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Running OSMOSE
This page gathers the documentation needed to install OSMOSE, prepare a model configuration, run simulations, understand the main technical components, and work with model outputs.
It is intended as the main entry point for users who want to use OSMOSE in practice. Some pages are written for new users running an existing configuration, while others are intended for users preparing inputs, modifying processes, activating modules, calibrating a model, or coupling OSMOSE with external environmental forcing.
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Getting Started
Helps new users install OSMOSE, prepare the required software environment, run a first simulation, and identify the next pages to read depending on their needs. -
Software Components
Introduces the OSMOSE software ecosystem, including the core simulator, the R package, input pre-processing, simulation execution, output reading, and post-processing tools. -
Inputs and Configuration
Describes the main configuration files and input data used by OSMOSE, including species parameters, species distribution maps, time series, resource forcing, fishing files, and observation files. -
Initialisation
Explains how populations, schools, eggs, and restart files can be used to initialise an OSMOSE simulation. -
Outputs and Observation
Describes the outputs produced by OSMOSE and the tools used to transform simulated ecosystem states into quantities that can be analysed or compared with data. -
Calibration and Validation
Introduces the calibration and validation of OSMOSE configurations, including data requirements, objective functions, optimisation, diagnostics, and troubleshooting. -
Coupling and Environmental Forcing
Describes how OSMOSE can use environmental forcing and how it can be coupled with lower-trophic-level, biogeochemical, or climate-driven models.
New users should start with Getting Started, then continue with Software Components to understand how the OSMOSE tools fit together.
Users preparing or modifying a model should read Inputs and Configuration, Initialisation, Processes, and Modules.
Users analysing simulations should continue with Outputs and Observation. Users fitting a model to data should read Calibration and Validation. Users working with environmental forcing, climate scenarios, or end-to-end ecosystem modelling should read Coupling and Environmental Forcing.
For task-oriented guides, see Tutorials, Workflows and Examples.