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Zonation

Zonation is a spatial conservation prioritization framework for large-scale conservation planning. It identifies areas, or landscapes, important for retaining high habitat quality and connectivity for multiple biodiversity features (eg. species), providing a quantitative method for enhancing species' long term persistence.

Available

Zonation is available in Puhti with following versions:

  • 5.0.0 (including Graphical User Interface)

Usage

Zonation is available in the zonation module and the command line interface can be loaded with

module load zonation

After loading the Zonation module you can run zonation commands in the following way:

z5 <command arguments>

Alternatively, if you want to use the Zonation Graphical User Interface (GUI) tool, Zonation can be started in Puhti web interface :

  1. Log in to Puhti web interface.
  2. Open Desktop app.
  3. After launching the Desktop, double-click Zonation icon.

Example

Here is an example with the Zonation tutorial data.

Zonation 5

Download the zonation5-tutorial data to your project's projappl or scratch folder, unzip it; then

cd /scratch/<your_project>/manual_and_example_setups/example\ setups\ and\ data/1_w
srun --ntasks=1 --time=00:15:00 --mem=1G --account=project_<your_project_number> --partition=test --pty z5 -w --mode=ABF minimal_settings.z5 $HOME/example1_out
which will show you the process in the terminal and create the example1_out file in your $HOME folder.

Example batch job script

#!/bin/bash
#SBATCH --account=<YOUR-PROJECT>
#SBATCH --cpus-per-task=1
#SBATCH --partition=test
#SBATCH --time=00:15:00
#SBATCH --mem=1G

module load zonation
cd /scratch/<your_project>/manual_and_example_setups/example\ setups\ and\ data/1_w
srun z5 -w --mode=ABF minimal_settings.z5 <path_to_where_you_want_to_store_the_result>/example1_out

License

Zonation 5 is distributed as is, freely under GNU General Public License (GPL) version 3 (#GNUGPL) (#GNUGPLv3) license.

Citation

Moilanen, A., Lehtinen, P., Kohonen, I., Virtanen, E., Jalkanen, J. and Kujala, H. 2022. Novel methods for spatial prioritization with applications in conservation, land use planning and ecological impact avoidance. Methods in Ecology and Evolution

Acknowledgement

Please acknowledge CSC and Geoportti in your publications, it is important for project continuation and funding reports. As an example, you can write "The authors wish to thank CSC - IT Center for Science, Finland (urn:nbn:fi:research-infras-2016072531) and the Open Geospatial Information Infrastructure for Research (Geoportti, urn:nbn:fi:research-infras-2016072513) for computational resources and support".

Installation

Zonation was installed to Puhti with Apptainer using Zonation Apptainer definition file written by CSC.

The container was finally wrapped with Tykky's wrap-container functionality: wrap-container -w /usr/bin/z5 --prefix install_dir z5.sif

References

Last update: November 3, 2023