User: Renato De Giovanni

Name: Renato De Giovanni

Joined: Sunday 27 November 2011 12:53:38 (UTC)

Last seen: Thursday 11 June 2015 13:23:24 (UTC)

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28 Workflows

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Renato De Giovanni has been credited 6 times

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Taverna 2

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Renato De Giovanni

Project

ENM resolution mix - single run version (6)

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Single run version of the workflow for comparing results of two kinds of ecological niche models: one using only low resolution layers and the other using a random mix of low and high resolution layers. Users select the study region and the environmental variables considered to be the main drivers of a virtual species niche. The workflow is all based on the ENM components, which use the openModeller Web Service (OMWS). After getting initial parameters from the user, the workflow generates a r...

Created: 2014-11-18 | Last updated: 2015-04-04

Credits: Renato De Giovanni BioVeL

Taverna 2

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Renato De Giovanni

Project

ENM resolution mix - multiple runs version (10)

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Multiple runs version of the workflow for comparing results of two kinds of ecological niche models: one using only low resolution layers and the other using a random mix of low and high resolution layers. Users select the study region and the environmental variables considered to be the main drivers of a virtual species niche. The workflow is all based on the ENM components, which use the openModeller Web Service (OMWS). After getting initial parameters from the user, the workflow generates ...

Created: 2014-11-13 | Last updated: 2015-05-12

Credits: Renato De Giovanni BioVeL

Taverna 2

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Renato De Giovanni

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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: BioVeL

Taverna 2

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Renato De Giovanni

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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: BioVeL

Taverna 2

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Renato De Giovanni

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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: BioVeL

Taverna 2

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Renato De Giovanni

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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

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Renato De Giovanni

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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: BioVeL

Taverna 2

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Renato De Giovanni

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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: BioVeL

Taverna 2

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Renato De Giovanni

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sample_points (11)

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Randomly samples a specified number of absence and/or presence points in a given environment (set of layers + mask).

Created: 2014-03-19 | Last updated: 2015-05-11

Credits: BioVeL

Taverna 2

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Renato De Giovanni

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loop_until_progress_complete (4)

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Loops until an asynchronous openModeller Web Service job is finished, i.e., keeps calling getProgress until it returns 100 (completed), -2 (aborted) or -3 (cancelled). NOTE: this is a "low level" component that was created to be used by other existing components, so end users may never need to use it at all.

Created: 2014-02-13 | Last updated: 2015-05-11

Taverna 2

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Renato De Giovanni

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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

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Renato De Giovanni

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biostif_show_projections (4)

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Displays model projections and points in the BioSTIF web interface (requires previous upload steps).

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

Taverna 2

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Renato De Giovanni

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configure_external_test (5)

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Displays an interface allowing configuration of external test. Currently can be used to skip external test or run a cross validation procedure. In the later case, it is possible to specify the number of replicates, if AUC should be calculated, if confusion matrix should be calculated (using either a fixed threshold or lpt - lowest precision threshold).

Created: 2013-12-24 | Last updated: 2015-04-04

Taverna 2

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Renato De Giovanni

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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

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Renato De Giovanni

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biostif_upload_points (5)

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Uploads species occurrence points to BioSTIF server.

Created: 2013-12-24 | Last updated: 2014-10-24

Taverna 2

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Renato De Giovanni

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select_matching_layers (5)

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Displays an interface where users can select matching layers (same variables) based on the labels of previously selected layers. This is typically needed when projecting a model into a different scenario, where the same variables selected for model creation need to be used on a different chronologic or geographic context. The interaction page may optionally include a label field.

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

Taverna 2

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Renato De Giovanni

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biostif_upload_raster (4)

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Uploads a raster from a given URL to a BioSTIF server, from where it can be displayed through the BioSTIF web interface.

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

Taverna 2

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Renato De Giovanni

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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

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Renato De Giovanni

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evaluate_model (9)

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Evaluates a model, returning model values for a given set of points and layers.

Created: 2013-12-10 | Last updated: 2014-12-04

Taverna 2

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Renato De Giovanni

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test_model (11)

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Tests a model based on the specified parameters (confusion matrix and/or ROC curve).

Created: 2013-12-10 | Last updated: 2014-12-04

Taverna 2

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Renato De Giovanni

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create_model (10)

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Creates a model based on the specified parameters.

Created: 2013-12-10 | Last updated: 2014-12-04

Taverna 2

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Renato De Giovanni

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select_or_create_mask (7)

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Displays an interface so that users can select or create a mask.

Created: 2013-12-10 | Last updated: 2015-04-04

Taverna 2

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Renato De Giovanni

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select_algorithm_and_set_parameters (2)

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Displays an interface to select one of the algorithms and then another interface to set algorithm parameter values. Returns selected algorithm and parameter values as XML.

Created: 2013-12-06 | Last updated: 2015-04-04

Taverna 2

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Renato De Giovanni

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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

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Renato De Giovanni

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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

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Renato De Giovanni

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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

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Renato De Giovanni

Project

Bioclim workflow (6)

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This workflow takes as input a file containing species occurrence points to create a model with the openModeller Web Service using the Bioclim algorithm. Environmental layers and mask are selected during the workflow. Points are filtered so that only environmentally unique points are used to create the model. You can use this workflow to either filter a set of species occurrence points excluding redundant points with the same environmental conditions (you can get the result in the output "se...

Created: 2013-09-02 | Last updated: 2015-04-04

Credits: Renato De Giovanni BioVeL

Taverna 2

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Renato De Giovanni

Project

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: Renato De Giovanni Alan Williams Robert Kulawik Francisco Quevedo Vhernand BioVeL

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