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Quantitative kinetic modeling software tools

Kinetic modeling of complex biochemical systems is central to the emerging field of systems biology (Kitano, 2002; Le Novère, 2015). Kinetic models require definition of numerous free parameters, usually obtained by calibration to…
Aevol
Desktop

Aevol

Allows the study of selection pressures on genomic architecture. Aevol is an…

Allows the study of selection pressures on genomic architecture. Aevol is an individual-based model of evolution. It is based on genetic algorithms and individual based modeling and permits to…

PottersWheel
Desktop

PottersWheel

Allows users to mathematically model dynamical systems. PottersWheel is a…

Allows users to mathematically model dynamical systems. PottersWheel is a comprehensive framework for data-based modelling in Systems Biology comprising multi-experiment fitting in normal and…

ModelPolisher
Desktop
Web

ModelPolisher

Connects genome-scale models to genome annotations and external databases. BiGG…

Connects genome-scale models to genome annotations and external databases. BiGG Models is a completely redesigned Biochemical, Genetic and Genomic knowledge base. It contains more than 75…

SBMLsqueezer
Web
Desktop

SBMLsqueezer

Generates automatically kinetic rate equations for metabolic and…

Generates automatically kinetic rate equations for metabolic and gene-regulatory networks given in SBML format. SBMLsqueezer is a software package designed for rapid, consistent prototyping of…

DBNizer
Desktop

DBNizer

Constructs abstractions using information Dynamic Bayesian Network (DBN).…

Constructs abstractions using information Dynamic Bayesian Network (DBN). DBNizer reduces the number of variables from 92 to 10, and accelerates numerical simulation by an order of magnitude, yet…

SED-ML Web Tools
Web

SED-ML Web Tools Simulation Experiment Description Markup Language Web Tools

Supports users in generating, modifying, simulating, and exporting standard…

Supports users in generating, modifying, simulating, and exporting standard compliant simulation experiments. SED-ML Web Tools implement all current SED-ML specifications and, thus, support complex…

AMIGO
Desktop

AMIGO

A MATLAB environment to solve mathematical optimization problems which in…

A MATLAB environment to solve mathematical optimization problems which in dynamic modeling and control of biological systems. AMIGO2 is organized in four main modules: the pre-processor, the…

BIOCHAM
Web
Desktop

BIOCHAM BIOCHemical Abstract Machine

Designs formal languages for describing qualitative or quantitative models of…

Designs formal languages for describing qualitative or quantitative models of biochemical systems. BIOCHAM is based on a s rule-based language and on a temporal logic language. It permits continuous…

ASPASIA
Desktop
Web

ASPASIA Automated Simulation Parameter Alteration and SensItivity Analysis

Addresses a key deficiency in software tools for understanding the impact an…

Addresses a key deficiency in software tools for understanding the impact an intervention has on system behaviour for models specified in Systems Biology Markup Language (SBML). ASPASIA can generate…

Bifurcation…
Desktop

Bifurcation Discovery Tool

Allows discovery of Hopf bifurcations, turning points, and bistable switches.…

Allows discovery of Hopf bifurcations, turning points, and bistable switches. Bifurcation Discovery Tool employs a genetic algorithm to proceed. It starts by creating a population of networks having…

bnstruct
Desktop

bnstruct Bayesian Network Structure Learning from Data with Missing Values

Provides algorithms to i) learn the structure and the parameters of a Bayesian…

Provides algorithms to i) learn the structure and the parameters of a Bayesian Network from data in the presence of missing values and ii) perform reasoning and inference on the learned Bayesian…

FAStGGM
Desktop

FAStGGM Fast Gaussian Graphical Model

Provides an algorithm able to analyze and speed up the inference of Gaussian…

Provides an algorithm able to analyze and speed up the inference of Gaussian graphical model (GGM) on large-scale networks, such as gene/protein networks. FastGGM is a package which includes three…

CamOptimus
Desktop

CamOptimus

Overcomes the concerns and limitations associated with the various platforms…

Overcomes the concerns and limitations associated with the various platforms available. CamOptimus is a simple-to-use and freely available tool. The algorithm guides the search towards a more…

SpaceScanner
Desktop

SpaceScanner adjustable parameter solution space scanner

Allows to manage global stochastic studies. SpaceScanner supports: (1) parallel…

Allows to manage global stochastic studies. SpaceScanner supports: (1) parallel optimization runs with automated recognition of consensus and stagnation situations, (2) automatic switching between…

Microvessel…
Desktop

Microvessel Chaste

Builds spatial models of vascularized tissue growth. Microvessel Chaste can be…

Builds spatial models of vascularized tissue growth. Microvessel Chaste can be used to simulate vessel growth and adaptation in response to mechanical and chemical stimuli, intra- and extra-vascular…

simbTUM
Desktop

simbTUM

Allows users to simulate stochastic processes and ordinary differential…

Allows users to simulate stochastic processes and ordinary differential equations (ODE) models.

