A portal site for systems biology.

Spatio-temporal simulation environment (STSE): the overall goal of this project is to provide a software platform: a set of tools and workflows facilitating spatio-temporal simulations (preferably of biological systems) based on microscopy data. The framework currently contains modules to digitize, represent, analyze, and model spatial distributions of molecules in static and dynamic structures (e.g. growing). A strong accent is put for the experimental verification of biological models by actual, spatio-temporal data acquired using microscopy techniques.

http://www.stse-software.org

GNU MCSim is a free simulation package which allows you to design your own statistical or simulation models, and perform Bayesian inference through Markov Chain Monte Carlo simulations. Starting with version 5.3.0, GNU MCSIm can import and simulate SBML models.

http://www.gnu.org/software/mcsim/

BALSA is a prototype cell systems modeling environment written in Java.

http://www.csi.washington.edu/teams/modeling/projects/BALSA

BIOCHAM is a programming environment for modeling biochemical systems, making simulations and querying the model in temporal logic CTL.

http://contraintes.inria.fr/BIOCHAM/

BioCharon is a language for modular specification of interacting hybrid systems based on the notions of agent and mode.

http://www.cis.upenn.edu/biocomp

BioNetGen is a software for generating mathematical/computational models that account comprehensively and precisely for the full spectrum of molecular species implied by user-specified activities, potential modifications and interactions of the domains of signaling molecules.

http://cellsignaling.lanl.gov/bionetgen

Bio-SPICE, an open source framework and software toolset for Systems Biology, is intended to assist biological researchers in the modeling and simulation of spatio-temporal processes in living cells. In addition, our goal is to develop and serve a user community committed to using, extending and exploiting these tools to further our knowledge of biological processes.

http://www.biospice.org/

http://biocomp.ece.utk.edu/tools.html

Cellerator is a Mathematica® package designed to facilitate biological modeling via automated equation generation. Cellerator was designed with the intent of simulating at least the following essential biological processes: signal transduction networks (STNs); cells that are represented by interacting signal transduction networks; and multi-cellular tissues that are represented by interacting networks of cells that may themselves contain internal STNs.

http://www-aig.jpl.nasa.gov/public/mls/cellerator/

Cellware is a grid based modeling and simulation tool.

http://www.bii.a-star.edu.sg/sbg/cellware

Copasi (Complex Pathway Simulator) is a software for simulation and analysis of biochemical networks developed by Pedro Mendes (VT) and Ulsla Kummer (EML Research) groups.

http://www.copasi.org/

Version 4.4 (Build 26) released May 8, 2008

http://biosim.genebee.msu.su/dbsdownload_en.html

Dizzy is a chemical kinetics stochastic simulation software package written in Java. It provides a model definition environment and an implementation of the Gillespie, Gibson-Bruck, and Tau-Leap stochastic algorithms. Dizzy is capable of importing and exporting the SBML model definition language, as well as displaying models graphically using the Cytoscape software system. Dizzy is based on the ISBJava library.

http://labs.systemsbiology.net/bolouri/software/Dizzy/

E-Cell System is an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems.

http://ecell.sourceforge.net/

http://biocomp.ece.utk.edu/

http://arep.med.harvard.edu/moma/FluxorPipeline.tar.gz

Gepasi is a software package for modeling biochemical systems. It simulates the kinetics of systems of biochemical reactions and provides a number of tools to fit models to data, optimize any function of the model, perform metabolic control analysis and linear stability analysis.(from Gepasi web page)

http://www.gepasi.org/

INSILICO discovery is an advanced computational tool for network oriented "in silico" analysis and design of cellular properties.
http://www.insilico-biotechnology.com/discovery_en.html

A fast simulator of reaction networks. This is one of the main modules in SBW, it provides may computational services, includes time course simulation (ODE or stochastic), steady state analysis, basic structural properties of networks, dynamic properties like the Jacobian, elasticities, sensitivities, eigenvalues etc. It also supports a scripting language that allows experienced users to directly interact with the computational engine.

http://www.sys-bio.org/

JigCell is a modeling and simulation software that also enable parameter estimation. JigCell is a joint effort by members of the Departments of Biology and Computer Science at Virginia Tech.
http://jigcell.biol.vt.edu/

