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TimeCourse Implementation #2450

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3 of 5 tasks
FFroehlich opened this issue May 15, 2024 · 0 comments · May be fixed by #2452
Open
3 of 5 tasks

TimeCourse Implementation #2450

FFroehlich opened this issue May 15, 2024 · 0 comments · May be fixed by #2452

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@FFroehlich
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FFroehlich commented May 15, 2024 •
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Overview of implementations to implement support for timecourse format in petab v2

  • add additional AmiciExpDataVector-like data structure for timeseries (to be generated by petab library)
  • add field to ExpData that specifies the ExpData for initialization
  • provide additional overload for timeseries object in in

    AMICI/python/sdist/amici/swig_wrappers.py

    Line 76 in 7487607

    def runAmiciSimulations(
  • add c++ implementation similar to

    AMICI/src/amici.cpp

    Line 266 in 7487607

    std::vector<std::unique_ptr<ReturnData>> runAmiciSimulations(
    (initially non-parallelized) that handles initialisation
  • add testcase based on

    AMICI/python/tests/test_preequilibration.py

    Line 90 in 7487607

    def test_manual_preequilibration(preeq_fixture):
@dweindl dweindl linked a pull request May 28, 2024 that will close this issue
Timeseries #2452
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Timeseries AMICI-dev/AMICI
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@FFroehlich