Fröhlich, Fabian
Weindl, Daniel
Schälte, Yannik
Pathirana, Dilan
Paszkowski, Lukasz
Lines, Glenn Terje
Stapor, Paul
Hasenauer, Jan
2022-03-15
<p>New features:</p>
<ul>
<li>Import of BioNetGenLanguage (BNGL) models by @FFroehlich in <a href="https://github.com/AMICI-dev/AMICI/pull/1709">https://github.com/AMICI-dev/AMICI/pull/1709</a></li>
<li>Added support for observable-dependent sigmas by @dweindl, @FFroehlich in <a href="https://github.com/AMICI-dev/AMICI/pull/1692">https://github.com/AMICI-dev/AMICI/pull/1692</a></li>
<li>Added support for pysb local functions by @FFroehlich in <a href="https://github.com/AMICI-dev/AMICI/pull/1666">https://github.com/AMICI-dev/AMICI/pull/1666</a></li>
<li>Added experimental support for conservation laws for non-constant species to SBML import: conservation laws for non-constant species
by @stephanmg, @dweindl in <a href="https://github.com/AMICI-dev/AMICI/pull/1669">https://github.com/AMICI-dev/AMICI/pull/1669</a>
Enable this feature by setting environment variable <code>AMICI_EXPERIMENTAL_SBML_NONCONST_CLS</code> to any value<ul>
<li>Allow using states eliminated by conservation laws to be used in root functions by @dweindl in <a href="https://github.com/AMICI-dev/AMICI/pull/1677">https://github.com/AMICI-dev/AMICI/pull/1677</a></li>
<li>Added support for parameter-dependent conservation laws by @dweindl, @FFroehlich in <a href="https://github.com/AMICI-dev/AMICI/pull/1678">https://github.com/AMICI-dev/AMICI/pull/1678</a></li>
</ul>
</li>
<li>Added optional caching for symbolic simplifications in ODE export by @dilpath in <a href="https://github.com/AMICI-dev/AMICI/pull/1672">https://github.com/AMICI-dev/AMICI/pull/1672</a></li>
<li>Added CLI option <code>--no-sensitivities</code> to <code>amici_import_petab</code> by @dweindl in <a href="https://github.com/AMICI-dev/AMICI/pull/1688">https://github.com/AMICI-dev/AMICI/pull/1688</a></li>
</ul>
<p>Fixes:</p>
<ul>
<li>SBML import: Raise in case of nested observables by @dweindl in <a href="https://github.com/AMICI-dev/AMICI/pull/1690">https://github.com/AMICI-dev/AMICI/pull/1690</a></li>
<li>Sympy 1.10 compatibility by @dweindl in <a href="https://github.com/AMICI-dev/AMICI/pull/1694">https://github.com/AMICI-dev/AMICI/pull/1694</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a href="https://github.com/AMICI-dev/AMICI/compare/v0.11.25...v0.11.26">https://github.com/AMICI-dev/AMICI/compare/v0.11.25...v0.11.26</a></p>
If you use this software, please cite both the article from preferred-citation and the software itself.
https://doi.org/10.5281/zenodo.6355611
oai:zenodo.org:6355611
Zenodo
https://github.com/AMICI-dev/AMICI/tree/v0.11.26
https://doi.org/10.5281/zenodo.597928
info:eu-repo/semantics/openAccess
Other (Open)
AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models
info:eu-repo/semantics/other