The parameter estimation tables (PEtab) format version 2

Abstract

Parameter estimation is a central task in data-driven computational modeling, and a clear, unambiguous, and commonly understood specification of parameter estimation problems is essential for reproducibility and interoperability. PEtab provides a standardized framework for defining such problems in systems biology and systems medicine, particularly for ordinary differential equation models. This document describes the second version of the PEtab format, PEtab 2.0. PEtab 2.0 simplifies and clarifies how estimation problems are defined, while also extending the standard to support more complex and realistic experimental setups. Key improvements include support for additional model formats beyond SBML, expanded and improved specification of parameter priors for Bayesian parameter estimation, and a more flexible description of experiments that allows multiple conditions, time periods, and pre-equilibration steps within a single simulation. Additional updates refine the definition of model parameters, measurement noise, and observation models, and remove ambiguous or confusing features from earlier versions. Version 2 also includes a general extension mechanism, to add functionality for specialized applications not covered by the core standard.