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Taverna 1

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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 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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Taverna 1

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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 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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Taverna 1

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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 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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Taverna 1

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Workflow Download pathways for external references list (v2)

Created: 16/09/08 @ 11:32:47 | Last updated: 14/11/08 @ 14:38:31

Credits: User Thomaskelder

Attributions: Workflow CloneItemsInList

License: Creative Commons Attribution-Share Alike 3.0 License

Download_pathways_for_external_references_list
Takes a list of external references to genes/proteins/metabolites, finds all pathways on WikiPathways that contain one of the given genes/proteins/metabolites and downloads them in a given file format.

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Taverna 1

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Workflow Get pathways by external reference (v2)

Created: 16/09/08 @ 11:18:51 | Last updated: 14/11/08 @ 14:21:46

Credits: User Thomaskelder

License: Creative Commons Attribution-Share Alike 3.0 License

Get_pathways_by_external_reference
Finds pathways on WikiPathways by an external gene/protein/metabolite reference. See http://www.pathvisio.org/Help_1.1#Supported_database_systems for a list of supported database systems.

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Taverna 1

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Workflow Write pathway to disk (v2)

Created: 16/09/08 @ 11:20:54 | Last updated: 14/11/08 @ 14:21:13

Credits: User Thomaskelder

License: Creative Commons Attribution-Share Alike 3.0 License

Write_pathway_to_disk
Downloads and writes a pathway from WikiPathways to a local disk in the given file type.

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Taverna 1

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Workflow firstwf (v1)

Created: 13/11/08 @ 20:45:09 | Last updated: 13/11/08 @ 20:45:10

Credits: User Rory

License: Creative Commons Attribution-Share Alike 3.0 License

Firstwf
No description

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Taverna 1

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Workflow multi-gridsam-gopher (v1)

Created: 11/11/08 @ 17:26:55 | Last updated: 13/11/08 @ 16:41:33

Credits: User Soton sbs

License: Creative Commons Attribution-Share Alike 3.0 License

Multi-gridsam-gopher
Generation of Orthologous Proteins from High-Throughput Estimation of Relationships This workflow uses GOPHER to take in two protein sequence files and generate datasets of orthologous sequence alignments. The first [seqin] sequence set is the 'queries' around which orthologous datasets are to be assembled. This is now optimised for a dataset consisting of one protein per protein-coding gene, although splice variants should be dealt with OK and treated as paralogues. The second [orthdb] ...

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Taverna 1

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Workflow AppendToFile (v2)

Created: 10/11/08 @ 16:36:53 | Last updated: 11/11/08 @ 15:14:43

Credits: User Wassinki

License: Creative Commons Attribution-Share Alike 3.0 License

Appendtofile
Processor to add content to a (existing)  file. The content is added to the end of the file. The inputs: Filename: the file name of a file, if the file does not exists, a new file is added Content: the string to append NewLine [default = true]: if true, a newline is added to the end of the line (useful if you want to add a record each time)   The processor supports Multi-Threading since version 2.

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Taverna 1

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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 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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Taverna 1

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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 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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Taverna 1

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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 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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Taverna 1

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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 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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Taverna 1

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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 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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Chemistry Plan

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Workflow Liliopsida Protein Alignment (v2)

Created: 30/10/08 @ 18:59:45 | Last updated: 05/11/08 @ 21:51:52

Credits: User Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 License

Graphdraw
This workflow retrieves Liliopsida chloroplast petb gene sequences from NCBI Nucleotide, removes duplicate sequences and saves the results at BioExtract Server. These results are then converted into GenBank format and fed into Fetch Translation, which removes the translation from the CDS coding region. Translations are then used to build a multiple alignment using ClustalW.

Rating: 4.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 2 | Citations: 1

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Taverna 1

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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 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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Taverna 1

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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 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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Taverna 1

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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 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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Taverna 1

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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 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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Taverna 1

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Workflow Sample grid workflow (v1)

Created: 24/10/08 @ 14:30:26 | Last updated: 31/10/08 @ 12:13:24

Credits: User Glatard

License: Creative Commons Attribution-Share Alike 3.0 License

Untitled
This is a sample workflow submitting jobs to the EGEE grid using the Generic Application Service Wrapper (GASW). The job submission service has to be installed locally.

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