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Showing 24 results. Use the filters on the left and the search box below to refine the results.
Type: Taverna 2
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Taverna 2
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Avatar De Sonja Holl

Workflow ENM Maxent workflow used for optimization (1)

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This workflow was used for the optimization of the Maxent algorithm from the openModeller toolbox (http://openmodeller.sourceforge.net/). The workflow uses 10-fold cross-validation and then calculates the average AUC, which can be used as fitness value during parameter optimization.

Created: 2013-08-09 | Last updated: 2013-09-04

Credits: User Sonja Holl User Renato De Giovanni

Taverna 2
Uploader
Avatar De Sonja Holl

Workflow ENM SVM workflow used for optimization (1)

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This workflow was used for the optimization of the SVM algorithm from the openModeller toolbox (http://openmodeller.sourceforge.net). The workflow uses 10-fold cross-validation and then calculates the average AUC, which can be used as fitness value during parameter optimization.

Created: 2013-08-09 | Last updated: 2013-09-04

Credits: User Sonja Holl User Renato De Giovanni

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

Workflow get_available_layers (8)

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Retrieves all available environmental layers from the openModeller web service and optionally from the BioSTIF service. In the first case, a single XML is returned according to the openModeller XML Schema, and in the second case a list of XML is returned for each BioSTIF workspace.

Created: 2013-12-06 | Last updated: 2015-03-26

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

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

Workflow project_model (9)

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Projects a model based on the specified parameters.

Created: 2013-12-24 | Last updated: 2014-12-04

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

Workflow get_available_algorithms (3)

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Retrieves all available algorithms from the openModeller web service, returning an XML.

Created: 2013-12-06 | Last updated: 2014-11-04

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

Workflow parse_csv_points (4)

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Parses csv content with species occurrence points in the DarwinCore archive format, determining column indexes and returning the records as a list of points in openModeller format (XML). No distinction is made between presences or absences.

Created: 2013-12-24 | Last updated: 2014-11-18

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

Workflow select_layers (4)

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Displays an interface to select one or more environmental layers. Returns a list of labels and a list of ids for the selected layers, both lists separated by line feed.

Created: 2013-12-06 | Last updated: 2015-05-11

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

Workflow show_test_results (4)

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Displays test results (ROC curve and confusion matrix) on an interface, allowing users to decide to continue the workflow or not.

Created: 2013-12-24 | Last updated: 2015-05-11

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

Workflow Ecological niche modelling workflow (28)

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This workflow takes as input a file containing species occurrence points to create a model with the openModeller Web Service. Algorithm, environmental layers and mask are selected during the workflow. The model is tested (internal test and optional cross validation external test) and then projected one or more times. All points from the input file are used to create a single model, even if there are differences in the scientific names. Cross validation calculates the mean AUC. Model projectio...

Created: 2013-01-07 | Last updated: 2015-06-11

Credits: User Renato De Giovanni User Alan Williams User Robert Kulawik User Francisco Quevedo User Vhernand Network-member BioVeL

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Funded by: BioVeL, EPSRC, JISC, Microsoft

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