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Add PumasQSP to README (#565)
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‎README.md‎

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@@ -71,6 +71,8 @@ Where PEtab is supported (in alphabetical order):
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- [PEtab.jl](https://github.com/sebapersson/PEtab.jl) ([HOWTO](https://sebapersson.github.io/PEtab.jl/stable/))
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- [PumasQSP.jl](https://help.juliahub.com/pumasqsp/stable/) ([HOWTO](https://help.juliahub.com/pumasqsp/stable/tutorials/petabimport/))
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- [pyABC](https://github.com/ICB-DCM/pyABC/) ([Example](https://pyabc.readthedocs.io/en/latest/examples/petab.html))
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- [pyPESTO](https://github.com/ICB-DCM/pyPESTO/)
@@ -89,24 +91,24 @@ different tools, based on passed test cases of the
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[PEtab test suite](https://github.com/PEtab-dev/petab_test_suite):
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| ID | Test | AMICI<br>`>=0.11.19` | Copasi | D2D | dMod | MEIGO | parPE<br>`develop` | PEtab.jl <br>`>=1.1.0` | pyABC<br>`>=0.10.1` | pyPESTO<br>`>=0.0.11` | SBML2Julia |
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|----|----------------------------------------------------------------|----------------------|--------|-----|------|-------|--------------------|------------------------|---------------------|-----------------------|------------|
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| 1 | Basic simulation | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ |
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| 2 | Multiple simulation conditions | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ |
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| 3 | Numeric observable parameter overrides in measurement table | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ |
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| 4 | Parametric observable parameter overrides in measurement table | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ |
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| 5 | Parametric overrides in condition table | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ |
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| 6 | Time-point specific overrides in the measurement table | --- | --- | +++ | +++ | +++ | --- | +++ | --- | --- | +++ |
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| 7 | Observable transformations to log10 scale | +++ | +++ | +++ | ++- | +++ | --+ | +++ | +++ | +++ | +++ |
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| 8 | Replicate measurements | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ |
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| 9 | Pre-equilibration | +++ | --- | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ |
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| 10 | Partial pre-equilibration | +++ | --- | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ |
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| 11 | Numeric initial concentration in condition table | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ |
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| 12 | Numeric initial compartment sizes in condition table | --- | +++ | +++ | +++ | +++ | --- | +++ | --- | --- | +++ |
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| 13 | Parametric initial concentrations in condition table | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ |
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| 14 | Numeric noise parameter overrides in measurement table | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ |
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| 15 | Parametric noise parameter overrides in measurement table | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ |
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| 16 | Observable transformations to log scale | +++ | +++ | +++ | ++- | +++ | --+ | +++ | +++ | +++ | +++ |
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| ID | Test | AMICI<br>`>=0.11.19` | Copasi | D2D | dMod | MEIGO | parPE<br>`develop` | PEtab.jl <br>`>=1.1.0` | PumasQSP | pyABC<br>`>=0.10.1` | pyPESTO<br>`>=0.0.11` | SBML2Julia |
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|----|----------------------------------------------------------------|----------------------|--------|-----|------|-------|--------------------|------------------------|----------|---------------------|-----------------------|------------|
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| 1 | Basic simulation | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ | +++ |
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| 2 | Multiple simulation conditions | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ | +++ |
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| 3 | Numeric observable parameter overrides in measurement table | +++ | +++ | +++ | +++ | +++ | --+ | +++ | --- | +++ | +++ | +++ |
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| 4 | Parametric observable parameter overrides in measurement table | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ | +++ |
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| 5 | Parametric overrides in condition table | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ | +++ |
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| 6 | Time-point specific overrides in the measurement table | --- | --- | +++ | +++ | +++ | --- | +++ | --- | --- | --- | +++ |
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| 7 | Observable transformations to log10 scale | +++ | +++ | +++ | ++- | +++ | --+ | +++ | +-+ | +++ | +++ | +++ |
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| 8 | Replicate measurements | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ | +++ |
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| 9 | Pre-equilibration | +++ | --- | +++ | +++ | +++ | --+ | +++ | --- | +++ | +++ | +++ |
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| 10 | Partial pre-equilibration | +++ | --- | +++ | +++ | +++ | --+ | +++ | --- | +++ | +++ | +++ |
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| 11 | Numeric initial concentration in condition table | +++ | +++ | +++ | +++ | +++ | --+ | +++ | +++ | +++ | +++ | +++ |
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| 12 | Numeric initial compartment sizes in condition table | --- | +++ | +++ | +++ | +++ | --- | +++ | --- | --- | --- | +++ |
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| 13 | Parametric initial concentrations in condition table | +++ | +++ | +++ | +++ | +++ | --+ | +++ | --- | +++ | +++ | +++ |
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| 14 | Numeric noise parameter overrides in measurement table | +++ | +++ | +++ | +++ | +++ | --+ | +++ | --- | +++ | +++ | +++ |
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| 15 | Parametric noise parameter overrides in measurement table | +++ | +++ | +++ | +++ | +++ | --+ | +++ | --- | +++ | +++ | +++ |
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| 16 | Observable transformations to log scale | +++ | +++ | +++ | ++- | +++ | --+ | +++ | --- | +++ | +++ | +++ |
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Legend:
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* First character indicates whether computing simulated data is supported and simulations are correct (+) or not (-).

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