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Items tagged with "cdk-taverna" (22)

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Workflows (20)

Taverna 1 Original Uploader Thomasku	Insert Molecules into Database (v1) Created: 29/08/08 @ 09:59:06 \| Last updated: 29/08/08 @ 10:17:02 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 179 times \| Downloaded: 50 times Tags (6): cdk-taverna \| database storing \| iterative file reader \| pgchem::tigress \| postgres \| reading mdl sd-file	View Download (v1)
Taverna 1 Original Uploader Thomasku	QSAR workflow to measure the time used for calculating different qsar properties (v1) Created: 29/08/08 @ 13:31:12 \| Last updated: 29/08/08 @ 13:40:52 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 119 times \| Downloaded: 90 times Tags (5): aromaticity detection \| atomtyping \| cdk-taverna \| qsar \| time distribution	View Download (v1)
Taverna 1 Original Uploader Thomasku	Atom typing of molecules from database (v1) Created: 06/09/08 @ 11:08:43 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 143 times \| Downloaded: 36 times Tags (6): atom typing \| cdk-taverna \| loading molecules from database \| molecules to pdf table \| pgchem::tigress \| postgres	View Download (v1)
Taverna 1 Original Uploader Thomasku	Iterative loading of molecules from database with aromaticity detection (v1) Created: 03/11/08 @ 14:28:31 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 67 times \| Downloaded: 25 times Tags (7): aromaticity detection \| atom typing \| atomtyping \| cdk-taverna \| loading molecules from database \| pgchem::tigress \| postgres	View Download (v1)
Taverna 1 Original Uploader Thomasku	InsertMoleculesIntoDatabase (v1) Created: 05/11/08 @ 10:30:38 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 57 times \| Downloaded: 26 times Tags (5): cdk-taverna \| database storing \| pgchem::tigress \| postgres \| reading mdl sd-file	View Download (v1)
Taverna 1 Original Uploader Thomasku	Load Molecules from a database and create a PDF file showing the structures of the loaded molecules (v1) Created: 05/11/08 @ 16:15:58 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 38 times \| Downloaded: 33 times Tags (3): cdk-taverna \| loading molecules from database \| molecules to pdf table	View Download (v1)
Taverna 1 Original Uploader Thomasku	Extraction of atom typing problems after loading of molecules from database (v1) Created: 05/11/08 @ 17:30:37 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 35 times \| Downloaded: 23 times Tags (3): atom typing \| cdk-taverna \| loading molecules from database	View Download (v1)
Taverna 1 Original Uploader Thomasku	Substructure Search On Database (v1) Created: 06/11/08 @ 12:02:18 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 88 times \| Downloaded: 36 times Tags (5): cdk-taverna \| molecules to pdf table \| pgchem::tigress \| smiles parsing \| substructure search	View Download (v1)
Taverna 1 Original Uploader Thomasku	Extract ChEBI molecules from TSV file and upload them into a database (v1) Created: 06/11/08 @ 16:11:54 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 52 times \| Downloaded: 28 times Tags (5): cdk-taverna \| chebi \| database storing \| loading molecules from database \| pgchem::tigress	View Download (v1)
Taverna 1 Original Uploader Thomasku	Topological Substructure Search Workflow (v1) Created: 06/11/08 @ 16:59:02 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 94 times \| Downloaded: 28 times Tags (6): cdk-taverna \| cml generation \| inchi generation \| reading mdl sd-file \| smiles parsing \| substructure search	View Download (v1)
Taverna 1 Original Uploader Thomasku	Analyse the Atom Typing Result (v1) Created: 06/11/08 @ 22:25:28 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 32 times \| Downloaded: 22 times Tags (5): atom typing \| atomtyping \| cdk-taverna \| pdf \| visualise	View Download (v1)
Taverna 1 Original Uploader Thomasku	Molecular Weight Distribution (v1) Created: 07/11/08 @ 14:18:32 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 49 times \| Downloaded: 25 times Tags (4): cdk-taverna \| loading molecules from database \| molecular weight distribution \| pgchem::tigress	View Download (v1)
Taverna 1 Original Uploader Thomasku	Calculation of molecular descriptors for molecules loaded from database (v1) Created: 15/11/08 @ 15:12:05 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 105 times \| Downloaded: 39 times Tags (9): aromaticity detection \| atom typing \| cdk-taverna \| iterative molecule from database loading \| loading molecules from database \| pgchem::tigress \| postgres \| qsar \| save qsar vector in database	View Download (v1)
Taverna 1 Original Uploader Thomasku	ART2A Classification Workflow (v1) Created: 17/11/08 @ 13:48:19 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 39 times \| Downloaded: 20 times Tags (5): art2a \| cdk-taverna \| classification \| loading vector from database \| qsar	View Download (v1)
Taverna 1 Original Uploader Thomasku	Get ART2A classification result showing the different origins of the vectors (v1) Created: 17/11/08 @ 14:21:24 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 36 times \| Downloaded: 23 times Tags (5): art2a \| cdk-taverna \| classification \| diversity analysis \| result visualizing	View Download (v1)
Taverna 1 Original Uploader Thomasku	Reaction Enumeration Workflow (v1) Created: 21/11/08 @ 15:25:01 Credits: Thomasku License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 47 times \| Downloaded: 20 times Tags (5): cdk-taverna \| molecules to pdf table \| pdf \| reaction enumeration \| reading mdl sd-file	View Download (v1)
Taverna 1 Original Uploader Thomasku	Reaction Enumeration Workflow (v1) Created: 22/11/08 @ 16:55:34 Credits: Thomasku Attributions: Reaction Enumeration Workflow License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 49 times \| Downloaded: 25 times Tags (5): cdk-taverna \| molecules to pdf table \| pdf \| reaction enumeration \| reading mdl sd-file	View Download (v1)
Taverna 2 Original Uploader Kalai	Generate Atom Signatures of molecules given SDF as input (v1) Created: 13/05/11 @ 17:14:06 \| Last updated: 13/05/11 @ 19:47:24 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 28 times \| Downloaded: 9 times Tags (22): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| re-use \| synthetic \| taverna 2 \| workflow \| workflows	View Download (v1)
Taverna 2 Original Uploader Kalai	Scoring small molecules for metabolite likeness/ Natural product likeness (v1) Created: 13/05/11 @ 17:22:28 \| Last updated: 13/05/11 @ 17:26:17 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 structural data SM_file:... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 30 times \| Downloaded: 8 times Tags (22): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| re-use \| structure \| synthetic \| workflow \| workflows	View Download (v1)
Taverna 2 Original Uploader Kalai	Plotting distribution of natural product likeness scores (v1) Created: 13/05/11 @ 17:34:58 \| Last updated: 13/05/11 @ 17:35:08 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 26 times \| Downloaded: 8 times Tags (24): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| plot \| re-use \| structure \| synthetic \| taverna2 \| workflow \| workflows	View Download (v1)

Packs (2)

Creator:

Katy Wolstencroft

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

21 items in this pack

Comments: 0 | Viewed: 146 times | Downloaded: 23 times

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Creator:

Kalai

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...

3 items in this pack

Comments: 0 | Viewed: 32 times | Downloaded: 15 times

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