Bioclim workflow

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

Download Workflow

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 "selected_csv_points") or to know the environmental ranges for each variable considering all input points. In the later case, you can inspect the "model_xml" to find this information in the Maximum and MInimum attributes of the Bioclim element. Values are separated by a space in the same order of the layers. Please note that there are no model tests or projections in this workflow.

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.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/3725/download?version=6
[ More Info Expand ]

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 (17)

Name	Type	Description
algorithm_xml	stringconstant	Value
parse_csv_points	component	Component parse_csv_points
biostif_upload_points	component	Component biostif_upload_points
get_available_layers	component	Component get_available_layers
select_layers	component	Component select_layers
caption1	stringconstant	Value Select enviromental layers
no	stringconstant	Value no
exclude_masks	stringconstant	Value masks
select_or_create_mask	component	Component select_or_create_mask
caption2	stringconstant	Value Select or create a mask
empty_string	stringconstant	Value
create_model	component	Component create_model
yes	stringconstant	Value yes
latlong_wgs84	stringconstant	Value GEOGCS["WGS84", DATUM["WGS84", SPHEROID["WGS84", 6378137.0, 298.257223563]], PRIMEM["Greenwich", 0.0], UNIT["degree", 0.017453292519943295], AXIS["Longitude",EAST], AXIS["Latitude",NORTH]]
convert_points_xml_to_csv	component	Component convert_points_xml_to_csv
use_biostif	stringconstant	Value yes
exclude_layers	stringconstant	Value marine terrestrial

Beanshells (0)

Outputs (5)

Name	Description
model_xml
model_log
selected_csv_points
layers
num_points

Datalinks (30)

Source	Sink
input_points	parse_csv_points:points_csv
input_points	biostif_upload_points:csvDataContent
use_biostif:value	get_available_layers:use_biostif_layers
get_available_layers:biostif_layers_xml_list	select_layers:biostif_layers_xml_list
get_available_layers:om_layers_xml	select_layers:om_layers_xml
caption1:value	select_layers:interface_caption
exclude_masks:value	select_layers:om_skip_labels
select_layers:selected_layers_ids	select_or_create_mask:selected_layers_ids
select_layers:selected_layers_labels	select_or_create_mask:selected_layers_labels
get_available_layers:om_layers_xml	select_or_create_mask:om_layers_xml
get_available_layers:biostif_layers_xml_list	select_or_create_mask:biostif_layers_xml_list
biostif_upload_points:csvDataURI	select_or_create_mask:csvDataURI
caption2:value	select_or_create_mask:interface_caption
exclude_layers:value	select_or_create_mask:om_skip_labels
parse_csv_points:points_xml	create_model:presence_points_xml
algorithm_xml:value	create_model:algorithm_xml
no:value	create_model:spatially_unique
yes:value	create_model:environmentally_unique
empty_string:value	create_model:absence_points_xml
select_or_create_mask:mask_id	create_model:mask_id
parse_csv_points:first_taxon_name	create_model:species_label
latlong_wgs84:value	create_model:srs
select_layers:selected_layers_ids	create_model:layers_ids
parse_csv_points:first_taxon_name	convert_points_xml_to_csv:species_label
create_model:full_serialized_final_model	convert_points_xml_to_csv:points_xml
create_model:model_xml	model_xml
create_model:log	model_log
convert_points_xml_to_csv:points_csv	selected_csv_points
select_layers:selected_layers_labels	layers
convert_points_xml_to_csv:num_points	num_points

Coordinations (6)

Controller	Target
parse_csv_points	get_available_layers
select_layers	select_or_create_mask
get_available_layers	select_layers
create_model	convert_points_xml_to_csv
parse_csv_points	biostif_upload_points
select_or_create_mask	create_model

Information Workflow Type

Taverna 2

Information Uploader

Renato De Giovanni

Information License

All versions of this Workflow are licensed under:

Information Version 6 (latest) (of 6)

Information Credits (2)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (13)

Uploader tags

Log in to add Tags

Information Shared with Groups (2)

Information Featured In Packs (2)

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

5341 viewings

1678 downloads

[ see breakdown ]

Citations (0)

None

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.

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (0)

There are no workflows in myExperiment that use similar services to this Workflow.