Purpose Features User Interface Publications Team Contact

Purpose

Persefone.jl is a mechanistic model of social-ecological systems in agriculture in Europe. It simulates agricultural practices, crop growth, and biodiversity at a landscape scale.

Its aim is to help us:

  • better understand biodiversity dynamics in agricultural landscapes,
  • explore interactions between political, economic, and ecological processes,
  • advise decision-makers on the (social-)ecological implications of policy choices.

To this end, Persefone.jl provides a collection of fully functioning farm, crop, and animal models that can be easily set up and configured for agroecological studies or policy impact assessments. It is also designed to be easily extensible, and offers an open-source platform that modellers can adapt to their needs, for example as a basis for new species models. The software is written in Julia for high performance.

A field of ripe grain in Thuringia, © Daniel Vedder

Features

Persefone.jl consists of a collection of submodels to represent different parts of agricultural socio-ecological systems:

Farm submodels

At the moment, Persefone.jl simulates typical crop rotations for different regions in Germany. Each crop rotation is accompanied by normal management practices, (currently implemented: sowing harvest, mowing). These standard processes can be modified by different policy scenarios (e.g. new regulations or subsidies).

We have also begun to work on expanding the model to include a more comprehensive agent-based model of farmer decision making. This will take into account the economic, social, environmental, and political context within which farmers work. With it, the model will be able to analyse how farms are likely to respond to regulatory and market changes, and how their responses affect agricultural landscapes and ecosystems.

Crop submodels

Persefone.jl simulates the growth of multiple European crop types based on weather data and simulated farmers’ actions. We use two different crop models, one based on that implemented in ALMaSS , and the other using the FAO’s more detailed AquaCrop model .

Animal submodels

Persefone.jl includes individual-based models of multiple animal species that are known to be indicator species for agroecosystems. Each species model includes life-history and movement processes.

Currently, Persefone.jl there are models available for skylark (Alauda arvensis) and marbled white butterflies (Melanargia galathea). More models (e.g. for yellowhammer or small heath) will be added in future.

A valley in the Hohenlohe region of Germany, © Daniel Vedder

User Interface

Persefone Desktop screenshot

Persefone.jl is primarily designed to be run on a High-Performance Computer (HPC), due to the computational demands of simulating large numbers of individual animals at high resolution. To this end, the main model is intended to be run on the command line (e.g. a Linux shell or the Julia REPL). To make running large simulation experiments easier, the model supports parallelisation and the automated launch of full-factorial experimental setups.

For exploratory simulations, there is also a graphical user interface (GUI) available that can be run on a personal computer. Persefone Desktop can be used to explore how the model works, try out new model setups, or to help during development. It allows stepping forwards and backwards through a simulation run and visualises the model state in real time (see screenshot above).

Documentation      Source code      Download

Publications

Publications about Persefone.jl:

  • Vedder, D., Matthies, M. C., Iturry, G. D., & Pe’er, G. (2025). Persefone.jl: Modelling Biodiversity in Dynamic Agricultural Landscapes. doi:10.32942/X20S8K

Publications relevant for Persefone.jl:

  • Díaz Iturry, G., Matthies, M. C., Pe’er, G., & Vedder, D. (2025). AquaCrop.jl: A Process-Based Model of Crop Growth. Journal of Open Source Software, 10(110), 7944. https://doi.org/10.21105/joss.07944
  • Vedder, D., Fischer, S. M., Wiegand, K., & Pe’er, G. (2024). Developing multidisciplinary mechanistic models: Challenges and approaches. Socio-Environmental Systems Modelling, 6, 18701. doi:10.18174/sesmo.18701

If you build on or modify Persefone.jl in your own code, please follow the terms of the MIT license.

Team

Project and institutional logos

Persefone.jl is developed as part of the CAP4GI project . This project brings together ecologists, economists, NGOs, and farmers to develop recommendations for improving the EU’s Common Agricultural Policy. It is funded by the German Federal Ministry for Education and Research (BMBF) through FEdA , the Research Initiative for the Conservation of Biodiversity.

The model is developed by scientists at the Helmholtz Center for Environmental Research - UFZ and the German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig .

A field of green grain in Thuringia, © Daniel Vedder

All pictures © Daniel Vedder.