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Items tagged with "cdk-taverna" (22)

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Workflows (20)
Original Uploader

Workflow Insert Molecules into Database (1)

Created: 29/08/08 @ 09:59:06 | Last updated: 29/08/08 @ 10:17:02

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow reads the molecules form the an MDL SD File and stores them into a database. The database used here is a Postgres SQL database which uses the PGChem::Tigress chemoinformtic extension. To run this workflow you have to install the CDK-Taverna Plug-in for Taverna 1.7.1.0 from http://cdk-taverna.de/plugin

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

Viewed: 195 times | Downloaded: 53 times

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Original Uploader

Workflow QSAR workflow to measure the time used for... (1)

Created: 29/08/08 @ 13:31:12 | Last updated: 29/08/08 @ 13:40:52

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow loads molecules from a database. Each molecule goes through the atom typing, gets its explecite hydrogens and the detection of the hueckel aromaticity. After that different qsar properties will be calculated. The output of this workflow will be a qsar vector as a csv file and a file which contains the time needed to calculate each qsar property.

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

Viewed: 134 times | Downloaded: 98 times

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Original Uploader

Workflow Atom typing of molecules from database (1)

Created: 06/09/08 @ 11:08:43

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow loads molecules from a database. For each molecule the atom type gets perceived. The output of this workflow are a couple of text files. The frist text file contains all molecule id's which are loaded from the database. The second text file contains all molecules which had problems with the atom typing. This file contains the molecule id and the atom which caused the problem. The last output file, a pdf, contains all structures of the molecules which caused problems during the a...

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

Viewed: 150 times | Downloaded: 39 times

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Original Uploader

Workflow Iterative loading of molecules from databa... (1)

Created: 03/11/08 @ 14:28:31

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow loads molecules from a database in an iterative manner using the SQL commands LIMIT and OFFSET. After the loading each molecule goes through an atom typing perception before the Hueckel Aromaticity Detector tries to detect the aromaticity. All id of the aromatic molecules will be written wo a text file.

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

Viewed: 70 times | Downloaded: 30 times

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Original Uploader

Workflow InsertMoleculesIntoDatabase (1)

Created: 05/11/08 @ 10:30:38

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow load molecules into a database. The molecules originally are stored in a MDL SD file. As workflow input an origin is added to each molecule which gets stored into the database. The output of the workflow shows logs from the database insert process.

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

Viewed: 61 times | Downloaded: 30 times

Tags (5):

Original Uploader

Workflow Load Molecules from a database and create ... (1)

Created: 05/11/08 @ 16:15:58

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow loads molecules from a database. The 2D structure of these molecules are shown within a table of a PDF document.

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

Viewed: 42 times | Downloaded: 36 times

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Original Uploader

Workflow Extraction of atom typing problems after l... (1)

Created: 05/11/08 @ 17:30:37

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow load molecules from the database and than checks whether the perception of the atom types works or not. After the extraction of the database identifier from all molecules which caused problems during this process will the identifier be written to a file.

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

Viewed: 40 times | Downloaded: 25 times

Tags (3):

Original Uploader

Workflow Substructure Search On Database (1)

Created: 06/11/08 @ 12:02:18

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes as input a SMILES. This represents the substructure, for which the database gets searched. The output of this workflow is a PDF showing the 2D structures of the matched structure from the substructure search on the database.

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

Viewed: 97 times | Downloaded: 43 times

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Original Uploader

Workflow Extract ChEBI molecules from TSV file and ... (1)

Created: 06/11/08 @ 16:11:54

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This worklfow load a TSV file from the ChEBI database. (normally structures.tsv) After the extraction of the molecules from the TSV file all non MDL mol files are removed before the valid molecules are inserted into a database.

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

Viewed: 59 times | Downloaded: 30 times

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Original Uploader

Workflow Topological Substructure Search Workflow (1)

Created: 06/11/08 @ 16:59:02

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow performs a topological substructure search. The molecules to be searched are loaded from a MDL SD file. The substructure is loaded from a SMILES (workflow input). The matched molecules are converted to CML and for the molecules which do not contain the substructure the InChI is generated.

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

Viewed: 106 times | Downloaded: 32 times

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Original Uploader

Workflow Analyse the Atom Typing Result (1)

Created: 06/11/08 @ 22:25:28

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow is used to analyse the result of the atom typing workflow. It creates a pdf document contains a diagram to visualise the outcome from the atom typing test to detect the for the cdk unknown atom types.

