Group: CDK-Taverna

The CDK-Taverna plug-in provides chemoinformatic functionality to Taverna. This group contains workflows using the CDK-Taverna plug-in.

Created at: Friday 29 August 2008 @ 10:08:28 (BST)

Unique name: CDKTaverna


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Workflow

Taverna 1

Original Uploader

Workflow Insert Molecules into Database (v1)

Created: 29/08/08 @ 09:59:06 | Last updated: 29/08/08 @ 10:17:03

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Insert_molecules_into_database_17355_1
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

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Workflow

Taverna 1

Original Uploader

Workflow 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 @ 13:40:53

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Qsar_workflow_to_measure_the_time_used_for_calculating_different_qsar_properties_26743_1
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.

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Workflow

Taverna 1

Original Uploader

Workflow Atom typing of molecules from database (v1)

Created: 06/09/08 @ 11:08:44

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Atom_typing_of_molecules_from_database_14696_1
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...

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Workflow

Taverna 1

Original Uploader

Workflow Iterative loading of molecules from database with aromaticity detection (v1)

Created: 03/11/08 @ 14:28:32 | Last updated: 03/11/08 @ 14:28:34

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Iterative_loading_of_molecules_from_database_with_aromaticity_detection
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.

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Workflow

Taverna 1

Original Uploader

Workflow InsertMoleculesIntoDatabase (v1)

Created: 05/11/08 @ 10:30:39 | Last updated: 05/11/08 @ 10:30:40

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Insertmoleculesintodatabase
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.

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Workflow

Taverna 1

Original Uploader

Workflow Load Molecules from a database and create a PDF file showing the structures of the loaded molecules (v1)

Created: 05/11/08 @ 16:15:59 | Last updated: 05/11/08 @ 16:16:00

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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Workflow

Taverna 1

Original Uploader

Workflow Extraction of atom typing problems after loading of molecules from database (v1)

Created: 05/11/08 @ 17:30:38 | Last updated: 05/11/08 @ 17:30:39

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Extraction_of_atom_typing_problems_after_loading_of_molecules_from_database
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.

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Workflow

Taverna 1

Original Uploader

Workflow Substructure Search On Database (v1)

Created: 06/11/08 @ 12:02:18 | Last updated: 06/11/08 @ 12:02:19

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Substructure_search_on_database
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.

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Workflow

Taverna 1

Original Uploader

Workflow Extract ChEBI molecules from TSV file and upload them into a database (v1)

Created: 06/11/08 @ 16:11:54 | Last updated: 06/11/08 @ 16:11:56

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Extract_chebi_molecules_from_tsv_file_and_upload_them_into_a_database
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.

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Workflow

Taverna 1

Original Uploader

Workflow Topological Substructure Search Workflow (v1)

Created: 06/11/08 @ 16:59:02 | Last updated: 06/11/08 @ 16:59:03

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Topological_substructure_search_workflow
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.

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Workflow

Taverna 1

Original Uploader

Workflow Analyse the Atom Typing Result (v1)

Created: 06/11/08 @ 22:25:29 | Last updated: 06/11/08 @ 22:25:30

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Analyse_the_atom_typing_result
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.

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Viewed: 24 times | Downloaded: 13 times

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Workflow

Taverna 1

Original Uploader

Workflow Molecular Weight Distribution (v1)

Created: 07/11/08 @ 14:18:33 | Last updated: 07/11/08 @ 14:18:34

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Molecular_weight_distribution
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.

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Viewed: 38 times | Downloaded: 16 times

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Workflow

Taverna 1

Original Uploader

Workflow Calculation of molecular descriptors for molecules loaded from database (v1)

Created: 15/11/08 @ 15:12:06 | Last updated: 15/11/08 @ 15:12:08

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Calculation_of_molecular_descriptors_for_molecules_loaded_from_database
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.

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Workflow

Taverna 1

Original Uploader

Workflow ART2A Classification Workflow (v1)

Created: 17/11/08 @ 13:48:20 | Last updated: 17/11/08 @ 13:48:21

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Art2a_classification_workflow
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.

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Workflow

Taverna 1

Original Uploader

Workflow Get ART2A classification result showing the different origins of the vectors (v1)

Created: 17/11/08 @ 14:21:25 | Last updated: 17/11/08 @ 14:21:26

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_art2a_classification_result_showing_the_different_origins_of_the_vectors
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.

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Viewed: 29 times | Downloaded: 14 times

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Workflow

Taverna 1

Original Uploader

Workflow Reaction Enumeration Workflow (v1)

Created: 21/11/08 @ 15:25:02 | Last updated: 21/11/08 @ 15:25:03

Credits: User Thomasku

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Reaction_enumeration_workflow
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.

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Workflow

Taverna 1

Original Uploader

Workflow Reaction Enumeration Workflow (v1)

Created: 22/11/08 @ 16:55:35 | Last updated: 22/11/08 @ 16:55:36

Credits: User Thomasku

Attributions: Workflow Reaction Enumeration Workflow

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Reaction_enumeration_workflow
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.

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Workflow

Taverna 1

Original Uploader

Workflow CDK Example (v1)

Created: 26/02/09 @ 16:31:22

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Cdk_example
This workflow reads a library from an SD file (change the default value of Read_MDL_SD_File) and identifies those structures that conform to Lipinski's Rule of Five. It then performs a substructure query, represented as SMILES (change the default value on Parse_SMILES), on the structures that pass Lipinski, and creates PNG images of those structures that contain the substructure. The image results will be found in your Taverna Data folder.

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File

Uploader:

Blob Smiles Search of ChemSpider

Created: 27/02/08 @ 16:21:30 | Last updated: 04/03/09 @ 10:01:13

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A Pipeline Pilot protocol to search ChemSpider by structure (smiles string) to illustrate use of the ChemSpider wsdl

File type: XML

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