IBRENA
Desktop

IBRENA In silico Biochemical REaction Network Analysis

Allows analysis of complex biological reaction networks. IBRENA is a software…

Allows analysis of complex biological reaction networks. IBRENA is a software package coupling forward sensitivity analysis with multivariate analysis techniques, especially principal component…

JSBML
Desktop

JSBML

Aims to provide an SBML parser and library that maps all SBML elements to a…

Aims to provide an SBML parser and library that maps all SBML elements to a flexible and extended type hierarchy. JSBML is a community-driven project to create a free, open-source, pure Java library…

PyEMMA
Desktop

PyEMMA

Provides accurate and efficient algorithms for kinetic model construction.…

Provides accurate and efficient algorithms for kinetic model construction. PyEMMA can read all common molecular dynamics data formats and helps in the selection of input features. It provides easy…

DBSolve Optimum
Desktop

DBSolve Optimum

Allows users to develop, analyze kinetic models and visualize simulation…

Allows users to develop, analyze kinetic models and visualize simulation results. DBSolve Optimum focuses on comprehensive work with kinetic model of a biological system including model development,…

PADA
Desktop

PADA PAthway Dynamics Approximator

Allows users to approximate the ordinary differential equation (ODE)-based…

Allows users to approximate the ordinary differential equation (ODE)-based biopathway dynamics. PADA is a graphical processing unit (GPU)-based implementation for constructing the dynamic Bayesian…

SensSB
Desktop

SensSB Sensitivity analysis for Systems Biology

Allows users to develop and analyse systems biology models. SensSB’s main…

Allows users to develop and analyse systems biology models. SensSB’s main features are: (i) Global sensitivity analysis (GSA), (ii) Pseudo-Global a priori identifiability analysis, (iii) optimal…

ORAC
Desktop

ORAC

Includes constant pressure and constant temperature simulations, smooth…

Includes constant pressure and constant temperature simulations, smooth particle mesh Ewald method, and multiple time steps integration. ORAC is a program for the molecular dynamics (MD) simulation…

SBaddon
Desktop

SBaddon

Provides features for parameter estimation problems. SBaddon is an extension to…

Provides features for parameter estimation problems. SBaddon is an extension to the Systems Biology Toolbox for MATLAB. The software aims to exemplify how the modular concept of the SBtoolbox can be…

ModelDiscrimina…
Desktop

ModelDiscriminationToolkit

Allows computation of optimal experiments for biochemical kinetic systems with…

Allows computation of optimal experiments for biochemical kinetic systems with underlying ordinary differential equation (ODE) models. ModelDiscriminationToolkit is the implementation of a model…

BioJazz
Desktop

BioJazz

A tool for evolving and designing biochemical reaction networks using genetic…

A tool for evolving and designing biochemical reaction networks using genetic algorithm (GA). Typically, a BioJazz user wishes to evolve or design a small network or motif which accomplishes a…

Mean-Field…
Algorithm

Mean-Field Approximation of ASEP with Langmuir Kinetics

Provides a monotone and contractive dynamical system. MFALK is a deterministic…

Provides a monotone and contractive dynamical system. MFALK is a deterministic mathematical model that can be interpreted as the dynamic mean-field approximation of asymmetric simple exclusion…

PhysiCell
Desktop

PhysiCell Physics-based multiCellular simulator

An agent-based model for 3-D multicellular simulations. PhysiCell provides both…

An agent-based model for 3-D multicellular simulations. PhysiCell provides both the stage and the players for studying many interacting cells in dynamic tissue microenvironments. It includes…

MOCCASIN
Desktop

MOCCASIN Model ODE Converter for Creating Automated SBML INteroperability

Takes ordinary differential equation (ODE) models written in MATLAB and export…

Takes ordinary differential equation (ODE) models written in MATLAB and export them as SBML files. MOCCASIN aims to facilitate scripting and automation. The tool offers (1) a module that parses…

