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Published December 10, 2024 | Version v0.30.0
Software Open

AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models

Creators

Description

Please note that the amici JAX model generation introduced in v0.29.0 is experimental, the API may substantially change in the future. Use at your own risk and do not expect backward compatibility.

Features

  • Added serialisation for JAX models

    by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2608

  • Disabled building the C++ extension by default when generating a JAX model

    by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2609

  • Separate pre-equilibration and dynamic simulation in jax

    by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2617

  • State reinitialisation in JAX

    by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2619

Fixes

  • Fixed ModelStateDerived copy ctor (fixes potential segfaults)

    by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2612

  • PEtab parameter mapping: fill in fixed parameter values for initial values

    by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2613

  • nan-safe log&divide for JAX models

    by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2611

Full Changelog: https://github.com/AMICI-dev/AMICI/compare/v0.29.0...v0.30.0

Notes

If you use this software, please cite both the article from preferred-citation and the software itself.

Files

AMICI-dev/AMICI-v0.30.0.zip

Files (7.2 MB)

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md5:af4f796dfacc292292ce7f3c40071397
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Additional details

Related works

Is supplement to
Software: https://github.com/AMICI-dev/AMICI/tree/v0.30.0 (URL)

Software

Repository URL
https://github.com/AMICI-dev/AMICI