Welcome to AMICI’s documentation!

Version: 1.0.1.dev

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
  • History
  • Publications on various features of AMICI
  • Third-Party numerical algorithms used by AMICI
• Changelog
  • v1.X Series
  • v0.X Series
  • What’s Changed
• Versioning policy
  • Versioning
  • Deprecation policy
  • Python compatibility
• 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
  • SBML import, observation model, sensitivity analysis, data export and visualization
  • Using PEtab
  • PEtab 2.0 import
  • AMICI Python example “Experimental Conditions”
  • Steady-state computation in AMICI
  • Debugging simulation failures
  • Speeding up model import and simulation - with a focus on large models
  • AMICI & JAX
  • Simulating AMICI models using JAX
  • AMICI Python example “splines”
• Usage
  • Model definition
  • Environment variables affecting model import
  • Miscellaneous
• Caveats
  • Sensitivity analysis
  • Steady states
  • Discontinuities
• FAQ
• API reference
  • amici
  • amici.importers.sbml
  • amici.importers.sbml.splines
  • amici.importers.pysb
  • amici.importers.bngl
  • amici.importers.antimony
  • amici.importers.petab
  • amici.importers.petab.v1
  • amici.importers.utils
  • amici.sim.jax
  • amici.sim.sundials
  • amici.sim.sundials.plotting
  • amici.sim.sundials.gradient_check
  • amici.sim.sundials.petab
  • amici.sim.sundials.petab.v1
  • amici.adapters.fiddy

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

Developer's guide

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

Indices and tables

• Index

• Module Index

• Search Page