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Items tagged with "bioclipse" (35)

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Workflows (31)

Bioclipse Scripting Language Original Uploader Egon Willighagen	/me is having Bioclipse/XMPP/RDF fun.js (v1) Created: 21/08/09 @ 15:39:04 Credits: 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: 30 times \| Downloaded: 14 times Tags (6): bioclipse \| cdk \| cheminformatics \| chemistry \| dbpedia \| xmpp	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Lists all Taverna 2 workflows (v1) Created: 21/08/09 @ 17:09:07 \| Last updated: 22/08/09 @ 05:54:06 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Uses Bioclipse and the MyExperiment SPARQL end point. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 82 times \| Downloaded: 20 times Tags (4): bioclipse \| myexperiment \| rdf \| sparql	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Extract RDF from HTML+RDFa (v2) Created: 30/09/09 @ 12:18:29 \| Last updated: 23/06/10 @ 20:04:25 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 79 times \| Downloaded: 68 times Tags (5): bioclipse \| extraction \| html \| rdf \| rdfa	View Download (v2)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Visualize Molecules from DBPedia as Molecule Table (v3) Created: 14/03/10 @ 20:57:58 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 133 times \| Downloaded: 37 times Tags (7): bioclipse \| cdk \| cheminformatics \| chemistry \| dbpedia \| rdf \| sparql	View Download (v3)
Bioclipse Scripting Language Original Uploader Egon Willighagen	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: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 119 times \| Downloaded: 28 times Tags (10): bio2rdf \| bioclipse \| cheminformatics \| drug development \| hiv \| jmol \| pdb \| proteins \| rdf \| sparql	View Download (v3)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Download CAS numbers and save as SD file (v1) Created: 15/10/09 @ 09:05:39 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 72 times \| Downloaded: 54 times Tags (5): bioclipse \| cas_number \| cheminformatics \| file \| services	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Kabsch Alignment of Small Molecules (v1) Created: 30/10/09 @ 22:12:57 Credits: 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: 69 times \| Downloaded: 45 times Tags (5): alignment \| bioclipse \| cheminformatics \| chemistry \| kabsch	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Convert a SMILES string into a connection table in LaTeX (v1) Created: 16/12/09 @ 19:52:33 Credits: 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: 14 times \| Downloaded: 24 times Tags (3): bioclipse \| cheminformatics \| chemistry	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Download all data sets from a OpenTox API capable web resource (v3) Created: 01/04/10 @ 12:20:18 \| Last updated: 13/11/10 @ 13:53:22 Credits: 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: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 22 times \| Downloaded: 16 times Tags (7): bioclipse \| cheminformatics \| data \| opentox \| rdf \| rest \| toxicity	View Download (v3)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Calculate molecular mass for entries in a SD file (v1) Created: 08/03/10 @ 09:46:03 Credits: 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: 10 times \| Downloaded: 18 times Tags (6): bioclipse \| cheminformatics \| chemistry \| mdl sd file \| molecular mass \| sdf	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Spectrum similarity search witn SWI-Prolog in Bioclipse (v1) Created: 13/03/10 @ 02:07:23 \| Last updated: 19/03/10 @ 13:15:41 Credits: Samuel Lampa License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 30 times \| Downloaded: 19 times Tags (5): bioclipse \| nmrshiftdb \| prolog \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Download QSAR data sets using the OpenTox API 1.1 (v1) Created: 22/03/10 @ 11:10:25 Credits: 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: 36 times \| Downloaded: 31 times Tags (5): bioclipse \| cheminformatics \| data \| opentox \| toxicology	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	List all algorithms and descriptors an OpenTox service provides (v2) Created: 01/04/10 @ 12:25:01 \| Last updated: 13/11/10 @ 13:49:17 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 45 times \| Downloaded: 21 times Tags (5): bioclipse \| opentox \| rdf \| sparql \| toxicity	View Download (v2)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in Jena with In-memory RDF Store (v1) Created: 14/05/10 @ 17:36:38 \| Last updated: 14/05/10 @ 17:43:00 Credits: Samuel Lampa License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 14 times \| Downloaded: 8 times Tags (4): bioclipse \| nmrshiftdb \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in Jena with TDB RDF Store (v1) Created: 14/05/10 @ 17:37:47 \| Last updated: 14/05/10 @ 17:43:03 Credits: Samuel Lampa License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 13 times \| Downloaded: 15 times Tags (4): bioclipse \| nmrshiftdb \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in Pellet with In-memory RDF Store (v1) Created: 14/05/10 @ 17:38:46 \| Last updated: 14/05/10 @ 17:43:09 Credits: Samuel Lampa License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 12 times \| Downloaded: 7 times Tags (4): bioclipse \| nmrshiftdb \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in SWI-Prolog (v1) Created: 14/05/10 @ 17:40:14 \| Last updated: 14/05/10 @ 17:43:13 Credits: Samuel Lampa License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 13 times Tags (6): benchmarks \| bioclipse \| nmrshiftdb \| prolog \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in SWI-Prolog, minimal version (v1) Created: 14/05/10 @ 17:41:04 \| Last updated: 14/05/10 @ 17:42:46 Credits: Samuel Lampa License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 13 times Tags (6): benchmarks \| bioclipse \| nmrshiftdb \| prolog \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Downloads all Bioclipse Scripting Language scripts from MyExperiment.org (v1) Created: 23/06/10 @ 19:55:03 \| Last updated: 23/06/10 @ 19:55:04 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Downloads all Bioclipse Scripting Language scripts uploaded to MyExperiment into the Bioclipse workspace, and opens them in JavaScript editors. