Biomedical Engineering Reference
In-Depth Information
1.
A-Cell
(http://www.fujixerox.co.jp/crc/cng/A-Cell/) is a tool for model-
ing biochemical reactions that provides backward compatibility with previously
constructed models.
2.
BioUML
(http://www.biouml.org) is a Java framework for systems biol-
ogy ranging from databases with experimental data, tools for formalized de-
scription of biological systems structure, and functioning, as well as tools for
visualization and simulation.
3.
CellDesigner
(http://www.systems-biology.org) is a biochemical net-
work modeling tool with a graphical user interface. It is designed to be SBW
(Systems Biology Workbench) compliant and to support the SBML (Systems
Biology Markup Language) format.
4.
Cellware
(http://www.cellware.org) is the first grid-enabled quantitative
tool for modeling and simulating cellular processes. It is capable of multi-
algorithmic simulation from a few reactions to the whole-cell level.
5.
Dbsolve
(http://websites.ntl.com/~igor.goryanin/) is an integrated devel-
opment environment based on ordinary differential equations. It is especially
useful for calculation of steady-state, fitting, and optimization procedures.
6. The
Discrete Metabolic Simulation System
(DMSS) (http://www.bio.
cam.ac.uk/~mw263/ftp/doc/ISMB99.ps) models reactions based on competing
metabolite concentrations or metabolite affinities to enzymes, including metabo-
lite and enzyme concentrations.
7.
Gepasi
(http://www.gepasi.org/) is also based on ordinary differential
equations and simulates the steady-state and time-course behavior of reactions
based on stoichiometry and reaction kinetics values.
8.
Jarnac
(http://www.cds.caltech.edu/~hsauro/Jarnac.htm) is a cell model-
ing language employed to describe metabolic, signal transduction, and gene
networks. Jarnac interacts with the user through the Jdesigner frontend.
9.
Netbuilder
(http://strc.herts.ac.uk/bio/maria/NetBuilder/) is an interac-
tive graphical tool for representing and simulating genetic regulatory networks
in multicellular organisms, using electronic engineering principles for pathway
layout.
10.
SigPath
(http://icb.med.cornell.edu/crt/SigPath/index.xml) is an infor-
mation system designed to support quantitative studies on the signaling path-
ways and networks of the cell. It helps manage information on protein-protein
interactions, protein-small molecule interactions, elementary chemical reac-
tions, and enzymatic reactions.
11.
StochSim
(http://info.anat.cam.ac.uk/groups/comp-cell/StochSim.html)
is a program that provides a stochastic simulator in which individual bio-
molecules or molecular complexes are represented as individual software ob-
jects.
12.
Trelis
(http://sourceforge.net/projects/trelis) is a graphical Monte Carlo
simulation tool for modeling the time evolution of chemical reaction systems
