AMICI
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About

  • About AMICI
  • Availability
  • License conditions
  • How to cite AMICI
  • References
  • Background
  • Changelog
  • Glossary
  • Contributing

Python

  • Installation
  • Examples
  • Usage
  • FAQ
  • API reference

C++

  • Installation
  • Usage
  • API reference

MATLAB

  • Installation
  • Usage
  • FAQ
  • API reference

Developer's guide

  • AMICI developer’s guide
  • Handling of Discontinuities
AMICI
  • Python interface
  • Edit on GitHub

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
    • 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
    • Preparation
    • JAX implementation
    • Testing
    • AMICI Python example “splines”
    • Spline implementation of JAK2-STAT5 signaling pathway
  • 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.de_export
    • amici.de_model
    • amici.plotting
    • amici.pandas
    • amici.logging
    • amici.gradient_check
    • amici.parameter_mapping
    • amici.conserved_quantities_demartino
    • amici.conserved_quantities_rref
    • amici.numpy
    • amici.sbml_utils
    • amici.splines

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