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Showing 2916 results. Use the filters on the left and the search box below to refine the results.
Taverna 2
Uploader
4080?size=60x60 Renato De Giovanni
Project Biovel

Workflow select_random_points_based_on_threshold (2)

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Selects random presence and/or absence points given a threshold and a set of points with the corresponding model values.

Created: 2014-11-13 | Last updated: 2015-05-11

Credits: Network-member BioVeL

Taverna 2
Uploader
4080?size=60x60 Renato De Giovanni
Project Biovel

Workflow define_frequently_used_constants (3)

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Defines constants that are frequently used as parameters for ENM Components. When building a new workflow with ENM Components, some constant values will likely be used multiple times as parameters. This component conveniently defines the most frequently used constants so that users can directly connnect them to the corresponding input ports without needing to manually create each constant.

Created: 2014-11-10 | Last updated: 2015-05-11

Credits: Network-member BioVeL

Taverna 2
Uploader
3505?size=60x60 At Markus Plangg

Workflow wc - Comparative File Size (2)

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SCAPE QA Object Component. Measures the file size and comparative file size of two images.

Created: 2014-11-06 | Last updated: 2014-11-06

Credits: User Markus Plangg

Taverna 2
Uploader
3505?size=60x60 At Markus Plangg

Workflow fits - TIFF image characterisation - image... (3)

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Extracts image width, image height, file size, and validity and compression type of a tiff image.

Created: 2014-11-06 | Last updated: 2014-11-06

Credits: User Markus Plangg

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-image-graph... (1)

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Converts any GraphicsMagick supported image format to TIFF

Created: 2014-11-06

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-image-gimp-... (1)

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Converts PNG to TIFF

Created: 2014-11-06

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-image-image... (1)

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Converts any ImageMagick supported image format to TIFF

Created: 2014-11-06

Taverna 2
Uploader
4080?size=60x60 Renato De Giovanni
Project Biovel

Workflow convert_points_xml_to_csv (4)

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Converts points in openModeller XML format into CSV format (header: occurrenceID,nameComplete,decimalLongitude,decimalLatitude). Most input/output ports related with presence or absence points expect/return data in openModeller XML format. This component can be used to simply convert such data back to a more human friendly format.

Created: 2014-11-05 | Last updated: 2015-05-11

Credits: Network-member BioVeL

Document
Uploader
4260?size=60x60 Ua Igor Lutsenko

Workflow Fundamentals of the theory of efficiency (1)

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The study expanded the target operation efficiency has allowed to derive a formula that can be used as the sole criterion of optimal control.

Created: 2014-10-27

Credits: User Igor Lutsenko

KNIME
Uploader
Avatar Ch Christine Chichester

Workflow Q4: For a given interaction profile, give ... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Compound Information followed by Compound Information (Batch) followed by Chemical Structure Search: Similarity with filter search...

Created: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

KNIME
Uploader
Avatar Ch Christine Chichester

Workflow Q19: For the targets in a given pathway, r... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Pathway Information: Get Targets followed by Target Pharmacology with filter minEx-pChembl=5 to answer scientific competency quest...

Created: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

KNIME
Uploader
Avatar Ch Christine Chichester

Workflow Q18:For pathway X, find compounds that ago... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Pathway Information: Get Targets followed byTarget Pharmacology with filters activity_type=Potency, max-activity_value=1000, activ...

Created: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

KNIME
Uploader
Avatar Ch Christine Chichester

Workflow Q16:Targets in Parkinson's disease or Alzh... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Target for Disease followed by Target Pharmacology with filter minEx-pChembl=5 to answer scientific competency question Q16:Target...

Created: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

KNIME
Uploader
Avatar Ch Christine Chichester

Workflow Q15: a) Which chemical series have been sh... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call a) Classification of Compounds for Target with filter minEx-pChembl=5 and b) Associations for Disease to answer scientif...

Created: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

KNIME
Uploader
Avatar Ch Christine Chichester

Workflow Q11: Retrieve all data for a given list of... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Chemical Structure Search: Exact with filter searchOptions.MatchType=2 followed by Compound Pharmacology and Compound Information ...

