********
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

    equilibration
        In AMICI, equilibration refers to the process of simulating or
        solving a dynamical system for :term:`steady state`.
        "Equilibration" refers to approaching an
        `equilibrium point <https://en.wikipedia.org/wiki/Equilibrium_point_(mathematics)>`__
        of a dynamical system and does not imply thermodynamic equilibrium.

    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:`pre-equilibration`, :term:`pre-simulation` and the main
        simulation. See also :term:`simulation periods`.

    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

    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.

    post-equilibration
        :term:`equilibration` after the main simulation.
        See also :term:`simulation periods`.

    pre-equilibration
        :term:`Equilibration <equilibration>` before the :term:`pre-simulation`
        or main simulation. Pre-equilibration is useful if the system is
        assumed to be at steady state at the start of some experiment, but the
        initial state is not known.
        The model time is reset to its initial time after pre-equilibration.
        See also :term:`simulation periods`.

    pre-simulation
        Simulation for a fixed time before the regular simulation. Can be used
        to specify pretreatments. Pre-simulation starts at
        :math:`t_0 - t_{presim}`. Dedicated fixed parameters can be
        specified for pre-simulation.
        See also :term:`simulation periods`.

    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.

    simulation periods
        In AMICI a model simulation may consist of multiple periods:

        * A :term:`pre-equilibration` period, which is used to simulate the
          system until it reaches :term:`steady state`.
        * A :term:`pre-simulation` period, which is used to simulate the system
          for a fixed time before the main simulation.
        * The main simulation period.
        * A :term:`post-equilibration` period, to simulate the system until it
          reaches :term:`steady state`.

        The main simulation and post-equilibration periods are the only
        periods for which output timepoints can be specified and during which
        measurements are assumed to be taken.

        (Non-fixed) model parameters (:math:`p`) are the same throughout those
        periods, but different sets of :term:`fixed parameters` (:math:`k`) can
        be specified for each period, except for post-equilibration, which
        always uses the fixed parameters of the main simulation period.

        For SBML models, initial assignments and initial values of event
        triggers are only applied once at the start of the first period.

    steady state
        In AMICI, a model is considered to be at steady state if the time
        derivative of the state variables is zero, up to the specified
        tolerances, even if there are discontinuities in the model
        (e.g., due to events) that may change the model state at a later time
        point.

    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.