Data2Dynamics
Desktop

Data2Dynamics

It is designed for computationally efficient and user-friendly integration of…

It is designed for computationally efficient and user-friendly integration of complex experimental data into models consisting of coupled non-linear ordinary differential equations (ODE). The…

saCeSS
Desktop

saCeSS self-adaptive Cooperative enhanced Scatter Search

Accelerates the solution of the problem of parameter estimation in nonlinear…

Accelerates the solution of the problem of parameter estimation in nonlinear dynamic models. saCeSS is based on the scatter search optimization metaheuristic and incorporates several key new…

MASS Toolbox
Desktop

MASS Toolbox Mass Action Stoichiometric Simulation Toolbox

Constructs and analyzes kinetic and constraint-based models of biochemical…

Constructs and analyzes kinetic and constraint-based models of biochemical reactions systems. MASS Toolbox is based on an omics and data driven approach. It can reconstruct networks that can be…

DOTcvpSB
Desktop

DOTcvpSB

Allows definition and solution of dynamic optimization problems where decision…

Allows definition and solution of dynamic optimization problems where decision variables are time dependent. DOTcvpSB is based on the control vector parameterization (CVP) method. It can handle very…

VisId
Desktop

VisId

Characterizes high-order relationships among parameters and allows…

Characterizes high-order relationships among parameters and allows visualisation of the results. VisId is the implementation of an identifiability and visualization methodology as a MATLAB toolbox.

COSMOS
Desktop

COSMOS Computation of Sensitivities in Model ODE Systems

Allows sensitivity analyses of metabolic reaction systems. COSMOS is a program…

Allows sensitivity analyses of metabolic reaction systems. COSMOS is a program that automates assessments of model stability and sensitivity for essentially arbitrary pathway models. A key feature of…

C-elegans
Desktop

C-elegans

Quantifies the analgesic-like effects of chemical stimuli or genetic mutations.…

Quantifies the analgesic-like effects of chemical stimuli or genetic mutations. C-elegans has been designed to build a statistical model of the heat stimulus and infer the changes in the perceived…

LimitsExptDesig…
Desktop

LimitsExptDesign

Quantifies the systematic error in a simple hyper-model. In addition,…

Quantifies the systematic error in a simple hyper-model. In addition, LimitsExptDesign can quantify the model’s discrepancy from the physical system and discuss the potential limits of accurate…

PySB/cupSODA
Desktop

PySB/cupSODA

Allows graphics processing unit (GPU)-based kinetic simulations. PySB/cupSODA…

Allows graphics processing unit (GPU)-based kinetic simulations. PySB/cupSODA is a high-performance GPU-based kinetic simulator for the modeling community. It can run thousands of parallel…

mboost
Desktop

mboost

Intends for modern regression modeling and stands in-between classical…

Intends for modern regression modeling and stands in-between classical generalized linear and additive models. Mboost implements functional gradient descent algorithms (boosting) for optimizing…

Cellware
Desktop

Cellware

Offers a multi-algorithmic environment for modeling and simulating both…

Offers a multi-algorithmic environment for modeling and simulating both deterministic and stochastic events in the cell. Cellware uses a proprietary file format (Cellware model or CWM) that stores…

REDEMPTION
Desktop

REDEMPTION REduced Dimension Ensemble Modeling and Parameter estimaTION

A MATLAB toolbox for the identification of parameters and parameter ensembles…

A MATLAB toolbox for the identification of parameters and parameter ensembles of ODE models from time-series data. The tools within REDEMPTION are accessible through a user-friendly MATLAB UI and…

libRoadRunner
Desktop

libRoadRunner

An extensible, high-performance, cross-platform, open-source software library…

An extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language (SBML). SBML is the most widely…

Biocellion
Desktop

Biocellion

Simulates systems at multiple scales using parallel computers. To support a…

Simulates systems at multiple scales using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the…

Antimony
Desktop

Antimony

A text-based model definition language originally based on Jarnac, and extended…

A text-based model definition language originally based on Jarnac, and extended to be fully modular. Antimony models can be converted to and from SBML, flattening the modularity in the process. The…

CellDesigner
Desktop

CellDesigner

A structured diagram editor for drawing gene-regulatory and biochemical…

A structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored…

JSim
Desktop

JSim

Allows users to construct quantitative numeric models. JSim aims to facilitate…

Allows users to construct quantitative numeric models. JSim aims to facilitate attempts to fit models to data, and to support the efficient development of computational models that describe and…

VCell
Desktop

VCell Virtual Cell

A problem solving environment, built on a central database, for analysis,…

A problem solving environment, built on a central database, for analysis, modelling and simulation of cell biological processes. VCell integrates a growing range of molecular mechanisms, including…

