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1
E-Cell
Masaru Tomita
Japan
http://www.e-cell.org/
A model-building kit
2
Gepasi
Pedro Mendes
USA
http://www.gepasi.org/
Biochemical Kinetics Simulator
3
PathDB
NCGR
USA
http://www.ncgr.org/research/pathdb/index.html
A Metabolic Pathway Database, PathDB attempts to include very rich descriptions of the kinetic, thermodynamic and physico-chemical properties of pathway components.
4
Jarnac
Herbert M Sauro
UK
http://members.tripod.co.uk/sauro/biotech.htm
an interactive and interpreted language for modelling integrated cellular systems, such as metabolic, gene regulation and signal transduction circuits
5
SCAMP
Herbert M Sauro
UK
http://www.fssc.demon.co.uk/Scamp/scamp.htm or http://bms-mudshark.brookes.ac.uk/sware.html
Metabolic Simulation and Analysis (PC)
41
Linear Pathway Modeller
Herbert M Sauro
UK
http://www.fssc.demon.co.uk
Linear Pathway Modeller*****
42
MetabVis
Andreas Freier
Germany
http://edradour.cs.uni-magdeburg.de/~freier/servlets/webmain.server
Metabolic Pathway Simulation and Visualization
6
JDesigner
Herbert M Sauro
UK
http://members.tripod.co.uk/sauro/biotech.htm
draw a biochemical network and export the network in the form of SBML.
7
MetaTool
Stefan Schuster, Juan Carlos Nu??nd Thomas Pfeiffer
Germany, UK
http://www.biologie.hu-berlin.de/biophysics/Theory/tpfeiffer/metatool.html
a program for studying stuctural properties of metabolic
networks by using methods of linear and convex algebra
8
Dynafit
BioKin, Ltd. (P. Kuzmic)
USA
http://www.biokin.com/dynafit/
Analysis of (bio)chemical kinetics and equilibria. Performing nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data.
9
BatchKi
BioKin, Ltd.
USA
http://www.biokin.com/batchki/
automatic determination of enzyme inhibition constants (both "classical" and "tight-binding") from enzyme kinetic data.
10
SCoP
NBSR et al.
USA
http://www.simresinc.com/scopinfo.html
Simulation Control Program
11
DBSolve
Igor Goryanin
UK
http://homepage.ntlworld.com/igor.goryanin/
DBsolve: software for metabolic, enzymatic and receptor-ligand binding simulation. Import SCAMP format cmd files for project migration from SCAMP and entering reactions in traditional way.
12
MetaModel
Athel Cornish-Bowden and Jannie Hofmeyr
France
http://bip.cnrs-mrs.fr/bip10/modeling.htm
MetaModel: a program for modelling and control analysis of metabolic pathways on the IBM PC and compatibles.
13
MIST
Magnus Ehlde
Sweden
ftp://wwwce1.kat.lth.se/program/mist/
Metabolic Interactive Simulation Tool. Dynamically simulate user-defined metabolic pathways, solve the steady state of the pathways, determine stoichiometric constraints in the pathways, calculate the control coefficients of the pathways.
14
CONTROL
Letellier et al.
France
http://www.u-bordeaux2.fr/recherche/labos/aigle.html
calculate control coefficients from values of elasticities.
15
MetaCon
Thomas, S. and Fell, D.A.
UK
http://bms-mudshark.brookes.ac.uk/sware.html
calculates algebraic expressions of the control coefficients as functions of the elasticities and can substitute polynomial expressions or numerical values for any or all variables (metabolite concentrations, fluxes and enzyme elasticities).
16
StochSim
Carl Firth
UK
http://www.zoo.cam.ac.uk/comp-cell/StochSim.html
a discrete, stochastic simulator for (bio)chemical
reactions
17
EMPath
UK
http://bms-mudshark.brookes.ac.uk/sware.html
18
MetaNet
Michael C.Kohn
USA
http://dir.niehs.nih.gov/dirlcbra/kohn/
a graph representation of a biochemical pathway
19
BioJAKE
IMCBBC
Singapore
http://sandstorm.bic.nus.edu.sg/BioJAKE/
providing mechanisms for the creation, edition and visualization of biological pathway diagrams.
20
BioQUEST
Brian White
USA
http://omega.cc.umb.edu/~bwhite/ek.html
Metabolic Pathways/Enzyme Kinetics Simulation
21
DMSS
Michael J. Wise and Peter Meric
UK
http://www.ccsr.cam.ac.uk/projects/dmss.html
Scalable, Discrete Event Metabolic Simulation System
22
ElectricArc
Gene Selkov Jr.
USA
http://home.xnet.com/~selkovjr/ElectricArc/
a perl and Tk-based diagram drawing tool
23
Virtual Cell
Schaff, J., et al.
USA
http://www.nrcam.uchc.edu/
a collection of still images, texts and movies covering the structure and functioning of a typical plant cell
24
Discrete Dynamics Lab
Santa Fe Institute
USA
htp://www.santafe.edu/~wuensch/ddlab.html
Tools for researching discrete dynamical networks - from Cellular Automata to Random Boolean Networks and beyond.
25
CKS
IBM
USA
http://www.almaden.ibm.com/st/msim/index.html
Reactions are simulated by a stochastic approach rather than the usual numerical solution of differential equations, which can provide advantages for some systems.
26
ENCORA
R.J.W. Slats, et al.
Netherland
http://www.bt.tudelft.nl/miscell/freewf.htm
obtaining steady-state kinetic parameters by fitting progress curves.
