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Welcome to the documentation wiki for OSMOSE, a marine ecosystem model. This wiki is the main place to find: documentation on the model itself; its inputs and outputs; its main processes and modules, and the tools needed to develop, run and understand OSMOSE configurations. It is intended for both new users discovering OSMOSE and more advanced users looking for technical details on a specific component of the model.
If you are new to OSMOSE, a good place to begin is the Getting started section. There you will find the main practical information needed to get started, including Download requirements, OSMOSE install, Running OSMOSE, Updating a configuration and Datarmor install.
This wiki is also a collaborative space; all contributions are welcome. Whether you want to improve an existing page, add a useful note, clarify a section or start a new topic, please see How to contribute. The documentation is meant to grow progressively, and contributors should not hesitate to expand pages, improve explanations or create links to topics that still need to be developed.
If you are looking for a general introduction to the model, start with OSMOSE. This page serves as the main entry point for understanding the overall structure, scope and philosophy of the model. Other useful pages are Model concepts, Glossary, Frequently asked questions and Troubleshooting.
The documentation is organised around some main themes.
If you are working on model setup and inputs, the OSMOSE inputs section brings together the main required files and forcing data, including Configuration files, LTL forcings, Spatial maps, Accessibility and catchability matrix and Time series.
If you want to understand how the model works internally, the Processes section describes the main simulated processes, including Growth, Reproduction, Incoming flux, School initialisation, LTL update, Mortality and Movement.
If you want a more general view, see Life cycle overview and Process interactions.
OSMOSE also includes several specialised modules that extend the core model. These are documented in their respective pages: Bioenergetic module, Ecogenetic module, Bioeconomic module, Initialisation module, Observation module and Multispecies Fisheries module. These sections are especially useful for users interested in more advanced or specific implementations.
For users working on parameter estimation and model fitting, the OSMOSE calibration section gathers the relevant material on calibration workflows and tools. This includes Install, Optimisation method, Calibrar description and Calibration process. You can also see Calibration examples and Good practices for calibration.
If you prefer to learn through worked examples, the OSMOSE tutorials and worked case studies pages are the main place to look.
Information on model updates and recent changes are available in the release notes, including notes for specific versions, such as v4.4.0. This part of the wiki helps track how the model and its documentation evolve over time.
For a complete page tree, see the full documentation index. This index is intended as a more exhaustive map of the wiki, while the present page serves as a general entry point to the documentation.