 times | Downloaded: 0 times

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Taverna 2

Original Uploader

Workflow SmilesToInchi (v1)

Created: 09/07/10 @ 15:37:08 | Last updated: 09/07/10 @ 15:37:10

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Smilestoinchi
Convert SMILES to InChI. Result is v1.02s InChI.

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

Viewed: 0 times | Downloaded: 0 times

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Taverna 2

Original Uploader

Workflow Convert chemical identifier (v1)

Created: 09/07/10 @ 15:45:53 | Last updated: 09/07/10 @ 15:46:31

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Convert_chemical_identifier
Converts a chemical compound identifier from one format to another using the open babel web service provided by ChemSpider

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

Viewed: 5 times | Downloaded: 0 times

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Taverna 2

Original Uploader

Workflow Get list of chemspider databases (v1)

Created: 12/07/10 @ 09:53:38 | Last updated: 12/07/10 @ 09:53:40

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_list_of_chemspider_databases
Returns a list of databases catalogedReturns a list of databases cataloged by ChemSpider

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Taverna 2

Original Uploader

Workflow Get extended compound information (v1)

Created: 12/07/10 @ 10:06:37 | Last updated: 12/07/10 @ 10:06:39

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_extended_compound_information
Returns information from chemspider for a given chemical represented by its chemspider identifier

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

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Taverna 2

Original Uploader

Workflow Get extended compound information for a list of chemspider identifiers (v1)

Created: 12/07/10 @ 10:33:31 | Last updated: 12/07/10 @ 10:34:11

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_extended_compound_information_for_a_list_of_chemspider_identifiers_
 Returns information for a given list of chemspider compound identifiers.

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Taverna 2

Original Uploader

Workflow Get ChemSpider record in MOL format (v1)

Created: 12/07/10 @ 10:47:44 | Last updated: 12/07/10 @ 10:47:46

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_chemspider_record_in_mol_format
Returns ChemSpider record in MOL format or empty string in case of failure.

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Taverna 2

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Workflow Get spectra information (v1)

Created: 13/07/10 @ 09:32:27 | Last updated: 13/07/10 @ 09:32:28

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_spectra_information
Returns information about the spectra stored in ChemSpider

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Taverna 2

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Workflow Get compound spectra information (v1)

Created: 13/07/10 @ 09:42:03 | Last updated: 13/07/10 @ 09:42:04

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_compound_spectra_information
Returns information about spectra stored in ChemSpider for a given compound represented by its chemspider identifier

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Taverna 2

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Workflow Get spectrum information (v1)

Created: 13/07/10 @ 09:48:50 | Last updated: 13/07/10 @ 09:48:51

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_spectrum_information
Returns information about a spectrum identified by its chemspider spectrum identifier

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Taverna 2

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Workflow Asynchronous chemspider simple search (v1)

Created: 13/07/10 @ 11:08:34 | Last updated: 13/07/10 @ 11:08:35

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Asynchronous_chemspider_simple_search
Performs an asynchronous simple search on ChemSpider

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Taverna 2

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Workflow Get compound information (v1)

Created: 13/07/10 @ 11:17:08 | Last updated: 13/07/10 @ 11:17:09

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_compound_information
Returns information about a given compound represented by its chemspider id

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Taverna 2

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Workflow Get compound thumbnail (v1)

Created: 13/07/10 @ 11:29:03 | Last updated: 13/07/10 @ 11:29:04

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_compound_thumbnail
Returns a small image of the 2D structure of given chemical compound represented by its chemspider identifier

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Taverna 2

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Workflow Get structure synonyms (v1)

Created: 13/07/10 @ 11:38:56 | Last updated: 13/07/10 @ 11:38:57

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_structure_synonyms
Returns synonyms for a given compound represented by a MOL fileReturns synonyms for a given compound

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Taverna 2

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Workflow chemspider identifier to MOL format (v1)

Created: 13/07/10 @ 13:52:02

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Chemspider_identifier_to_mol_format
Returns the MOL file for a given compound represented by its chemspider identifier

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Taverna 2

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Workflow getLiteEntity (v1)

Created: 13/07/10 @ 14:14:52 | Last updated: 13/07/10 @ 14:14:53

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Getliteentity
Retrieves a list of "lite" entities containing only the ChEBI ASCII name and ChEBI identifier. The input parameters are a search string and a search category. If the search category is null then it will search under all fields. The search string accepts the wildcard character "*" and also unicode characters. You can get maximum results upto 5000 entries at a time.

