Expand description
§COPASI-RS
Revival of COPASI biochemical network simulator in Rust.
§History
COPASI (Complex Pathway Simulator) was developed at the Virginia Bioinformatics Institute and EML Research. It simulates biochemical networks using ODEs, stochastic methods, and hybrid approaches.
§SBML Support
This crate also provides SBML (Systems Biology Markup Language) import capabilities, the standard format for biochemical models.
§Features
- ODE Simulation: Deterministic simulation with LSODA
- Stochastic: Gillespie’s SSA (Stochastic Simulation Algorithm)
- Hybrid: Adaptive switching between deterministic/stochastic
- Steady State: Newton’s method for equilibrium
- Parameter Estimation: Levenberg-Marquardt, genetic algorithms
- Sensitivity Analysis: Local and global sensitivity
Modules§
Structs§
- Assignment
Rule - Assignment rule (algebraic constraint)
- Compartment
- Compartment (reaction container)
- Copasi
Simulation - COPASI-style simulator
- Event
- Event (discrete state change)
- Event
Assignment - Event assignment
- Parameter
- Parameter (kinetic constant)
- Rate
Rule - Rate rule (ODE definition)
- Reaction
- Reaction
- Sbml
Model - Complete SBML model
- Sbml
Version - SBML Level/Version
- Simulation
Result - Simulation result
- Species
- Species (molecule, protein, metabolite)
- Species
Reference - Species reference in a reaction
- Unit
- SBML Unit
- Unit
Definition - SBML Unit definition
Enums§
- Kinetic
Law - Kinetic law expression
- Simulation
Method - Simulation method
- Unit
Kind - Standard unit kinds