We present Bio-Stark, an extension of Stark for the simulation and analysis of biological systems. Specifically, to simulate the stochastic, dynamical, behaviour of these systems, Bio-Stark exploits the core simulation model of Stark, the evolution sequence model, and it extends it by refining the discrete step modelling into a time point modelling. We show how Bio-Stark allows us to verify robustness properties in systems biology, by capturing the effects of (unpredictable) perturbations on species in biochemical networks, as well as on the oscillatory behaviour of gene regulatory networks.
Bio-Stark: A Tool for the Time-Point Robustness Analysis of Biological Systems
Tini S.
2024-01-01
Abstract
We present Bio-Stark, an extension of Stark for the simulation and analysis of biological systems. Specifically, to simulate the stochastic, dynamical, behaviour of these systems, Bio-Stark exploits the core simulation model of Stark, the evolution sequence model, and it extends it by refining the discrete step modelling into a time point modelling. We show how Bio-Stark allows us to verify robustness properties in systems biology, by capturing the effects of (unpredictable) perturbations on species in biochemical networks, as well as on the oscillatory behaviour of gene regulatory networks.
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