Created: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

KNIME
Uploader
Avatar Ch Christine Chichester

Workflow Q10:For a given compound, summarize all si... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Chemical Structure Search: Similarity with filters searchOptions.SimilarityType=0 and searchOptions.Threshold=0.80, followe by Com...

Created: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

KNIME
Uploader
Avatar Ch Christine Chichester

Workflow Q9:For a given compound, give me the inter... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Compound Pharmacology with filter activity_type=IC50|EC50|AC50|Ki|Kd|Potency to answer scientific competency question Q9: For a gi...

Created: 2014-10-22 | Last updated: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

KNIME
Uploader
Avatar Ch Christine Chichester

Workflow Q8:Identify all known protein-protein inte... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Target Class Pharmacology and filters target_type=ppi and minEx-pChembl=5 to answer scientific competency question Q8: Identify al...

Created: 2014-10-22 | Last updated: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

KNIME
Uploader
Avatar Ch Christine Chichester

Workflow Q7: For a target, give me all active compo... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Target Pharmacology and filter minEx-pChembl=5 to answer scientific competency question Q7; For a target, give me all active compo...

Created: 2014-10-22 | Last updated: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

KNIME
Uploader
Avatar Ch Christine Chichester

Workflow Q6:For a specific target family, retrieve ... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Target Class Pharmacology to answer scientific competency question Q6; For a specific target family, retrieve all compounds in spe...

Created: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

KNIME
Uploader
Avatar Ch Christine Chichester

Workflow Q3: Given a target find me all actives aga... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Target Pharmacology with filter minEx-pChembl=5 followed by Compound Pharmacology with minEx-pChembl=0. to answer scientific compe...

Created: 2014-10-22 | Last updated: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

KNIME
Uploader
Avatar Ch Christine Chichester

Workflow Q1: Give me all oxidoreductase inhibitors ... (2)

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A new version of the Open PHACTS drug discovery question 1 workflow (answers the question: Give me all oxidoreductase inhibitors active <100nM in human and mouse) with improvements contributed by Ellert van Koperen.  To run workflow the parameters for Human and Mouse in the OPS_Swagger node must be re-entered. They become corrupted upon on export to zip file.

Created: 2014-10-22 | Last updated: 2015-06-02

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

Taverna 2
Uploader
30?size=60x60 Nl Marco Roos

Workflow HPO-UMLS-ConceptID mapping (1)

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Generate HPO-Concept profiles via HPO-UMLS mappings. The result is a list of Concept IDs corresponding to Concept profiles for UMLS concepts that approximate HPO concepts. The output is a table of UMLS-ID, HPO- ID, COncept-ID rows.

Created: 2014-10-20

Credits: User Marco Roos Network-member BioSemantics

Taverna 2
Uploader
30?size=60x60 Nl Marco Roos

Workflow Get HPO concept label and synonym (1)

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This workflow queries bioportal for label and synonyms of Human Phenotype Ontology concepts.Note: this workflow requires a BioPortal API key to work. It can be requested from bioportal.bioontology.org

Created: 2014-10-20 | Last updated: 2014-10-20

Credits: User Rajireturn Network-member BioSemantics

Taverna 2
Uploader
30?size=60x60 Nl Marco Roos

Workflow Match concept to HPO profiles (1)

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This workflow matches a query concept to the list of Human Phenotypes. The Human Phenotypes are the subset of the Human Phenotype Ontology for which we have a mapped UMLS concept available and a concept profile. HPO-UMLS mapping: Winnenburg, R., & Bodenreider, O. (2014). Coverage of Phenotypes in Standard Terminologies. In Proceedings of the ISMB’2014 SIG meeting “BioLINK.” Retrieved from http://phenoday2014.bio-lark.org/pdf/5.pdf Concept Profile Database: July 2012

Created: 2014-10-20

Credits: User Marco Roos Network-member BioSemantics

Attributions: Workflow Match concept profiles Workflow Get concept information

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Funded by: BioVeL, EPSRC, JISC, Microsoft

Affiliates: myGrid, Taverna, BioCatalogue
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