GINsim 3.1: Qualitative modelling and dynamical analysis of logical regulatory networks

Abstract

GINsim is a software for the definition and dynamical analysis of qualitative (Boolean and multi-valued) models of biological regulatory networks. Building on its modular architecture, based on the MDDlib decision-diagram and bioLQM model-manipulation libraries, GINsim version 3.1 introduces new functionalities aimed at the analysis of large logical models: the symbolic computation of trap-spaces, the Booleanisation of multilevel models and the reversal of model dynamics. GINsim 3.1 also extends the estimation of attractor reachability (Monte Carlo and Avatar algorithms), the computation of stable states, as well as model reduction functionalities. Analyses can be applied to perturbed models, and scripted, in particular from the CoLoMoTo interactive notebook. We illustrate the main functionalities of GINsim on a reference multilevel model of regulatory network that control the mammalian cell cycle, including the computation of its stable states and cyclic attractor, the assessment of their reachability, and the identification of the regulatory circuits driving multistability and oscillations. GINsim is freely available under GPL-3.0 at https://ginsim.github.io/, runs on any platform supporting Java, and is interoperable with the other tools of the CoLoMoTo community. Its website provides installation instructions and reference documentation, as well as a repository of Boolean and multilevel logical models.