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 12 times \| Downloaded: 13 times Tags (2): bioclipse \| myexperiment	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Resolve an InChIKey on ChemSpider (v1) Created: 23/06/10 @ 21:16:09 \| Last updated: 23/06/10 @ 21:16:10 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Resolves an InChIKey on ChemSpider and opens the search results in a molecules table. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 8 times Tags (4): bioclipse \| chemspider \| inchikey \| search	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Create an OpenTox API dataset and add molecules (v2) Created: 04/08/10 @ 13:33:51 \| Last updated: 13/11/10 @ 14:04:08 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Bioclipse script that creates a data set at an OpenTox API capable server, and adds molecules to it. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 9 times Tags (4): bioclipse \| data \| database \| opentox	View Download (v2)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Count the number of MetaPrint2D predicted metabolization sites for the Novartis malaria data (v1) Created: 04/08/10 @ 16:41:35 \| Last updated: 04/08/10 @ 16:42:15 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License 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). Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 7 times Tags (6): bioclipse \| data \| drug \| malaria \| metabolism \| metaprint2d	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	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: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 26 times \| Downloaded: 12 times Tags (9): bioclipse \| boiling point \| cheminformatics \| chemistry \| html \| matrix \| qspr \| rdfa \| wiener	View Download (v1)
Bioclipse Scripting Language Original Uploader jonalv	Performing a double sided T-test on Brunn data (v1) Created: 13/09/10 @ 10:20:52 \| Last updated: 13/09/10 @ 11:14:48 Credits: jonalv License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 2 \| Citations: 0 Viewed: 12 times \| Downloaded: 8 times Tags (4): assays \| bioclipse \| brunn \| statistics	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Calculate molecular descriptors with OpenTox services (v1) Created: 30/10/10 @ 17:03:27 \| Last updated: 30/10/10 @ 17:03:31 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Queries an OpenTox ontology server for available molecular descriptor, picks one, and calculates the descriptor value for a few molecules. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 8 times Tags (10): bioclipse \| cheminformatics \| descriptor \| molecular \| ontology \| opentox \| qsar \| rdf \| services \| toxicology	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Search OpenTox data sets by title. (v1) Created: 14/11/10 @ 11:40:43 \| Last updated: 14/11/10 @ 11:40:46 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Use of an OpenTox ontology server to find data sets with a particular string in the title, such as 'EPA' as in this case. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 14 times \| Downloaded: 6 times Tags (7): bioclipse \| data \| epa \| ontology \| opentox \| rdf \| toxicology	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Extract chemical structures from a Beilstein Journal of Organic Chemistry paper (v1) Created: 12/05/11 @ 07:54:39 \| Last updated: 12/05/11 @ 07:54:41 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Uses the Oscar4 text mining tool to extract chemical structures from a Beilstein Journal of Organic Chemistry paper and visualizes them in the molecules table. Jericho is used to extract text from the paper's HTML page. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 12 times \| Downloaded: 15 times Tags (5): bioclipse \| cheminformatics \| oscar4 \| text mining \| visualisation	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Create a molecules table from a list of IUPAC names (v1) Created: 25/05/11 @ 08:47:34 \| Last updated: 25/05/11 @ 08:47:36 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Scripts that uses OPSIN to convert IUPAC names into chemical structures, which are saved as SD file and openend in the Bioclipse molecules table. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 7 times \| Downloaded: 3 times Tags (7): bioclipse \| cdk \| convert \| iupac name \| mdl sd file \| opsin \| table	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Authenticate with the OpenTox network (v1) Created: 25/05/11 @ 09:11:15 \| Last updated: 25/05/11 @ 09:11:17 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Bioclipse script commands log authenticate with the OpenTox network. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 3 times \| Downloaded: 1 time Tags (5): authentication \| bioclipse \| opensso \| opentox \| security	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Download the ONS solubility data from Google docs into Bioclipse (v1) Created: 06/06/11 @ 10:34:13 \| Last updated: 06/06/11 @ 10:34:15 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Use the Bioclipse scripting langauge to authenticate with Google Docs, and download the Open Notebook Science solubility data into a local data structure. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 4 times \| Downloaded: 5 times Tags (5): bioclipse \| google \| onssolubility \| open notebook science \| spreadsheet	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Map a Entrez Gene ID to a Gene Ontology ID (v1) Created: 07/01/12 @ 10:01:05 Credits: Egon Willighagen License: MIT License BSL Groovy script that uses BridgeDB to convert a Entrez Gene identifier into a Gene ontology identifier. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 8 times \| Downloaded: 3 times Tags (5): bioclipse \| bridgedb \| entrez \| gene ontology \| groovy	View Download (v1)