Welcome to AMICI’s documentation!

Version: 0.16.1

Source code: https://github.com/AMICI-dev/amici

About

• About AMICI
  • Features
  • Interfaces & workflow
• Availability
  • Source code
  • Python package
  • Installation instructions
• License conditions
  • AMICI
  • AMICI Logo
  • Dependencies
• How to cite AMICI
• References
• Background
  • Publications on various features of AMICI
  • Third-Party numerical algorithms used by AMICI
• Changelog
  • v0.X Series
  • What’s Changed
• Glossary
• Contributing
  • Contributing to AMICI
  • Code of Conduct

Python interface

Python

• Installation
  • Short guide
  • Installation on Linux
  • Installation on OSX
  • Installation on Windows
  • Further topics
• Examples
  • Getting Started in AMICI
  • AMICI Python example “steadystate”
  • Using PEtab
  • AMICI Python example “Experimental Conditions”
  • AMICI documentation example of the steady state solver logic
  • Debugging simulation failures
  • Speeding up model import and simulation - with a focus on large models
• Usage
  • Model definition
  • Environment variables affecting model import
  • Miscellaneous
• FAQ
• API reference
  • amici
  • amici.amici
  • amici.sbml_import
  • amici.pysb_import
  • amici.bngl_import
  • amici.petab_import
  • amici.petab_import_pysb
  • amici.petab_objective
  • amici.petab_simulate
  • amici.import_utils
  • amici.ode_export
  • amici.ode_model
  • amici.plotting
  • amici.pandas
  • amici.logging
  • amici.gradient_check
  • amici.parameter_mapping
  • amici.conserved_quantities_demartino
  • amici.conserved_quantities_rref
  • amici.numpy

C++ interface

C++

• Installation
  • Supported CBLAS libraries
  • Optional SuperLU_MT support
• Usage
  • AMICI-generated C++ model files
  • Running a model simulation
  • Compiling and linking
  • Parameter estimation for AMICI models in high-performance computing environments
• API reference
  • Class Hierarchy
  • File Hierarchy
  • Full API

Matlab interface

MATLAB

• Installation
• Usage
  • Specifying models in Matlab
  • SBML
  • Model Compilation
  • Model simulation
• FAQ
• API reference
  • Class Hierarchy
  • File Hierarchy
  • Full API

Developer's guide

• AMICI developer’s guide
  • Branches / releases
  • When starting to work on some issue
  • Code contributions
  • Further topics
• Handling of Discontinuities
  • Mathematical Considerations
  • Algorithmic Considerations

Indices and tables

• Index

• Module Index

• Search Page