Software support

Where PEtab is supported (in alphabetical order):

• AMICI (Example)

• A PEtab -> COPASI converter

• d2d (HOWTO)

• dMod (HOWTO)

• MEIGO (HOWTO)

• parPE

• PEtab.jl (HOWTO)

• PumasQSP.jl (HOWTO)

• pyABC (Example)

• pyPESTO (Example)

• SBML2Julia (Tutorial)

If your project or tool is using PEtab, and you would like to have it listed here, please let us know.

PEtab features supported in different tools

The following table provides an overview of supported PEtab features in different tools, based on passed test cases of the PEtab test suite:

Tool support

ID	Test	AMICI;`>=0.11.19`	Copasi	D2D	dMod	MEIGO	parPE;`develop`	PEtab.jl;`>=1.1.0`	PumasQSP	pyABC;`>=0.10.1`	pyPESTO;`>=0.0.11`	SBML2Julia
1	Basic simulation	+++	+++	+++	+++	+++	–+	+++	+++	+++	+++	+++
2	Multiple simulation conditions	+++	+++	+++	+++	+++	–+	+++	+++	+++	+++	+++
3	Numeric observable parameter overrides in measurement table	+++	+++	+++	+++	+++	–+	+++	—	+++	+++	+++
4	Parametric observable parameter overrides in measurement table	+++	+++	+++	+++	+++	–+	+++	+++	+++	+++	+++
5	Parametric overrides in condition table	+++	+++	+++	+++	+++	–+	+++	+++	+++	+++	+++
6	Time-point specific overrides in the measurement table	—	—	+++	+++	+++	—	+++	—	—	—	+++
7	Observable transformations to log10 scale	+++	+++	+++	++-	+++	–+	+++	+-+	+++	+++	+++
8	Replicate measurements	+++	+++	+++	+++	+++	–+	+++	+++	+++	+++	+++
9	Pre-equilibration	+++	—	+++	+++	+++	–+	+++	—	+++	+++	+++
10	Partial pre-equilibration	+++	—	+++	+++	+++	–+	+++	—	+++	+++	+++
11	Numeric initial concentration in condition table	+++	+++	+++	+++	+++	–+	+++	+++	+++	+++	+++
12	Numeric initial compartment sizes in condition table	—	+++	+++	+++	+++	—	+++	—	—	—	+++
13	Parametric initial concentrations in condition table	+++	+++	+++	+++	+++	–+	+++	—	+++	+++	+++
14	Numeric noise parameter overrides in measurement table	+++	+++	+++	+++	+++	–+	+++	—	+++	+++	+++
15	Parametric noise parameter overrides in measurement table	+++	+++	+++	+++	+++	–+	+++	—	+++	+++	+++
16	Observable transformations to log scale	+++	+++	+++	++-	+++	–+	+++	—	+++	+++	+++

Legend:

• First character indicates whether computing simulated data is supported and simulations are correct (+) or not (-).

• Second character indicates whether computing chi2 values of residuals are supported and correct (+) or not (-).

• Third character indicates whether computing likelihoods is supported and correct (+) or not (-).