Simulation
StochSS
New capabilities of Version 1.5 include:
* A new model editor: Edit models faster and easier
* Cost analysis functionality: Measure the cost of running jobs in the cloud
* Cloud data reproduction: Delete cloud data and reproduce it only when it is needed
* Cloud instance type selection: Configure what instance types are used for cloud computation
Linda Petzold and Chandra Krintz
University of California Santa Barbara
posted 2015.03.03
Spatio Temporal Simulation Environment
http://www.stse-software.org
posted 2010.12.03
GNU MCSim
http://www.gnu.org/software/mcsim/
posted 2009.01.15
BALSA
BALSA is a prototype cell systems modeling environment written in Java.
posted 2006.04.25
BIOCHAM
posted 2006.04.25
BioCharon
BioCharon is a language for modular specification of interacting hybrid systems based on the notions of agent and mode.
posted 2006.04.25
BioNetGen
posted 2006.04.25
BioSPICE Dashboard
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.
posted 2006.04.25
BioSpreadsheet
posted 2006.04.25
Cellerator
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.
posted 2006.04.25
Cellware
Cellware is a grid based modeling and simulation tool.
posted 2006.04.25
Copasi
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.
Version 4.4 (Build 26) released May 8, 2008posted 2006.04.25
DBsolve
posted 2006.04.25
Dizzy
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.
posted 2006.04.25
E-Cell
E-Cell System is an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems.
posted 2006.04.25
ESS
posted 2006.04.25
Fluxor
posted 2006.04.25
Gepasi
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)
posted 2006.04.25
INSILICO discovery
http://www.insilico-biotechnology.com/discovery_en.html
posted 2006.04.25
Jarnac
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.
posted 2006.04.25
JigCell
http://jigcell.biol.vt.edu/
posted 2006.04.25
JSIM
http://nsr.bioeng.washington.edu/PLN/Members/butterw/JSIMDOC1.6/JSim_Home.stx/view
posted 2006.04.25
Kinsolver
http://lsdis.cs.uga.edu/%7Ealeman/kinsolver/
posted 2006.04.25
MesoRD
posted 2006.04.25
MMT2
http://www.simtec.mb.uni-siegen.de/software_mmt2.0.html
posted 2006.04.25
Moleculizer
posted 2006.04.25
NetBuilder
posted 2006.04.25
PathwayLab
http://innetics.com/
posted 2006.04.25
PathwayBuilder
posted 2006.04.25
PNK 2e
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.
posted 2006.04.25
PROTON
posted 2006.04.25
PySCeS
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.
posted 2006.04.25
runSBML
posted 2006.04.25
SBML ODE Solver
SBML ODE Solver is a high pecision ODE solver for SBML.
posted 2006.04.25
SBMLSim
SBMLSim provides a Matlab GUI that allows the user to import a SBML model, simulate it, and visualize the simulations.
posted 2006.04.25
SigTran
SigTran is a modeling environment especially designed to enable biological researchers to carry out large scale simulations and analysis of complex signal transduction networks.
posted 2006.04.25
SIMBA
posted 2006.04.25
Simpathica
posted 2006.04.25
StochSim
posted 2006.04.25
STOCKS
posted 2006.04.25
TERANODEÂ Suite
posted 2006.04.25
Trelis
posted 2006.04.25
Virtual Cell
posted 2006.04.25
WinSCAMP
posted 2006.04.25
CellDesigner
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.
posted 2006.04.25
CADLIVE
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.
posted 2006.04.25
BioUML
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.
posted 2006.04.25