eSTGt: A programming and simulation environment for population dynamics

Abstract

Background: We have previously presented a formal language for describing population dynamics based on environment-dependent Stochastic Tree Grammars (eSTG). The language captures in broad terms the effect of the changing environment while abstracting away details on interaction among individuals. An eSTG program consists of a set of stochastic tree grammar transition rules that are context-free. Transition rule probabilities and rates, however, can depend on global parameters such as population size, generation count and elapsed time. In addition, each individual may have an internal state, which can change during transitions. Results: This paper presents eSTGt (eSTG tool), an eSTG programming and simulation environment. When executing a program, the tool generates the corresponding lineage trees as well as the internal states values, which can then be analyzed either through the tool's GUI or using MATLAB's command-line environment. Conclusions: The presented tool allows researchers to use existing biological knowledge in order to model the dynamics of a developmental process and analyze its behavior throughout the historical events. Simulated lineage trees can be used to validate various hypotheses in silico and to predict the behavior of dynamical systems under various conditions. Written under MATLAB environment, the tool also enables to easily integrate the output data within the user's downstream analysis.