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Software Components Overview

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Ricardo Oliveros Ramos edited this page Jun 11, 2026 · 1 revision

Software Components Overview

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Wiki pages Pages 160

Home
Allocating Java memory for OSMOSE experiments
Bioeconomic Module Calibration
Bioeconomic Module Concepts and Assumptions
Bioeconomic Module Data Requirements
Bioeconomic Module Mathematical Formulation
Bioeconomic Module Parameters
Bioeconomic Module Scenarios and Outputs
Bioenergetic Module Energy Uptake
Bioenergetic Module Maintenance
Bioenergetic Module Maturation
Bioenergetic Module Mortality
Bioenergetic Module New Tissue Production
Bioenergetic Module Reproduction
Bioenergetic module Simplified equations
Calibration and Validation
Calibration and Validation Data Requirements
Calibration and Validation Diagnostics
Calibration and Validation Install
Calibration and Validation Multi Phase Calibration
Calibration and Validation Objective Functions
Calibration and Validation Optimisation
Calibration and Validation Overview
Calibration and Validation Troubleshooting
Calibration and Validation Using Calibrar
Coupling and Environmental Forcing
Coupling and Environmental Forcing Climate Scenarios
Coupling and Environmental Forcing Environmental Drivers
Coupling and Environmental Forcing One Way Coupling
Coupling and Environmental Forcing Overview
Coupling and Environmental Forcing Resource Species
Coupling and Environmental Forcing Two Way Coupling
Development and Contribution
Development and Contribution Coding Conventions
Development and Contribution Development Installation
Development and Contribution Documentation Standards
Development and Contribution GitHub Workflow
Development and Contribution Implementation Details
Development and Contribution Testing
Development and Contribution Wiki Editing
Documentation index
Ecogenetic Module Genetic Inheritance
Ecogenetic Module Genetic Structure
Ecogenetic Module Trait Determinism
Getting Started
Getting Started Installing OSMOSE
Getting Started Running a First Simulation
Getting Started Running OSMOSE on Datarmor
Getting Started Software Requirements
Getting Started Updating a Configuration
Growth Gompertz
Growth Von Bertalanffy
Influx
Initialisation
Initialisation Appendix Data layer example
Initialisation Appendix Direct school based example
Initialisation Appendix Egg seeding example
Initialisation Appendix Population initialization block
Initialisation Appendix Workflow diagram
Initialisation Concepts
Initialisation Conclusion
Initialisation Introduction
Initialisation Limitations and outlook
Initialisation Method overview
Initialisation NetCDF Restart
Initialisation Other methods
Initialisation Reconstructed Populations
Initialisation Relative biomass
Initialisation Seeding
Initialisation Summary
Initialisation Troubleshooting
Initialisation Workflows
Inputs and Configuration
Inputs and Configuration Accessibility Matrices
Inputs and Configuration Configuration Files
Inputs and Configuration Fishing Files
Inputs and Configuration Observation Files
Inputs and Configuration Resource Forcing
Inputs and Configuration Species Distribution Maps
Inputs and Configuration Species Parameters
Inputs and Configuration Time Series
LTL Update
Model Overview
Model Overview Main Assumptions
Model Overview Schools
Model Overview Spatial Domain
Model Overview Species Types
Model Overview State Variables
Model Overview Time Step
Modules
Modules Bioeconomic Module
Modules Bioenergetic Module
Modules Ecogenetic Module
Modules Individual Based Fisheries Module
Modules Multispecies Fisheries Module
Modules Observation Module
Modules Stable Isotopes Module
Mortality Additional mortality
Mortality Additional mortality Adult mortality
Mortality Additional mortality Larva mortality
Mortality Fishing By species mortality
Mortality Fishing Fisheries
Mortality Post‐reproduction mortality
Movement Gradient Based Movements
Movement Map distribution
Movement Random Distribution
Outputs and Observation
Outputs and Observation Aggregation
Outputs and Observation Ecosystem Indicators
Outputs and Observation Optional Outputs
Outputs and Observation Population Indicators
Outputs and Observation School Level Outputs
Outputs and Observation Standard Outputs
Outputs and Observation Survey Filtering
Processes
Processes Detritus
Processes Fishing
Processes Growth
Processes Maturation
Processes Mortality
Processes Movement
Processes Predation
Processes Reproduction
Processes Starvation
Processes Time Step
Reference
Reference Algorithms
Reference Configuration Keys
Reference Equation synthesis
Reference Glossary
Reference Input File Formats
Reference Output File Formats
Reference Parameters
Reference Units
Release Notes
Release Notes OSMOSE 4.4.0
Release Notes OSMOSE 4.4.1
Release Notes OSMOSE 4.4.2
Running OSMOSE
School Init
Software Components
Software Components Analysing and Plotting Results
Software Components Core Simulator
Software Components Input Pre Processing
Software Components Overview
- Software Components Overview
Software Components R Package
Software Components Reading Outputs
Software Components Running Simulations
Species Focal species
Species LTL species
Tutorials and Workflows
Tutorials and Workflows Add a Species
Tutorials and Workflows Add Fishing
Tutorials and Workflows Add Resource Forcing
Tutorials and Workflows Analyse Outputs
Tutorials and Workflows Build a New Configuration manually 4.3.3
Tutorials and Workflows Calibrate a Model
Tutorials and Workflows Run an Existing Configuration
Tutorials and Workflows Run Scenarios
Tutorials Workflows Examples

Home

Model Overview

Running OSMOSE

Tutorials, Workflows and Examples

Implementation details

Full Documentation

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