---
tags:
  - Free
catalog:
  name: Zonation
  description: Spatial conservation prioritization framework
  license_type: Free
  disciplines:
    - Geosciences
  available_on:
    - web_interfaces:
        - Puhti
        - Roihu
    - Puhti
    - Roihu
---

# Zonation

[Zonation](https://zonationteam.github.io/Zonation5/) 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__ including Graphical User Interface is available with following versions:

* 5.2.4 in Roihu
* 5.2.3 in Puhti
* 5.2.1 in Puhti
* 5.2.0.2 in Puhti
* 5.1.0 in Puhti


## Usage

Zonation is available in the __zonation__ module:

```
module load zonation
z5 <command arguments>
```

With version 5.2.1 you can also use `zonation5 <command arguments>`

Zonation can be used with command-line or graphical interface, as interactive job or with batch system. In any case reserve suitable amount of computing resources: cores and memory. Zonation 5 runs faster, if it can use several cores. It can use one node, which is max 40 cores in Puhti and 384 in Roihu.  

Before starting Zonation, move your data to your project's __scratch__ folder. For testing, [zonation5-tutorial data](https://github.com/zonationteam/Zonation5/releases/download/v1.0/manual_and_example_setups.zip) can be used.

### Zonation with Graphical User Interface

Zonation Graphical User Interface (GUI) can be started in Puhti web interface:

1. Log in to [Puhti web interface](https://puhti.csc.fi).
2. Open [Desktop app](../computing/webinterface/desktop.md)
3. After launching the Desktop, double-click Zonation icon.

### Working with Zonation interactively
For relatively short analysis jobs, it is possible to use Zonation in [interactive session](../computing/running/interactive-usage.md).

```
sinteractive -i
cd /scratch/project_200xxxx/<location_of_your_data>
z5 -w --mode=ABF minimal_settings.z5 /scratch/project_200xxxx/example1_out
```

### Using Zonation with batch job
For longer analysis jobs, Puhti batch system should be used.

```
#!/bin/bash
#SBATCH --account=project_200xxxx
#SBATCH --cpus-per-task=40
#SBATCH --partition=small
#SBATCH --time=00:15:00
#SBATCH --mem=4G

module load zonation
cd /scratch/project_200xxxx/<location_of_your_data>
srun z5 -w --mode=ABF minimal_settings.z5 /scratch/project_200xxxx/example1_out
```


## License 

Zonation 5 is distributed as is, freely under [GNU General Public License (GPL) version 3 (#GNUGPL) (#GNUGPLv3) license.](https://www.gnu.org/licenses/gpl-3.0.html)


## 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 files](https://github.com/CSCfi/singularity-recipes/tree/main/zonation) written by Pauli Lehtinen from University of Helsinki with slight modifications. 

The container was finally wrapped with [Tykky's wrap-container functionality](../computing/containers/tykky.md#container-based-installations): 
`wrap-container -w /squashfs-root/AppRun --prefix install_dir zonation5_v2.1.sif`

Symbolic links added for `z5` and `zonation5` to work as starting commands.

## References

* [Zonation homepage](https://zonationteam.github.io/Zonation5/)
* [Zonation Github](https://github.com/zonationteam/Zonation5)
* [Zonation 5 manual and tutorial data](https://github.com/zonationteam/Zonation5/releases/download/v1.0/manual_and_example_setups.zip)