MCMC_CLIB
Desktop

MCMC_CLIB

Allows users to sample ordinary differential equation (ODE) model parameters.…

Allows users to sample ordinary differential equation (ODE) model parameters. MCMC_CLIB is an implementation of SMMALA (simplified manifold Metropolis-adjusted Langevin algorithm), a sampling…

SensA
Desktop
Web

SensA

A web-based application for sensitivity analysis of mathematical models. The…

A web-based application for sensitivity analysis of mathematical models. The sensitivity analysis is based on metabolic control analysis, computing the local, global and time-dependent properties of…

EPISIM
Desktop

EPISIM

A graphical modeling system for multi-agent based simulation of tissue…

A graphical modeling system for multi-agent based simulation of tissue homeostasis. An editor allows the intuitive and hierarchically structured specification of cellular behavior. The models are…

Morpheus
Desktop

Morpheus

A modeling environment for the simulation and integration of cell-based models…

A modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of multiscale models in…

COPASI
Desktop

COPASI

A software application for simulation and analysis of biochemical networks and…

A software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their…

SmoothPCA
Desktop

SmoothPCA Smooth Principal Components Analysis

Assesses the predictive power of kinetic metabolic models. SmoothPCA is an…

Assesses the predictive power of kinetic metabolic models. SmoothPCA is an unsupervised data analysis method that can make use of also the underlying time profile and hence is suitable for time…

odeSD
Desktop

odeSD

Allows computation of parameter sensitivities. odeSD is an integrator for…

Allows computation of parameter sensitivities. odeSD is an integrator for ordinary differential equation (ODE) systems resulting from the modelling of chemical and biological reaction networks. Key…

Systems…
Desktop

Systems Biology Simulation Core Library

Provides a large collection of numerical solvers and a sophisticated interface…

Provides a large collection of numerical solvers and a sophisticated interface hierarchy for the definition of custom differential equation systems. the Systems Biology Simulation Core Library, a…

JWS Online
Web

JWS Online

Allows biological systems modelling. JWS Online (Java Web Simulation) is a web…

Allows biological systems modelling. JWS Online (Java Web Simulation) is a web server which permits to construct, modify and simulate kinetic models and also to store curated models. User can build…

MatCont
Desktop

MatCont Numerical Bifurcation Analysis Toolbox in Matlab

Permits numerical study of parameterized continuous and discrete dynamical…

Permits numerical study of parameterized continuous and discrete dynamical systems. MatCont computes phase response curves and their derivatives as a by-product of the continuation of limit cycles.…

SloppyCell
Desktop

SloppyCell

Provides support for model construction, simulation, fitting and validation.…

Provides support for model construction, simulation, fitting and validation. SloppyCell is a software environment that aims to provide a flexible environment that facilitates interactive exploratory…

SBMLsimulator
Web
Desktop

SBMLsimulator

Provides an intuitive graphical user interface (GUI) with various options as…

Provides an intuitive graphical user interface (GUI) with various options as well as a fully-featured command-line interface for large-scale and script-based model simulation and calibration.…

nsiGGM
Desktop

nsiGGM Node-structured Integrative Gaussian Graphical Model

Develops an estimation and variable selection algorithm for node-structured…

Develops an estimation and variable selection algorithm for node-structured integrative gaussian graphical model. nsiGGM is a statistical framework for fitting joint Gaussian graphical model…

JMCCM
Desktop

JMCCM

Fits a conditional Gaussian graphical model via the joint mean and constant…

Fits a conditional Gaussian graphical model via the joint mean and constant covariance model. JMCCM is an R package and an algorithm for estimation and variable selection for Joint Mean and Constant…

MEIGOR
Desktop

MEIGOR MEtaheuristics for bIoinformatics Global Optimization

Contains several algorithms such as a scatter search implementation and…

Contains several algorithms such as a scatter search implementation and variable neighbourhood search (plus cooperative multicore/multimachine implantations of these) and dynamic hill climbing.…

biosvd
Desktop

biosvd

Allows for high-throughput data processing, outlier detection, noise removal…

Allows for high-throughput data processing, outlier detection, noise removal and dynamic modeling, based on the framework of Singular Value Decomposition (SVD). Biosvd provides the user with summary…

GIM3E
Desktop

GIM3E Gene Inactivation Moderated by Metabolism Metabolomics and Expression

Enables the development of condition-specific models based on an objective…

Enables the development of condition-specific models based on an objective function, transcriptomics and cellular metabolomics data. GIM3E establishes metabolite use requirements with metabolomics…

