This database contains information on 181 internet pathway
resources that are categorized on
the basis of the type of pathway
data provided: protein-protein interaction, metabolic pathway,
signalling pathway and gene pathway.
The Center for
Systems Biology in the School of Natural Sciences
at the Institute for Advanced Study emphasizes
the interface of molecular biology and the
physical sciences. Research interests of the
group include genetics and genomics,
polymorphisms and molecular aspects of evolution,
signal transduction pathways and networks, stress
responses and pharmacogenomics in cancer
biology.
Bio-SPICE is 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
BioUML is a 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.
BSTLab is a
software toolbox compatible with Matlab,
a popular scientific
and engineering computing package that is
being developed to
facilitate wider application of biochemical
systems theory. The
toolbox, BSTLab, implements functions common
to BST-based studies
and is designed to integrate easily into
the widely used
Matlab environment, automate many
common tasks, and
allow expansion and customization by the user.
The toolbox also includes
functions needed to
reformulate and transport models from SBML.
CADLIVE is a system
for constructing large-scale biological networks
(metabolic and gene regulatory networks) using a GUI (Graphic User Interface)
and saving them as regulator reaction equations in a database in the format
compatible to a simulator.
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.
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:
1 signal transduction networks (STNs);
2 cells that are represented by interacting
signal transduction networks; and
3 multi-cellular tissues that are represented by interacting networks of cells
that may themselves contain internal STNs.
Cellware is a
grid-based modeling and simulation tool. It is a
computational
tool that integrates
and graphically models biological information
of varying
complexity, conducts large-scale simulations with
heavy number
crunching capability, is user friendly (especially
for the non-specialists)
and offers services over the web.
Cytoscape is an
open source bioinformatics software platform for
visualizing
molecular interaction
networks and integrating these interactions with
gene expression profiles and other state data.
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.
E-Cell is a
multi-algorithm, multi-timescale simulation
software environment.
The E-Cell system is
an object-oriented software suite for modelling,
simulation
and analysis of large
scale complex systems such as biological
cells.
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.
Gepasi simplifies the
task of model building by assisting the
user in translating
the language of chemistry (reactions) to
mathematics (matrices
and differential equations) in a transparent way.
This is combined
with a set of
sophisticated numerical algorithms that assure
the results are obtained fast and accurate.
Jarnac is 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.
JDesigner is a
Win32 application which allows one to draw a
biochemical
network and export
the network in the form of SBML. The Designer has
an
SBW interface that
allows it to be called from other SBW compliant
modules,
for example Python.
In addition, JDesigner has the ability to use
Jarnac
as a simulation
server (via SBW) thus allowing models to be run
from within
JDesigner. In this
mode JDesigner is both a network design tool and
simulator.
Full binaries and source code
is available in the download.
JSIM is a
Java-based simulation and animation environment
supporting
Web-Based Simulation.
In JSIM, simulation
models may be built using either the event package
(Event-Scheduling
Paradigm) or the process package
(Process-Interaction
Paradigm). In
addition, a graphical designer (jmodel package)
allows process
models to be be rapidly built graphically.
MathSBML is an
open-source package for working with SBML models
in Mathematica.
It provides
facilities for reading SBML models, converting
them
to systems of
ordinary differential equations for simulation
and plotting
in Mathematica,
and translating the
models to other formats. It supports both
Level 1
and Level
2
SBML.
PathArt is the
world's largest database, encompassing 600+
mammalian
disease and signaling
pathways, collated through manual curation
from literature and
public domain databases. PathArt is
organism-specific,
and covers diverse
physiologies: inflammation, apoptosis, cell
adhesion,
cell cycle,
development, myogenesis, etc. This signalling
pathway
database is
integrated with the commercial software
PathwayAssist
for pathway visualization and analysis.
SigTran is a
modeling environment especially designed to
enable biological
researchers to carry
out large scale simulations and analysis
of complex signal
transduction networks. SigTran offers biological
researchers a choice
of four major stochastic algorithms including (a)
the Firth-Bray
algorithm of StochSim
(b) Gillespie (c) Gillespie-Gibson and
(d) a novel uniform
time stepping algorithm developed at UW/CSI. In
addition
to running
simulations of
biological network models in a stochastic mode,
biological
researchers may, with no additional effort,
switch SigTran
into a deterministic
mode. SigTran
provides full simulation support for systems of
ordinary differential
and algebraic equations (DAEs).
STOCHSIM is a
stochastic simulator for (bio)chemical reactions.
The
particles are
represented as individual software objects which
react according
to probabilities
derived from concentrations and rate constants.
In the
version 1.4 of
STOCHSIM simple two-dimensional spatial
structures have
been implemented, in
which nearest-neighbour interactions of molecules
can be simulated.
