As the study of information processing in living cells moves from individual pathways to complex regulatory networks, mathematical models and simulation become indispensable tools for analyzing the complex behavior of such networks and can provide…

As the study of information processing in living cells moves from individual pathways to complex regulatory networks, mathematical models and simulation become indispensable tools for analyzing the complex behavior of such networks and can provide deep insights into the functioning of cells.

A free, open-source, biochemical reaction simulator designed to handle systems…

A free, open-source, biochemical reaction simulator designed to handle systems that have a large or even infinite number of possible molecular interactions or states. NFsim also has advanced and…

A generic simulation framework for BioPAX. BioASF explicitly separates the…

A generic simulation framework for BioPAX. BioASF explicitly separates the execution model from the model structure as provided by BioPAX, with the advantage that the modelling process becomes more…

A tool for modeling biological networks and simulating their discrete-time…

A tool for modeling biological networks and simulating their discrete-time dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network that enables researchers to…

Explores the space of alignments looking for ones scoring well according to M…

Explores the space of alignments looking for ones scoring well according to M (an objective function for alignment quality). SANA is based on a metaheuristic search algorithm with a rich history of…

Designed to efficiently rewire large bipartite networks. BiRewire3 is a…

Designed to efficiently rewire large bipartite networks. BiRewire3 is a one-stop tool to rewire in a meaningful way any type of unweighted networks (undirected, directed, and signed) currently used…

Simulates large-scale rule-based models. DYNSTOC is an opensource software that…

Simulates large-scale rule-based models. DYNSTOC is an opensource software that implements an extension of the StochSim simulation method that uses a set of rules specified in an expressive…

Serves for stochastic simulation and analysis of chemical reaction networks.…

Serves for stochastic simulation and analysis of chemical reaction networks. FERN is a Java framework for modeling and simulating biological systems which provides accurate and state-of-the-art…

Allows creation and manipulation of SBML format metabolic networks with…

Allows creation and manipulation of SBML format metabolic networks with reactions and compounds defined as in the KEGG LIGAND database. MetNetMaker is an application that uses the KEGG LIGAND…

Allows exploration of the dynamics of biochemical networks. Facile is…

Allows exploration of the dynamics of biochemical networks. Facile is especially designed for mathematicians, engineers, and physicists working in systems biology. It is provided with EasyStoch which…

An open-source in-browser tool for simulation and manipulation of Boolean…

An open-source in-browser tool for simulation and manipulation of Boolean networks. BooleSim can be used specifically for the modeling of gene regulatory or signal transduction networks.

Models and simulates reaction-diffusion systems. Meredys allows for the…

Models and simulates reaction-diffusion systems. Meredys allows for the simulation of multi-component, multi-feature state molecular species in two and three dimensions. The software employs a…

Assists in modelling and simulation of biological processes. PNK uses…

Assists in modelling and simulation of biological processes. PNK uses Stochastic Petri Nets(SPNs) and a graphical representation of Markov Jump Processes to work.

Allows users to model and simulate spatio-temporal processes in living cells.…

Allows users to model and simulate spatio-temporal processes in living cells. Bio-SPICE is a framework and software toolkit that consists of (i) the Dashboard, (ii) data analysis tools, (iii)…

Analyzes metabolic pathways, principally by using Flux Balance Analysis (FBA)…

Analyzes metabolic pathways, principally by using Flux Balance Analysis (FBA) and Open Dynamics Engine (ODE) simulation. Pathway Analyzer performs report on gene deletions and flux values from…

Computes attractors in Boolean Networks with Synchronous update. BNS is a…

Computes attractors in Boolean Networks with Synchronous update. BNS is a software tool used for the modeling of genetic regulatory networks. It implements an algorithm based on a SAT-based bounded…

Enables users to automatically convert networks for analysis with the signaling…

Enables users to automatically convert networks for analysis with the signaling petri net (SPN) simulator from the standard systems biology markup language. The automation of this step opens the SPN…

A stochastic tool for simulation of biochemical networks. Jdesigner allows…

A stochastic tool for simulation of biochemical networks. Jdesigner allows model builders to run stochastic simulations of their models and perform statistical analysis on the results. It also…

A Cytoscape plugin that conveniently simulates dynamics related to robustness,…

A Cytoscape plugin that conveniently simulates dynamics related to robustness, and examines structural properties with respect to feedforward/feedback loops. NetDS can evaluate how robustly a network…

Allows users to specify molecular complexes and their interactions as well as…

Allows users to specify molecular complexes and their interactions as well as the reaction-induced modifications of the molecules through a flexible visual interface. It can take into account the…

A visualization system for the integrated visualization, modeling and…

A visualization system for the integrated visualization, modeling and simulation of rule-based intracellular biochemistry. RuleBender has been adopted as both an educational and a research tool. A…

Implements a network-free method for simulation of rule-based models that is…

Implements a network-free method for simulation of rule-based models that is similar to Gillespie's method. The method is suitable for rule-based models that can be encoded in BNGL, including…

Allows simulation large reaction networks. KINSOLVER is a simulator that can…

Allows simulation large reaction networks. KINSOLVER is a simulator that can solve reaction networks of arbitrary size, topology, rate constants, and initial conditions by 5 standard methods. It also…

Allows users to build, visualize, and simulate multi-layered biological…

Allows users to build, visualize, and simulate multi-layered biological networks. NetBuilder aims to assist researchers in manipulating mathematical representations needed for the prediction of the…

Provides library and tools to support the SBML Layout and Rendering Extension.…

Provides library and tools to support the SBML Layout and Rendering Extension. SBML Layout is a web-server that allows users to layout and render SBML files. It provides a unified interface to a…

Allows communication between heterogeneous application components. SBW is a…

Allows communication between heterogeneous application components. SBW is a computational resource sharing framework that allows applications to communicate with each other efficiently and without…

Simulates metabolic and chemical networks. WinSCAMP allows users to proceed…

Simulates metabolic and chemical networks. WinSCAMP allows users to proceed metabolic control analysis calculations. The software is useful to detail reactions by using natural biochemical notation…

Detects rate constants in molecular network models. PET can be used as a…

Detects rate constants in molecular network models. PET can be used as a regulatory network models’ builder or for making comparison between models and results from experimentation. It allows…

Reproduces neural systems from biochemical signaling to complex models…

Reproduces neural systems from biochemical signaling to complex models including single neurons, circuits, and larges networks. Moose classifies biological concepts into classes and dispatch them…

Permits to model regulatory network systems. transsys (1) integrates several…

Permits to model regulatory network systems. transsys (1) integrates several methods for modelling gene regulatory systems, (2) facilitates interfacing with models of growth processes and (3) allows…

Provides a Boolean-based representations of Biological Systems.…

Provides a Boolean-based representations of Biological Systems. ccBooleanAnalysis is a modeling system that can visualize biological networks as logic gate circuits, and vice-versa.

A biological network topology simulator in which module structures of different…

A biological network topology simulator in which module structures of different type and size are replicated at different level of network organization and interconnected, so to obtain the desired…