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Taverna 2

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Workflow Asynchronous chemspider search by formula (v1)

Created: 13/07/10 @ 14:15:41 | Last updated: 13/07/10 @ 14:16:17

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Asynchronous_chemspider_search_of_compounds_by_molecular_formula
Performs an asynchronous search on ChemSpider by molecular formula

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Taverna 2

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Workflow Get complete chebi entity (v1)

Created: 13/07/10 @ 14:38:12 | Last updated: 13/07/10 @ 14:38:13

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_complete_chebi_entity
Returns informations for a given compound represented by its chebi identifier

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Taverna 2

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Workflow Get complete entity by list (v1)

Created: 13/07/10 @ 14:44:02 | Last updated: 13/07/10 @ 14:47:57

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_completle_entity_by_list
Returns information from the chebi database for a list of chebi identifiers

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Taverna 2

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Workflow Get ontology parents (v1)

Created: 13/07/10 @ 14:48:37 | Last updated: 13/07/10 @ 14:48:38

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_ontology_parents
Retrieves the ontology parents of an entity including the relationship type, using the ChEBI identifier.

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Taverna 2

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Workflow Get ontology children (v1)

Created: 13/07/10 @ 14:51:32 | Last updated: 13/07/10 @ 14:51:33

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_ontology_children
Retrieves the ontology children of an entity including the relationship type, using the ChEBI identifier.

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Taverna 2

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Workflow Search structures in ChEBI database (v1)

Created: 13/07/10 @ 15:08:20 | Last updated: 13/07/10 @ 15:10:10

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

_untitled_
 Does a substructure, similarity or identity search using a structure in the Chebi database

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Taverna 2

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Workflow Simple search (v1)

Created: 13/07/10 @ 15:18:44 | Last updated: 13/07/10 @ 15:18:45

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Simple_search
Performs a lite search on ChemSpider

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Taverna 2

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Workflow file-similarity-entrez-url (v2)

Created: 16/07/10 @ 09:34:45 | Last updated: 16/07/10 @ 09:43:39

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Filesimilarityentrezurl
Performs a 2D structure similarity search on PubChem. The input structure has to be in the form of a SDF file. The original SDF-based similarity search workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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Taverna 2

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Workflow smiles-identity-idlist (v1)

Created: 16/07/10 @ 09:50:50 | Last updated: 16/07/10 @ 09:53:16

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Smilesidentityidlist
Searches for similar structures in PubChem to an input SMILES string. This workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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Taverna 2

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Workflow smiles-identity-idlist (v2)

Created: 16/07/10 @ 10:20:48 | Last updated: 16/07/10 @ 10:25:06

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Perform_similarity_search_in_pubchem
Performs a search in Pubchem for compounds similar to an input compound represented in SMILES notation. This workflow is based on the original smiles-identity-idlist workflow written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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Taverna 2

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Workflow PubChem substructure search (v2)

Created: 16/07/10 @ 10:31:51 | Last updated: 16/07/10 @ 10:52:28

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Pubchem_substructure_search
Search PubChem Compound for structures containing the one given by the structure key input, based on a user-selected level of chemical identity: connectivity only, match isotopes and/or stereo, etc. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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Taverna 2

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Workflow download (v2)

Created: 16/07/10 @ 10:41:38 | Last updated: 16/07/10 @ 10:53:32

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Download_data_from_pubchem
Given a list key, prepare for download a file containing those records in the selected format. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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Taverna 2

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Workflow Predict chemical solubility in solvents (v2)

Created: 04/08/10 @ 11:42:55 | Last updated: 04/08/10 @ 11:43:30

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Predict_chemical_solubility_in_solvents
Predicts solubility in molar units for a given chemical compound represented as a SMILES string in a given solvent. Uses a beanshell script to enable the user to select the solvent from a list.

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Taverna 2

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Workflow Predict Abraham descriptors (v1)

Created: 05/08/10 @ 16:26:19 | Last updated: 05/08/10 @ 16:26:20

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Predict_abraham_descriptors
Predicts descriptor values using a model derived from a linear regression analysis of the Open Notebook Science solubility data and literature values. The workflow returns all the Abraham descriptors E, S, A, B and V in a HTML file.Predicts descriptor values using a model derived from a linear regression analysis of the Open Notebook Science solubility data and literature values

Rating: 4.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 2

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Workflow Generate CombiUgi library (v1)

Created: 10/08/10 @ 12:15:37 | Last updated: 10/08/10 @ 12:16:00

Credits: User Peter Li User Romney

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Generate_combiugi_library
Generates a CombiUgi library using data from a Goolgle spreadsheet containing smiles strings of compounds to undergo virtual Ugi reactions

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Bioclipse Scripting Language

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Workflow Visualize the boiling point data from the 1947 paper by H. Wiener (v1)

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

Atomcountboilingpoint
 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.

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