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BioDiVinE - Parallel Model-Checker for Multi-Affine ODE Models
BioDiVinE tool adapts parallel LTL model checking algorithms for rectangular abstraction of multi-affine ODE models. Biological models described in terms of mass action kinetics are supported. The tool is accompanied with a simple GUI that allows specification of reactions. The tool package includes a visualisation utility Simaff that allows untimed simulation and 2D depiction of rectangular phase spaces.

[ See link source release ]

 
BioDiVinE GUI
Stand-alone Java GUI for graphical specification of biological reaction networks. This prototype tool allows both graphical and textual editing of biological models which can be exported into .bio format readable by BioDiVinE. The tool is planned to serve also as an interface for BioDiVinE. As an example, visualization of reachable concentration levels is currently supported.

[ See link and binary release ]

 
GeNeSim GUI: Web Interface for Biological Models
GeNeSim GUI is a web interface which currently allows managing of piece-wise linear and multi-affine models, it supports import of models from GNA and SBML, and export to GNA and BioDiVinE tools. The models are represented in an internal XML format.

[ See link ]

 
GeNeSim-DiVinE - prototype of a distributed LTL model checker for genetic regulatory networks

GeNeSim/DiVinE is an experimental prototype extension of the parallel model-checker DiVinE which implements implicit representation of qualitative automata for piece-wise linear models.

[ See link or local copy ]

 
CADP
CADP (Construction and Analysis of Distributed Processes) is a popular toolbox   for the design of communication protocols and distributed systems. CADP is developed  by the VASY team at INRIA Rhone-Alpes and connected to various complementary tools.  CADP is maintained, regularly improved, and used in many industrial projects.   The toolbox offers a wide range of functionalities assisting the user throughout the  design process: compilation and rapid prototyping, interactive step-by-step and guided  simulation, model checking and equivalence checking, test case generation, and performance   evaluation. Several verification techniques (on-the-fly, compositional, and massively  parallel) are provided by CADP and can be combined in order to fight against state explosion.

[ See link ]

 
Genetic Network Analyzer (GNA)
Genetic Network Analyzer (GNA) is a computer tool for the modeling and simulation of genetic regulatory networks. The aim of GNA is to assist biologists and bioinformaticians in constructing a model of a genetic regulatory network using knowledge about regulatory interactions in combination with gene expression data.

[ See link ]

 
LTSmin - Minimization and Instantiation of Labelled Transition Systems
LTSmin is a toolset for manipulating large labelled transition systems.This can be done in two ways: by means of symbolic (BDD based) state space exploration or by means of distributed state space generation and reduction.

[ See link and source release ]

 
LTSmin/CADP plugins for GNA
Client and server side plugins for the GNA model checking service that use LTSmin to perform on-the-fly model checking with CADP.

[ See report and client plugin for GNA 7.0.0]