27
Equilibrate
GertJan C. Veenstra
http://equilibrate.homestead.com/files/
calculates steady state equilibria, simulates dynamic equilibria, and calculates dissociation constants.
28
kc
http://SAL.KachinaTech.COM/Z/2/KC.html
Kinetic Compiler, simulates reactions by integrating
differential equations
29
Kinetic
http://www.graphpad.com/www/kinetic.htm
simulates or models the kinetics of biochemical systems.
30
KINSIM/FITSIM
C. Frieden's lab
USA
http://wuarchive.wustl.edu/packages/kinsim/
simulation package in enzymology
31
Enzyme Kinetics
ChemSW, Inc.
Canada
http://www.chemsw.com/13022.htm
analyzing single-substrate steady-state kinetics.
32
Equilibrium Calculator
Robert D. Allendoerfer
USA
http://jchemed.chem.wisc.edu/JCESoft/Issues/Series_D/1D1/prog3-1D1.html
calculates the equilibrium concentrations of all the reagents in an arbitrary chemical reaction with as many as five reactants and products by minimizing the Gibbs free energy as a function of the extent of reaction using an iterative algorithm.
33
KINETICS
http://www.ari.net/ars/kin.html
Numeric Integration of Multistep Rate Equations
34
BioThermo
http://www.biotecnol.pt/
A simulation package that allows feasibility studies of metabolic pathways. Based on specification of the standard Gibbs free energies and ranges of metabolite concentrations the feasibility of the individual pathway reactions are evaluated.
35
FluxMap
Pissarra, P.N.
http://www.biotecnol.com/projecto_3.htm
A simulation package that allows calculation of metabolic fluxes based on metabolite balancing. The software works with a graphical interface, which can be custom designed for a specific network structure.
36
BioNet
Joe Vallino
USA
http://www.ibt.dtu.dk/cpb/metaboleng/metabol.htm or http://web.mit.edu/cheme/gnswebpage/index.shtml
A simple simulation package for metabolic flux analysis.
37
QS4WIN
William R. Smith
Canada
http://www.mathtrek.com/
an equilibrium analysis package for Windows
38
M-Cell
Bartol, Jr. T. M, et al.
USA
http://www.mcell.cnl.salk.edu/
A General Monte Carlo Simulator of Cellular Microphysiology
39
NetWork
Russia
http://www.csa.ru/Inst/gorb_dep/inbios/VarGenet/genes.htm
simulate the genetic network dynamics as a Boolean network
40
Elementary Modes
Klaus Mauch
Germany
http://einstein.ibvt.uni-stuttgart.de/
a Java simulation for computing elementary modes
43
SIMFIT
Holzhutter and Colosimo
Compu.Appl.Biosci.,6,23-28
a microcomputer software for modelistic studies in biochemistry
44
BioSpice
Arkin Lab
USA
http://gobi.lbl.gov/~aparkin/
45
BioSIM
K.R.Heidtke
Germany
http://www.molgen.mpg.de/~biosim/BioSim/BioSimHome.html
A New Qualitative Simulation Environment for Molecular Biology
46
QSim
Benjamin Kuipers
USA
http://www.cs.utexas.edu/users/qr/QR-software.html
A qualitative simulation engine with a variety of extensions and additions
47
QPC
Benjamin Kuipers
USA
http://www.cs.utexas.edu/users/qr/QR-software.html
a Qualitative Process Compiler. Compiles qualitative process theory models into qualitative differential equations that can be simulated using QSIM.
48
DMSP
Erik Gerdes, David Rhodes
USA
http://www.hort.purdue.edu/cfpesp/models/dmspj/dmspj.htm
DMSP Radiolabeling Kinetics Simulator
49
SAAM II
SAAM Institute,Inc.
USA
http://www.saam.com/
a powerful compartmental and numerical modeling program for pharmacokinetic/pharmacodynamic and metabolic kinetic analysis
50
A-Cell
Fuji Xerox Co.,Ltd.
Japan
http://www.fujixerox.co.jp/crc/cng/A-Cell/index.html
A platform for the construction of biochemical reaction and electrical equivalent circuit models in a biological cell and a neuron
51
NEURON
Hines,M. et al.
USA
http://www.neuron.yale.edu/
NEURON is a simulation environment for developing and exercising models of neurons and networks of neurons.
52
GENESIS
Bower,J. et al.
USA
http://genesis.bbb.caltech.edu/
GEneral NEural SImulation System
53
Virtual Cell
WWWIC
USA
http://www.ndsu.nodak.edu/instruct/mcclean/vc/
The Virtual Cell is an educational sofware development project to create an environment in which students can learn about the the structure and function of the cell.
54
Virtual Plant Cell
Matej Lexa
USA
http://www.life.uiuc.edu/plantbio/cell/
Virtual Cell is a collection of still images, texts and movies covering the structure and functioning of a typical plant cell. You can see and "manipulate" various cell images by zooming, cutting and turning images.
55
Genomic Object Net
Satoru Miyano / Hiroshi Matsuno
Japan
http://www.genomicobject.net/
Genomic Object Net is an enviroment for simulating and representing biological systems. It is an integrated tool consisting of several kinds of software tools for describing biopathways, visualizing simulation results, evaluating a hypothesis, biopathways recreation from biopathway databases, and so on
56
CellDesigner
Hiroaki kitano
Japan
http://www.systems-biology.org/002/
CellDesigner is a modeling tool of biochemical networks with graphical user interface. It is designed to be SBW (Systems Biology Workbench) compliant, and support SBML (Systems Biology Markup Language) format.