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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

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3791?size=60x60 Gb David De Roure
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Blob The Future of Scholarly Communications UKSG proofed ...

Created: 2014-11-06 00:16:53

Credits: User David De Roure

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The publisher's fulltext PDF is the final version of the paper. This is the Word version of the proof after revision, on which the published version was based, updated to include the figure and final page numbers.  

File type: Word 2007 document

Comments: 0 | Viewed: 18 times | Downloaded: 12 times

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3791?size=60x60 Gb David De Roure
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Blob Four quadrant diagram

Created: 2014-11-05 23:58:21 | Last updated: 2014-11-06 00:37:54

Credits: User David De Roure

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Powerpoint file for Figure 1.  This figure is based on an earlier diagram by Dave Robertson of University of Edinburgh which appeared in the EPSRC grant proposal EP/J017728/1 SOCIAM: The Theory and Practice of Social Machines

File type: PowerPoint 2007 presentation

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3791?size=60x60 Gb David De Roure
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Blob The Future of Scholarly Communications UKSG fulltext...

Created: 2014-11-05 23:50:39 | Last updated: 2014-11-05 23:59:51

Credits: User David De Roure

License: Creative Commons Attribution-Share Alike 3.0 Unported License

De Roure, D, The future of scholarly communications, Insights, 2014, 27(3), 233–238; DOI: http://dx.doi.org/10.1629/2048-7754.171 Please acknowledge Insights: the UKSG journal as the place of first publication. 

File type: Adobe PDF

Comments: 0 | Viewed: 14 times | Downloaded: 7 times

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3791?size=60x60 Gb David De Roure
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Pack The Future of Scholarly Communications


Created: 2014-11-05 23:43:27 | Last updated: 2014-11-06 00:38:53

Original materials for article "The Future of Scholarly Communications" in Insights: the UKSG journal, based on a paper presented at the 37th UKSG Conference, Harrogate, April 2014.Citation - Please acknowledge Insights: the UKSG journal as the place of first publication.De Roure, D, The future of scholarly communications, Insights, 2014, 27(3), 233–238; DOI: http://dx.doi.org/10.1629/2048-7754.171AuthorDavid De RoureProfessor of e-Research, University of O...

5 items in this pack

Comments: 0 | Viewed: 11 times | Downloaded: 1 time

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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

Creator
Avatar Ch Christine Chichester
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Pack Open PHACTS Drug Discovery FAQ Workflows


Created: 2014-11-05 11:12:18 | Last updated: 2014-11-05 11:15:59

Computational drug discovery using the KNIME workflow engine and the integrated resources of Open PHACTS for answering a number of important frequently asked pharmacology questions. 14 workflows for answering 16 different questions.

14 items in this pack

Comments: 0 | Viewed: 168 times | Downloaded: 39 times

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4260?size=60x60 Ua Igor Lutsenko
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Blob Deploed model of extremal system operation for solvi...

Created: 2014-10-27 21:01:16 | Last updated: 2015-05-13 05:46:35

Credits: User Igor Lutsenko

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The reduced, simplified registration mathematical model of the system operation, obtained by scaling the registration signals of the basic model and determining the sum of the reduced, integrated flow rates by the input and output of the system under study was constructed. The studies of this traditional, for today model have shown the problem, associated with the existing approach in operations identification. As a result of using the agent model and system approach, it was found that regist...

File type: Adobe PDF

Comments: 0 | Viewed: 63 times | Downloaded: 7 times

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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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30?size=60x60 Nl Marco Roos
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Blob Concept Profile of phenotype Chorea

Created: 2014-10-20 08:34:10

Credits: User Marco Roos Network-member BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Concept Profile generated from HPO term 'Chorea' via mapping to the corresponding UMLS phenotype concept.The profile contains ranked associations with Chorea conform mutual information content derived from co-occurrence in MedLine abstracts.Versions: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/...

File type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

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30?size=60x60 Nl Marco Roos
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Blob HTT-HPO concept profile match result

Created: 2014-10-20 08:26:32 | Last updated: 2014-10-20 08:35:28

Credits: User Marco Roos User Rajireturn Network-member BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example Concept Profile of the Human Phenotype named 'Chorea' also referred to by as Human Phenotype Ontology concept HP_0002072.This file contains a list of concepts from the Human Phenotype Ontology, ranked according to Concept Profile Matching with the profile of huntingtin, the protein whose aberrant form is the cause of Huntington's Disease.Versions:HPO-UMLS mapping: Winnenburg, R., & Bodenreider, O. (2014). Coverage of Phenotypes in Standard Terminologies. In Proceedings...

