Mathematical models based on Ordinary Differential Equations (ODEs) are
frequently used to describe and simulate biological systems. Nevertheless, such
models are often difficult to understand. Unlike ODE models, Rule-Based Models
(RBMs) utilise formal language to describe reactions as a cumulative number of
statements that are easier to understand and correct. They are also gaining
popularity because of their conciseness and simulation flexibility. However,
RBMs generally lack tools to perform further analysis that requires simulation.
This situation arises because exact and approximate simulations are
computationally intensive. Translating RBMs into ODEs is commonly used to reduce
simulation time, but this technique may be prohibitive due to combinatorial
explosion. Here, we present the software called Pleione to calibrate RBMs.
Parameter calibration is essential given the incomplete experimental
determination of reaction rates and the goal of using models to reproduce
experimental data. The software distributes stochastic simulations and
calculations and incorporates equivalence tests to determine the fitness of RBMs
compared with data. The primary features of Pleione were thoroughly tested on a
model of gene regulation in Escherichia coli. Pleione yielded satisfactory
results regarding calculation time and error reduction for multiple simulators,
models, parameter search strategies, and computing infrastructures.