JSim is a Java-based simulation system for building and analyzing quantitative numeric models. JSim's primary focus has been in physiology and bio-medicine, however its computation engine is quite general and applicable to a wide range of scientific domains.
http://nsr.bioeng.washington.edu/PLN/Members/butterw/JSIMDOC1.6/JSim_Home.stx/view

Kinsolver is a simulator for biochemical and gene regulatory networks
http://lsdis.cs.uga.edu/%7Ealeman/kinsolver/

MesoRD - Mesoscopic Reaction Diffusion Simulator
http://mesord.sourceforge.net/

Modeling and simulation software for metabolic networks.
http://www.simtec.mb.uni-siegen.de/software_mmt2.0.html

http://www.molsci.org/%7Elok/moleculizer/

http://strc.herts.ac.uk/bio/maria/NetBuilder/

PathwayLab is an in silico pathway analysis tool, enabling pharmaceutical R&D to reach their target decisions faster and with higher accuracy.
http://innetics.com/

http://biospice.lbl.gov/PathwayBuilder/

The PNK (Petri Net Kernel) 2e is a software environment for the modeling and simulation of biological processes. It was developed as part of a M.Sc. project at the University of Edinburgh, UK. The software uses Stochastic Petri Nets (SPNs), a graphical representation of Markov Jump Processes.

http://page.mi.fu-berlin.de/%7Etrieglaf/PNK2e/index.html

PROTON is an Integrative Modeling System (IMS). It has been initiated by the project MARG sponsored by the German Research Council (DFG). The purpose of the system is to support the modeling of large-scale systems by using integrative methods.

http://tunicata.techfak.uni-bielefeld.de/proton

Pysces is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis.

http://pysces.sourceforge.net/

A pathway simulation tool by Ariadne Genomics.

http://ariadnegenomics.com/technology/simulation.html

SBML ODE Solver is a high pecision ODE solver for SBML.

http://www.tbi.univie.ac.at/%7Eraim/odeSolver/

SBMLSim provides a Matlab GUI that allows the user to import a SBML model, simulate it, and visualize the simulations.

http://www.dim.uchile.cl/%7Edremenik/SBMLSim/

SigTran is a modeling environment especially designed to enable biological researchers to carry out large scale simulations and analysis of complex signal transduction networks.

http://csi.washington.edu/teams/modeling/projects/sigtran

http://www.ifak-system.com/swt/simulation/index.php?level=swtSIMBA4

Simpathica is a set of tools capable of simulating and analyzing biological pathways. It consists of a front end and a back end. The front end is a pathway editor which generates a set of Ordinary Differential Equations, which are in turn simulated using Octave. The back end, also known as XSSYS, is a temporal logic analysis tool which can answer queries about the time course behavior of a set of pathways. Developed by NYU Courant Institute of Mathematical Sciences.

http://bioinformatics.nyu.edu/Projects/Simpathica/

StochSim is a stochastic simultor for biological processes. StochSim was written by Carl Firth (formerly Carl Morton-Firth

http://info.anat.cam.ac.uk/groups/comp-cell/StochSim.html

STOCKS is a stochastic simulation software for biochemical reaction networks.

http://www.sysbio.pl/stocks/

Platform to Automate Experiments and Manage Data

http://teranode.com/products/index.php

Trelis is a graphical Monte Carlo simulation tool for modeling the time evolution of chemical reaction systems involving small numbers of reactant molecules, such as occur in subcellular biological processes like genetic regulatory networks.

Trelis

Cellular simulation software developed at University of Connecticut Health Center which is a part of the Center for Cell Analysis and Modeling, CCAM.

http://www.vcell.org/

Window version of SCAMP by H. Sauro.

http://www.sys-bio.org/

CellDesigner is a software suite for systems biology which enables grpahical editing of biological networks, simulation. It comply with SBML and SBGN, and can connect to SBW to utlize analysis packages.

http://celldesigner.org/

CADLIVE is a system for constructing large-scale biological networks (metabolic and gene regulatory networks) using GUI (Graphic User Interface) and saving them as regulator reaction equations in a database in the format compatible to a simulator. It has been developed by H. Kurata at the Kyushu Institute of Technology together with staffs at Mitsui Knowledge Industry Co., Ltd.

http://kurata21.bse.kyutech.ac.jp/cadlive/

BioUML is Java framework for systems biology. It spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization and simulations.

http://www.biouml.org/