File type: Excel workbook

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30?size=60x60 Nl Marco Roos
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Pack RD-Connect D4.03 Deliverable Pack


Created: 2014-10-19 21:05:07 | Last updated: 2014-10-20 16:34:40

This pack compiles workflows and workflow results for Deliverable D4.03 for RD-Connect (http://rd-connect.eu).

5 items in this pack

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

Workflow extract_confusion_matrix (1)

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Extracts confusion matrix data from a test result XML.

Created: 2014-10-13 | Last updated: 2014-12-04

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

Workflow extract_roc_points (1)

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Extracts the ROC points from a test result XML.

Created: 2014-10-13 | Last updated: 2014-12-04

Credits: Network-member BioVeL

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

Workflow extract_auc (2)

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Extracts the AUC value from a test result XML.

Created: 2014-10-09 | Last updated: 2014-10-13

Credits: Network-member BioVeL

Taverna 2
Uploader
3194?size=60x60 Hu Ferenc HORVATH
Project Biovel

Workflow Biome-BGC SA 1.3 (1)

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Biome-BGC is a process-based biogeochemical model that can be used to simulate carbon, nitrogen and water fluxes of different terrestrial ecosystems. Two models have been implemented: the Biome-BGC v4.1.1 Max Planck Institute model, and the newly developed Biome-BGC MuSo 3.0 model. Performance, success or failure of these models are highly dependent on parameter settings and variation. Due to the high number of parameters (around 40 and 60 for 4.1.1 MPI and MuSo respectively) and the non-line...

Created: 2014-10-04

Credits: User Ferenc HORVATH User Dora Krasser User Peter Ittzes User Zoltan BARCZA Network-member BioVeL

Taverna 2
Uploader
Avatar Renzo
Project Biovel

Workflow Microbial Metagenomic Trait Calculation an... (3)

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This workflow calculates the microbial traits of your metagenome and retrieves additional traits data from the Microbial Metagenomic Trait Database http://mb3is.megx.net/mg-traits. The list of traits: - GC content - Variance of GC content - Dinucleotides - Number of rRNA - Codon usage - Amino acid composition - Acidic to basic amino acids ratio - % of Transcriptional factors - % of classified reads - Functional content - Functional diversity - Taxonomic content - Taxonomic diversity As ...

Created: 2014-10-03 | Last updated: 2015-06-12

Credits: User Renzo User Antonio Fernandez-Guerra

Attributions: Workflow Microbial Metagenomic Trait Statistical Analysis Workflow

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1217?size=60x60 Gb Alan Williams
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Blob XPath service

Created: 2014-10-03 15:36:07

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to use the XPath service in Taverna

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob WoRMS and OBIS services

Created: 2014-10-03 15:35:11

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to use WoRMS and OBIS services in Taverna

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Working with BioVeL Portal

Created: 2014-10-03 15:34:08

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to work with the BioVeL portal

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Using R in Taverna

Created: 2014-10-03 15:33:06

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to use R in Taverna

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Tool service

Created: 2014-10-03 15:32:14

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a description of how to use the tool service in Taverna

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Using BiodiversityCatalogue

Created: 2014-10-03 15:31:21

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to use BiodiversityCatalogue

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Taverna introduction

Created: 2014-10-03 15:29:44

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation introducing Taverna

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Simple workflow

Created: 2014-10-03 15:28:51

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation about creating a simple workflow in Taverna

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Nested workflows

Created: 2014-10-03 15:27:58

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation about nested workflows within Taverna

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Introduction to myGrid

Created: 2014-10-03 15:27:06

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation introducing myGrid

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Installing Taverna

Created: 2014-10-03 15:26:12

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to install Taverna

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Inputting data

Created: 2014-10-03 15:25:25

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to input data into Taverna workbench

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1217?size=60x60 Gb Alan Williams
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Blob help

Created: 2014-10-03 15:24:36

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing help information for Taverna Biodiversity

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Embedding workflows in your website

Created: 2014-10-03 15:23:49

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation about how to embed the running of workflows in your website, and examples.

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Components

Created: 2014-10-03 15:22:22

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation about Taverna components

File type: Adobe PDF

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