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

Fröhlich, Fabian; Weindl, Daniel; Schälte, Yannik; Pathirana, Dilan; Paszkowski, Lukasz; Lines, Glenn Terje; Stapor, Paul; Hasenauer, Jan


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  <identifier identifierType="DOI">10.5281/zenodo.6524929</identifier>
  <creators>
    <creator>
      <creatorName>Fröhlich, Fabian</creatorName>
      <givenName>Fabian</givenName>
      <familyName>Fröhlich</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-5360-4292</nameIdentifier>
    </creator>
    <creator>
      <creatorName>Weindl, Daniel</creatorName>
      <givenName>Daniel</givenName>
      <familyName>Weindl</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-9963-6057</nameIdentifier>
    </creator>
    <creator>
      <creatorName>Schälte, Yannik</creatorName>
      <givenName>Yannik</givenName>
      <familyName>Schälte</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-1293-820X</nameIdentifier>
    </creator>
    <creator>
      <creatorName>Pathirana, Dilan</creatorName>
      <givenName>Dilan</givenName>
      <familyName>Pathirana</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-7000-2659</nameIdentifier>
    </creator>
    <creator>
      <creatorName>Paszkowski, Lukasz</creatorName>
      <givenName>Lukasz</givenName>
      <familyName>Paszkowski</familyName>
    </creator>
    <creator>
      <creatorName>Lines, Glenn Terje</creatorName>
      <givenName>Glenn Terje</givenName>
      <familyName>Lines</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-6294-1805</nameIdentifier>
    </creator>
    <creator>
      <creatorName>Stapor, Paul</creatorName>
      <givenName>Paul</givenName>
      <familyName>Stapor</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-7567-3985</nameIdentifier>
    </creator>
    <creator>
      <creatorName>Hasenauer, Jan</creatorName>
      <givenName>Jan</givenName>
      <familyName>Hasenauer</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-4935-3312</nameIdentifier>
    </creator>
  </creators>
  <titles>
    <title>AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2022</publicationYear>
  <dates>
    <date dateType="Issued">2022-05-06</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/6524929</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">https://github.com/AMICI-dev/AMICI/tree/v0.11.29</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.597928</relatedIdentifier>
  </relatedIdentifiers>
  <version>v0.11.29</version>
  <rightsList>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Features:&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;Performance: Limit newton step convergence check by @FFroehlich in &lt;a href="https://github.com/AMICI-dev/AMICI/pull/1780"&gt;https://github.com/AMICI-dev/AMICI/pull/1780&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;More informative NaN/Inf warnings by @dweindl in &lt;a href="https://github.com/AMICI-dev/AMICI/pull/1640"&gt;https://github.com/AMICI-dev/AMICI/pull/1640&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;SBML import can now handle initial events by @FFroehlich in &lt;a href="https://github.com/AMICI-dev/AMICI/pull/1789"&gt;https://github.com/AMICI-dev/AMICI/pull/1789&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;Fixes:&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;Avoid error if no measurements in PEtab problem; fixed type handling in PEtab parameter mapping by @dilpath in &lt;a href="https://github.com/AMICI-dev/AMICI/pull/1783"&gt;https://github.com/AMICI-dev/AMICI/pull/1783&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;Fixed substitution of expressions in root and stau by @dilpath in &lt;a href="https://github.com/AMICI-dev/AMICI/pull/1784"&gt;https://github.com/AMICI-dev/AMICI/pull/1784&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;Workaround for PEtab problems with state-dependent noise models by @dweindl in &lt;a href="https://github.com/AMICI-dev/AMICI/pull/1791"&gt;https://github.com/AMICI-dev/AMICI/pull/1791&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</description>
    <description descriptionType="Other">If you use this software, please cite both the article from preferred-citation and the software itself.</description>
  </descriptions>
</resource>
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