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BANJO | http://www.cs.duke.edu/~amink/software/banjo/ | Banjo is a software application and framework for structure learning of static and dynamic Bayesian networks, developed under the direction of Alexander J. Hartemink in the Department of Computer Science at Duke University. Banjo was designed from the ground up to provide efficient structure inference when analyzing large, research-oriented data sets, while at the same time being accessible enough for students and researchers to explore and experiment with the algorithms. Because it is implemented in Java, the framework is easy to maintain and extend. | |

Berkeley Madonna | http://www.berkeleymadonna.com/features.html | Differential equation solver | |

BioCyc | http://biocyc.org/ | BioCyc | |

Biolearn | http://www.c2b2.columbia.edu/danapeerlab/html/biolearn.html | Biolearn is a general package for applying probabilistic graphical models to biological applications. Biolearn release 1.0 is concentrated on structure learning for bayesian networks; future releases are expected to include other types of graphical models, support inference applications, and allow plug-and-play addition of new types of probability distributions, scoring functions and search algorithms. | |

BioModels Database | http://www.ebi.ac.uk/biomodels-main/ | a repository of peer-reviewed, published, computational models | |

BioNetGen | http://bionetgen.org/ | BioNetGen is software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. | |

BioNetS | http://frostbite.amath.unc.edu/~david/BioNetS.zip | Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks. See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC408466/ | Stochastic bistability example |

BooleanNet | http://code.google.com/p/booleannet/ | Boolean Network Modeling. The goal of this software package is to provide intuitive and accessible tools for simulating biological regulatory networks in a boolean formalism. Using this simulator biologist and bioinformaticians can specify their system in a simple textual language then explore various dynamic behaviors via a web interface or an application programming interface (API) each designed to facilitate scientific discovery, data collection and reporting. | |

CompuCell 3D | http://www.compucell3d.org/About | CompuCell is an open source modeling environment and pde solver, primarly used to study cellular behavior. CompuCell is based on the Cellular Potts Model (CPM). While the Potts model was originally developed to study ferromagentic and crystalline systems. | |

COPASI | http://www.copasi.org/ | COPASI (Complex Pathway Simulator) is a software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. COPASI also carries out several analyses of the network and the dynamics, such as steady state stability, parameter sensitivity, elementary flux modes, Lyapunov exponents. Any feature of a model can be optimized using a variety of diverse non-linear optimization algorithms. Parameter values can be estimated from data using a very customizable framework. | |

Cytoscape | http://www.cytoscape.org/ | ytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web. | |

JGI-IMG | http://img.jgi.doe.gov/ | Analysis across multiple genomes | |

MatCont | http://sourceforge.net/projects/matcont/ | MatCont is a Matlab software project for the numerical continuation and bifurcation study of continuous and discrete parameterized dynamical systems. Leaders of the project are Willy Govaerts (Gent,B) and Yuri A. Kuznetsov (Utrecht,NL). | |

MesoRD | http://mesord.sourceforge.net/ | Mesoscopic Reaction Diffusion Simulator is a tool for stochastic simulation of reactions and diffusion. In particular, it is an implementation of the Next Subvolume Method, which is an exact method to simulate the Markov process corresponding to the reaction-diffusion master equation. | |

NeuroRD | http://krasnow.gmu.edu/CENlab/software.html | Computationally efficient, neuronal reaction-diffusion stochastic simulator. | |

NFsim | http://emonet.biology.yale.edu/nfsim/ | NFsim is 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 flexible options for simulating coarse-grained representations of complex nonlinear reaction mechanisms. | |

PottersWheel | http://www.potterswheel.de/ | ottersWheel is a MATLAB® toolbox for mechanistic mathematical modeling, allows reaction network or ordinary differential equation (ODE) based modeling, fits a model to several data sets at once (multi-experiment fitting), is numerically fast based on FORTRAN integrators and C MEX ODE files, is accessible via graphical user interfaces, from command line and scripts, determines parameter identifiability and confidence intervals, imports and exports SBML models and supports biochemical network modeling, can be used in a computer cluster comprises 250,000 lines of Matlab and C Code, is freely available for academic users, is intensively used by experimentalists and modelers since 2005, originates from Systems Biology, but is applicable to any ODE based modeling. | |

ProcessDB | http://www.integrativebioinformatics.com/processdb.html | Biological system modeller | |

RuleBender | http://rulebender.org | Rule Based Modeling and Simulation with RuleBender. Rule-based languages for describing intracellular biochemistry allow for the construction and simulation of detailed models with unprecedented scope and precision. Rule-based Models can be used to suggest new hypotheses and new ideas for future experimentation. | |

SABIO-RK | http://sabiork.h-its.org/ | biochemical pathway and reaction kinetics. Includes rate constants. | |

SimBiology | http://www.mathworks.com/products/simbiology/ | SimBiology® provides graphical and programmatic tools for computational systems biology and pharmacokinetics. It contains functionality for creating, simulating, and analyzing biological models. The SimBiology desktop lets you build a model using a block diagram editor, a model wizard, or a tabular interface. You can also create a model at the command line or directly from SBML files. SimBiology lets you simulate a model using stochastic or deterministic solvers. The product supports parameter estimation, sensitivity analysis, parameter scans, and other model analysis methods. All SimBiology features can be used together with the MATLAB® programming language, letting you customize models, create or modify analysis tasks, and automate your workflow. | |

STEPS | http://steps.sourceforge.net/STEPS/Home.html | STEPS is a package for exact stochastic simulation of reaction-diffusion systems in arbitrarily complex 3D geometries. Our core simulation algorithm is an implementation of Gillespie's SSA, extended to deal with diffusion of molecules over the elements of a 3D tetrahedral mesh. | |

VCell | http://www.nrcam.uchc.edu/ | The Virtual Cell is a unique computational environment for modeling and simulation of cell biology . It has been specifically designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. The creation of biological or mathematical models can range from the simple, to evaluate hypotheses or to interpret experimental data, to complex multi-layered models used to probe the predicted behavior of complex, highly non-linear systems. | |

XPPAUT | http://www.math.pitt.edu/~bard/xpp/xpp.html | Numerical integration of ODEs, phase planes, and bifurcation analysis. Now available for the iPad! | |