Bioclim workflow

Created: 2013-09-02 13:44:59 Last updated: 2015-04-04 20:57:28

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This workflow takes as input a file containing species occurrence points to create a model with the openModeller Web Service 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.

For more information about the input file format, please look at the documentation for the corresponding parameter. If you use the default occurrence points you should know that Gammarus tigrinus is an aquatic species, so you need to choose marine environmental layers during the modelling procedure.

Workflow requirements: When running on Taverna workbench, this workflow requires Internet connection and the Taverna interaction plugin installed.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
input_points	This input takes a text file containing species occurrence points. The file must be formatted in the following way: each line corresponds to a different record, values are separated by comma and the first line must be a header (also separated by comma) containing the column names. The following column names are mandatory to run this workflow: occurrenceID, nameComplete, decimalLongitude and decimalLatitude. All records will be used to generate a single model regardless the species name.

Processors (12)

Name	Type	Description
parse_input_points	workflow	This part is responsible for parsing the input points, determining column indexes and returning the records as a single string (same original format) without the header.
allocate_points	workflow	This part is responsible for transforming the csv lines into a list of XML points. It returns a list of all points as well as two lists with 10 elements containig training and testing points to be used in 10-fold cross validation.
retrieve_layers	workflow	This part is reponsible for retrieving all available layers from the niche modelling service and from the GeoServer repository at Fraunhofer.
select_layers	workflow	This part displays an interface so that users can select layers for model creation.
upload_csv_data	workflow	This part is responsible for uploading the species occurrence points to the BioSTIF service.
input_mask_selection	workflow	This part displays an interface so that users can select or create a mask for model creation.
make_configuration_of_create_model	workflow	This part creates the XML configuration for model creation.
filter_environmentally_unique_points	stringconstant	Value yes
filter_spatially_unique_points	stringconstant	Value no
algorithm_xml	stringconstant	Value
create_model	workflow	This part is responsible for creating the model.
transform_filtered_points_to_csv	workflow

Beanshells (10)

Name	Inputs	Outputs
parse_header	csv_content	name_idx id_idx long_idx lat_idx
extract_taxon_points	csv_content name_idx taxon_name	taxon_points
get_first_taxon	csv_content name_idx	taxon_name
mask_was_selected	selected_mask	yes no
extract_first_element_1	inlist	first_element
extract_first_element_2	inlist	first_element
trimRESTurlResult	url	resultUrl
checkDataUpload	status	dataUpload_ok dataUpload_failed uploadStatus
allocate_points	all_points folds	training_points testing_points
csv_to_xml_list	csv_points id_idx long_idx lat_idx	all_points num_points

Outputs (5)

Name	Description
model_xml
model_log
selected_csv_points
layers
num_points

Datalinks (27)

Source	Sink
input_points	parse_input_points:csv_content
parse_input_points:id_idx	allocate_points:id_idx
parse_input_points:long_idx	allocate_points:long_idx
parse_input_points:taxon_points	allocate_points:csv_points
parse_input_points:lat_idx	allocate_points:lat_idx
retrieve_layers:biostif_layers_xml_list	select_layers:biostif_layers_xml_list
retrieve_layers:om_layers_xml	select_layers:om_layers_xml
input_points	upload_csv_data:csvDataContent
upload_csv_data:csvDataURI	input_mask_selection:csvDataURI
select_layers:selected_layers_labels	input_mask_selection:selected_layers_labels
select_layers:selected_layers_ids	input_mask_selection:selected_layers_ids
retrieve_layers:biostif_layers_xml_list	input_mask_selection:biostif_layers_xml_list
retrieve_layers:om_layers_xml	input_mask_selection:om_layers_xml
input_mask_selection:mask_id	make_configuration_of_create_model:mask_id
filter_environmentally_unique_points:value	make_configuration_of_create_model:environmentally_unique
filter_spatially_unique_points:value	make_configuration_of_create_model:spatially_unique
allocate_points:all_points	make_configuration_of_create_model:presence_points
select_layers:selected_layers_ids	make_configuration_of_create_model:layers
algorithm_xml:value	make_configuration_of_create_model:algorithm_xml
make_configuration_of_create_model:outputString	create_model:createModel_configuration
create_model:serialized_model	transform_filtered_points_to_csv:xml
parse_input_points:first_taxon_name	transform_filtered_points_to_csv:species_name
create_model:serialized_model	model_xml
create_model:output_log	model_log
transform_filtered_points_to_csv:csv	selected_csv_points
select_layers:selected_layers_labels	layers
transform_filtered_points_to_csv:num_points	num_points

Coordinations (4)

Controller	Target
allocate_points	retrieve_layers
retrieve_layers	select_layers
input_mask_selection	make_configuration_of_create_model
select_layers	input_mask_selection

Information Workflow Type

Taverna 2

Information Uploader

Renato De Giovanni

Information License

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Information Version 1 (earliest) (of 6)

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Information Statistics

5343 viewings

1679 downloads

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Version History

In chronological order:

Bioclim workflow with interaction

Created by Renato De Giovanni on Monday 02 September 2013 13:44:58 (UTC)
Bioclim workflow with interaction

Created by Renato De Giovanni on Monday 02 September 2013 13:55:14 (UTC)

Revision comment:

Improved documentation.
Bioclim workflow with interaction

Created by Renato De Giovanni on Tuesday 18 November 2014 18:46:37 (UTC)

Revision comment:

Replaced sub-workflows with the corresponding ENM components.
Bioclim workflow

Created by Renato De Giovanni on Thursday 04 December 2014 15:58:08 (UTC)

Revision comment:

Updated components versions.
Bioclim workflow

Created by Renato De Giovanni on Thursday 26 March 2015 20:07:23 (UTC)

Revision comment:

Updated get_available_layers component to order BioSTIF layers alphabetically.
Bioclim workflow

Created by Renato De Giovanni on Saturday 04 April 2015 20:57:28 (UTC)

Revision comment:

Upgraded interaction components to use github pages.