Systems Biology PortalStochSS
StochSS (Stochastic Simulation Service) is an integrated development environment for modeling and simulation of discrete stochastic biochemical systems. An easy to use GUI enables researchers to quickly develop and simulate biological models on a desktop or laptop, which can then be expanded or combined to incorporate increasing levels of complexity. As the demand for computational power increases, StochSS is able to seamlessly scale up by deploying cloud computing resources. The software currently supports simulation of ODE and well-mixed discrete stochastic models, parameter estimation of discrete stochastic models, and simulation of spatial stochastic models.
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
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
posted 2010.12.03
GNU MCSim
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/
posted 2009.01.15
BALSA
BALSA is a prototype cell systems modeling environment written in Java.
http://www.csi.washington.edu/teams/modeling/projects/BALSA
posted 2006.04.25
BIOCHAM
BIOCHAM is a programming environment for modeling biochemical systems,
making simulations and querying the model in temporal logic CTL.
http://contraintes.inria.fr/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.
http://www.cis.upenn.edu/biocomp
posted 2006.04.25
BioNetGen
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
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.
http://www.biospice.org/
posted 2006.04.25
BioSpreadsheet
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.
http://www.biouml.org/
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.
http://kurata21.bse.kyutech.ac.jp/cadlive/
posted 2006.04.25
CellDesigner
CellDesigner is a software suite for systems biology which enables graphical
editing of biological networks, simulation. It comply with SBML and SBGN,
and can connect to SBW to utilize analysis packages.
http://celldesigner.org/
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.
http://www-aig.jpl.nasa.gov/public/mls/cellerator/
posted 2006.04.25
Cellware
Cellware is a grid based modeling and simulation tool.
http://www.bii.a-star.edu.sg/sbg/cellware
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, 2008
http://www.copasi.org/
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.
http://labs.systemsbiology.net/bolouri/software/Dizzy/
posted 2006.04.25
DBsolve
http://biosim.genebee.msu.su/dbsdownload_en.html
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.
http://ecell.sourceforge.net/
posted 2006.04.25
ESS
posted 2006.04.25
Fluxor
http://arep.med.harvard.edu/moma/FluxorPipeline.tar.gz
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)
http://www.gepasi.org/
posted 2006.04.25
INSILICO discovery
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
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.
http://www.sys-bio.org/
posted 2006.04.25
JigCell
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/
posted 2006.04.25
JSIM
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
posted 2006.04.25
Kinsolver
Kinsolver is a simulator for biochemical and gene regulatory networks
http://lsdis.cs.uga.edu/%7Ealeman/kinsolver/
posted 2006.04.25
MesoRD
MesoRD - Mesoscopic Reaction Diffusion Simulator
http://mesord.sourceforge.net/
posted 2006.04.25
Moleculizer
http://www.molsci.org/%7Elok/moleculizer/
posted 2006.04.25
MMT2
Modeling and simulation software for metabolic networks.
http://www.simtec.mb.uni-siegen.de/software_mmt2.0.html
posted 2006.04.25
NetBuilder
http://strc.herts.ac.uk/bio/maria/NetBuilder/
posted 2006.04.25
PathwayLab
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/
posted 2006.04.25
PathwayBuilder
http://biospice.lbl.gov/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.
http://page.mi.fu-berlin.de/%7Etrieglaf/PNK2e/index.html
posted 2006.04.25
PROTON
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
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.
http://pysces.sourceforge.net/
posted 2006.04.25
runSBML
A pathway simulation tool by Ariadne Genomics.
http://ariadnegenomics.com/technology/simulation.html
posted 2006.04.25
SBML ODE Solver
SBML ODE Solver is a high pecision ODE solver for SBML.
http://www.tbi.univie.ac.at/%7Eraim/odeSolver/
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.
http://www.dim.uchile.cl/%7Edremenik/SBMLSim/
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.
http://csi.washington.edu/teams/modeling/projects/sigtran
posted 2006.04.25
SIMBA
http://www.ifak-system.com/swt/simulation/index.php?level=swtSIMBA4"
posted 2006.04.25
Simpathica
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/
posted 2006.04.25
StochSim
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
posted 2006.04.25
STOCKS
STOCKS is a stochastic simulation software for biochemical reaction
networks.
http://www.sysbio.pl/stocks/
posted 2006.04.25
TERANODEÂ Suite
Platform to Automate Experiments and Manage Data
http://teranode.com/products/index.php
posted 2006.04.25
Trelis
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.
http://www.sourceforge.net/projects/trelis
posted 2006.04.25
Virtual Cell
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/
posted 2006.04.25
WinSCAMP
Window version of SCAMP by H. Sauro.
http://www.sys-bio.org/
posted 2006.04.25