MOTIVATION: One of the main causes hampering predictability during the model identification and automated design of gene circuits in synthetic biology is the effect of molecular noise. Stochasticity may significantly impact the dynamics and function of gene circuits, specially in bacteria and yeast due to low mRNA copy numbers. Standard stochastic simulation methods are too computationally costly in realistic scenarios to be applied to optimization-based design or parameter estimation. RESULTS: In this work, we present IDESS (Identification and automated Design of Stochastic gene circuitS), a software toolbox for optimization-based design and model identification of gene regulatory circuits in the stochastic regime. This software incorporates an efficient approximation of the Chemical Master Equation as well as a stochastic simulation algorithm-both with GPU and CPU implementations-combined with global optimization algorithms capable of solving Mixed Integer Nonlinear Programming problems. The toolbox efficiently addresses two types of problems relevant in systems and synthetic biology: the automated design of stochastic synthetic gene circuits, and the parameter estimation for model identification of stochastic gene regulatory networks. AVAILABILITY AND IMPLEMENTATION: IDESS runs under the MATLAB environment and it is available under GPLv3 license at https://doi.org/10.5281/zenodo.7788692.

Mechanistic dynamic models have become an essential tool for understanding biomolecular networks and other biological systems. Biochemical stochasticity can be extremely important in some situations, e.g., at the single-cell level where there is a low copy number of the species involved. In these scenarios, deterministic models are not suitable to characterize the dynamics, so stochastic dynamic models should be considered. Here, we address the challenging problem of parameter estimation in stochastic dynamic models. Despite recent advances, this area is considerably less mature than its deterministic counterpart. We present a novel strategy based on two components: (i) global optimization via a hybrid stochastic-deterministic approach, and (ii) stochastic simulation techniques tailored to the sparsity of the available experimental data. Regarding the latter, for cases of dense population data we make use of a novel approach using a Partial Integro-Differential Equation (PIDE) model solved using a semilagrangian method. In order to further speed up the simulations, we also present efficient parallel implementations for multi-core CPUs and also for graphical processing units (GPUs). Importantly, whereas SDE and Fokker Planck approximations of the Chemical Master Equation (CME) apply when the reactant populations are sufficiently large, the PIDE approximation to the CME is valid for very low copy numbers, and therefore they enable us to tackle parameter estimation for systems with large intrinsic molecular noise, (highly stochastic regimes far from the thermodynamic limit). We test our strategy with four challenging problems: a Lotka-Volterra system, a polarization system in S. cerevisiae, a genetic toggle switch, and a genetic circadian oscillator. Our method could successfully solve these problems in very reasonable computation times (often a few minutes for the first two problems) using standard low-cost hardware, showing very significant speedups with respect to recent alternative methods. The code used to obtain the results reported here is available at https://doi.org/10.5281/zenodo.5195408.

Motivation: Gene regulation is inherently stochastic. In many applications concerning Systems and Synthetic Biology such as the reverse engineering and the de novo design of genetic circuits, stochastic effects (yet potentially crucial) are often neglected due to the high computational cost of stochastic simulations. With advances in these fields there is an increasing need of tools providing accurate approximations of the stochastic dynamics of gene regulatory networks (GRNs) with reduced computational effort. Results: This work presents SELANSI (SEmi-LAgrangian SImulation of GRNs), a software toolbox for the simulation of stochastic multidimensional gene regulatory networks. SELANSI exploits intrinsic structural properties of gene regulatory networks to accurately approximate the corresponding Chemical Master Equation with a partial integral differential equation that is solved by a semi-lagrangian method with high efficiency. Networks under consideration might involve multiple genes with self and cross regulations, in which genes can be regulated by different transcription factors. Moreover, the validity of the method is not restricted to a particular type of kinetics. The tool offers total flexibility regarding network topology, kinetics and parameterization, as well as simulation options. Availability and implementation: SELANSI runs under the MATLAB environment, and is available under GPLv3 license at https://sites.google.com/view/selansi. Contact: [email protected].