********
Glossary
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.. glossary::
    :sorted:

    BNGL
        `BioNetGenLanguage <https://bionetgen.org>`_ is a language for
        modular, structure-based modeling of biochemical reaction networks.

    CVODES
        `CVODES <https://computing.llnl.gov/projects/sundials/cvodes>`_ is a
        solver for stiff and non-stiff :term:`ODE` systems with sensitivity
        analysis capabilities and is used by AMICI. It is part of the
        :term:`SUNDIALS` solver suite.

    DAE
        Differential-Algebraic Equation

    fixed parameters
        In AMICI, *fixed parameters* are parameters with respect to which no
        sensitivities are computed. They usually correspond to experimental
        conditions. For fixed parameters, different values can be set for
        :term:`preequilibration`, :term:`presimulation` and simulation.

    IDAS
        `IDAS <https://computing.llnl.gov/projects/sundials/idas>`_ is a
        solver :term:`DAE` systems with sensitivity analysis capabilities
        and is used by AMICI. It is part of the :term:`SUNDIALS` solver suite.

    ODE
        Ordinary Differential Equation

    preequilibration
        Simulating or solving the dynamical system for the steadystate.

    presimulation
        Simulation for a fixed time before the regular simulation. Can be used
        to specify pretreatments.

    PEtab
        `PEtab <https://github.com/PEtab-dev/PEtab>`_ is a format for
        specifying parameter estimation problems. It is based on an
        :term:`SBML` model and tab-separated value files specifying the
        observation model and experimental conditions.

    PySB
        `PySB <http://pysb.org/>`_ is a tool for specifying rule-based systems
        biology models as Python code.

    SBML
        The `Systems Biology Markup Language <http://sbml.org/>`_ is a
        commonly used format for specifying systems biology models.

    SUNDIALS
        `SUNDIALS <https://computing.llnl.gov/projects/sundials/>`_:
        SUite of Nonlinear and DIfferential/ALgebraic equation Solvers.
        Provides the :term:`CVODES` and :term:`IDAS` solvers used by AMICI.

    SWIG
        `SWIG <http://www.swig.org/>`_ is a tool that creates interfaces for
        C(++) code to a variety of languages. Much of the AMICI Python
        interface is generated by SWIG.