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

Viewed: 35 times | Downloaded: 26 times

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Original Uploader

Workflow Molecular Weight Distribution (1)

Created: 07/11/08 @ 14:18:32

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow calculates the molecular weight of molecules stored in a postgres sql database with the Pgchem::tigress chemoinformatics cardridge. The cardridge perform the molecular weight calculation. The get a moleculear weight distribution worker creates a chart of the available data.

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

Viewed: 54 times | Downloaded: 27 times

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Original Uploader

Workflow Calculation of molecular descriptors for m... (1)

Created: 15/11/08 @ 15:12:05

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow loads iteratively molecules from a database. For each molecule the atom typse are perceived before the hydrogens are added and the aromaticity is detected. Than the QSAR worker calculates the selected descriptors. The result of this calculation is stored in database table.

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

Viewed: 115 times | Downloaded: 46 times

Tags (9):

Original Uploader

Workflow ART2A Classification Workflow (1)

Created: 17/11/08 @ 13:48:19

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow loads a vector from a database and performs an ART2A classification. The ART2A classificator contains various options which are changeable within the stored workflow configuration file. There is no UI for these content available.

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

Viewed: 43 times | Downloaded: 32 times

Tags (5):

Original Uploader

Workflow Get ART2A classification result showing th... (1)

Created: 17/11/08 @ 14:21:24

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow load an ART2A classifcation results and creates a diagram showing the origin allocation within the different cluster or classes. This is usable for performing a chemical diversity analysis. The result is stored within an PDF which contains a diagram and a table of the classification result.

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

Viewed: 40 times | Downloaded: 25 times

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Original Uploader

Workflow Reaction Enumeration Workflow (1)

Created: 21/11/08 @ 15:25:01

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow performs a reaction enumeration. Therefore it loads a generic reaction rxn file and two educt lists. This SD-Files contains molecules for the enumeration. The products of the enumerated reaction are stored as Mol Files and a PDF will be created which contains the product molecules.

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

Viewed: 53 times | Downloaded: 25 times

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Original Uploader

Workflow Reaction Enumeration Workflow (1)

Created: 22/11/08 @ 16:55:34

Credits: User Thomasku

Attributions: Workflow Reaction Enumeration Workflow

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow performs a reaction enumeration. Therefore it loads a generic reaction rxn file and two educt lists. This SD-Files contains molecules for the enumeration. The products of the enumerated reaction are stored as Mol Files and a PDF will be created which contains the product molecules.

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

Viewed: 56 times | Downloaded: 34 times

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Original Uploader

Workflow Generate Atom Signatures of molecules give... (1)

Created: 13/05/11 @ 17:14:06 | Last updated: 13/05/11 @ 19:47:24

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re...

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

Viewed: 65 times | Downloaded: 26 times

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Original Uploader

Workflow Scoring small molecules for metabolite lik... (2)

Created: 13/05/11 @ 17:22:28 | Last updated: 18/03/12 @ 16:41:39

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Prerequisite:   - CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow http://www.myexperiment.org/workflows/2120/download?version=1   Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structu...

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

Viewed: 85 times | Downloaded: 23 times

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Original Uploader

Workflow Plotting distribution of natural product l... (1)

Created: 13/05/11 @ 17:34:58 | Last updated: 13/05/11 @ 17:35:08

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Prerequisite:  CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow you need a Score file which is written to text file.  - This could be generated from ScorerActivity.t2flow http://www.myexperiment.org/workflows/2121/download?version=1   Description of input ports : score_file: Path to file name that has pre computed scores. Note: While passing file as input it could be passed as list of many files or single fi...

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

Viewed: 40 times | Downloaded: 17 times

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Packs (2)

Pack useful_for_sysmo


Created: 17/12/08 @ 12:31:48 | Last updated: 10/06/09 @ 09:43:20

These workflows have been collected as potentially useful protocols for the sysmo consortium

0 items in this pack

Comments: 0 | Viewed: 176 times | Downloaded: 27 times

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Pack Natural product likeness filter


Created: 13/05/11 @ 19:35:39 | Last updated: 29/08/11 @ 14:25:47

Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work...

0 items in this pack

Comments: 0 | Viewed: 45 times | Downloaded: 22 times

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