BioDiVinE 2.0 is an ongoing project aiming at the creation of a tool for the robustness analysis of stochastic biochemical systems.
BioDiVinE 1.0 is a tool set created for verifying properties of biochemical systems given as a system of ordinary differential equations.
Esther is an online interface to multiple tools, among others Parsybone, for analysis of discrete multi-valued models. Esther provides user-friendly interface for model creation, dynamical simulation connected with LTL model checking and result analysis.
Parsybone is a CLI based tool for synthesis of discrete kinetic parameters in gene regulatory networks and for their further analysis.
Parasim is a tool for robustness analysis. Given a SBML model, a property and perturbation set, it computes the robustness of the model over the perturbation set with respect to the property. A perturbation set consists of intervals over model parameters and initial variable values. Properties are entered in the form of signal temporal logic formulae.
GeNeSim is a web based GUI for managing models of biological interaction networks given either as Qualitative models defined by Piece-wise Linear Differential Equations (PLDEs) or Quantitative models defined by Multiaffine Ordinary Differential Equations (MODEs). These models are intended for analysis using the BioDiVinE 1.0 tool.