Dynetica
Desktop

Dynetica

A user-friendly simulator of dynamic networks for constructing, visualizing,…

A user-friendly simulator of dynamic networks for constructing, visualizing, and analyzing kinetic models of biological systems. In addition to generic reaction networks, Dynetica facilitates…

LibSBMLSim
Desktop

LibSBMLSim

A library for simulating an SBML model which contains ordinary differential…

A library for simulating an SBML model which contains ordinary differential equations (ODEs). LibSBMLSim provides simple command-line tool and several APIs to load an SBML model, perform numerical…

PySCeS
Desktop

PySCeS Python Simulator for Cellular Systems

An extendable research tool for the numerical analysis and investigation of…

An extendable research tool for the numerical analysis and investigation of cellular systems. For a network of coupled reactions PySCeS does a stoichiometric matrix analysis, calculates the time…

SOSlib
Desktop

SOSlib SBML ODE Solver Library

A programming library for symbolic and numerical analysis of chemical reaction…

A programming library for symbolic and numerical analysis of chemical reaction network models encoded in the Systems Biology Markup Language (SBML). The package employs libSBML structures for formula…

SYCAMORE
Web

SYCAMORE

A browser-based application that facilitates construction, simulation and…

A browser-based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Thus, SYCAMORE allows e.g. database supported modelling, basic model checking…

iBioSim
Desktop

iBioSim

Supports learning of genetic circuit models, efficient abstraction-based…

Supports learning of genetic circuit models, efficient abstraction-based analysis of these models and the design of synthetic genetic circuits. iBioSim includes project management features and a…

Tav4SB
Desktop

Tav4SB Taverna services for Systems Biology

Provides an access to services which are mainly related to the sequence…

Provides an access to services which are mainly related to the sequence annotation and analysis. Tav4SB is a workflow management application that aims to support the orchestration of physically…

MIRACH
Desktop

MIRACH

Validates the ever-growing biological pathway simulation models—both in…

Validates the ever-growing biological pathway simulation models—both in complexity and quantity. MIRACH is an on-the-fly probabilistic model checker for quantitative pathway models. It supports…

MCell
Desktop

MCell

Allows simulation of movements and reactions of molecules within and between…

Allows simulation of movements and reactions of molecules within and between cells. MCell permits simulation of specific instance of chemical signaling, diffusion, and reaction of discrete…

WholeCellViz
Desktop
Web

WholeCellViz

A web-based software program for visually exploring and analyzing whole-cell…

A web-based software program for visually exploring and analyzing whole-cell simulations. WholeCellViz provides 14 animated visualizations, including metabolic and chromosome maps. These…

CellBlender
Desktop

CellBlender

Allows construction of computational cell biology models. CellBlender’s…

Allows construction of computational cell biology models. CellBlender’s outputs can be used with cell simulation biophysics engines and specially MCell. It allows users to: (1) define molecules and…

AgentBase
Desktop

AgentBase

Allows users to build Agent Based Models (ABMs). AgentBase is a software…

Allows users to build Agent Based Models (ABMs). AgentBase is a software library optimized for quick development of illustrative ABM models. It values minimalism over complexity, readable and pretty…

SBMLR
Desktop

SBMLR

Contains a systems biology markup language (SBML) interface for R.

Contains a systems biology markup language (SBML) interface for R.

RSBML
Desktop

RSBML

Provides a systems biology markup language (SBML) interface library for R.

Provides a systems biology markup language (SBML) interface library for R.

G T A T C G C T A
MathSBML
Desktop

MathSBML

Supports biological community and SBML users in particular. MathSBML is an…

Supports biological community and SBML users in particular. MathSBML is an open-source package for working with SBML models in Mathematica. It provides facilities for reading SBML models, converting…

Ben(Zai)Ten
Desktop

Ben(Zai)Ten

Allows construction of kinetic biological models as well as production of…

Allows construction of kinetic biological models as well as production of standards compliant annotated computational models.

Jarnac
Desktop

Jarnac

Permits description and manipulation of cellular system model. Jarnac is a…

Permits description and manipulation of cellular system model. Jarnac is a language useful for the description of metabolic, signal transduction and gene networks. It is applicable to any physical…

Jacobian Viewer
Desktop

Jacobian Viewer

Allows dynamic analysis of Jacobian matrix. Jacobian Viewer permits users to…

Allows dynamic analysis of Jacobian matrix. Jacobian Viewer permits users to underline the influence of model variables on the rates of change. Users can customize the time-steps taken by the…

BioPARKIN
Desktop

BioPARKIN

Allows simulation and parameter identification in ordinary differential…

Allows simulation and parameter identification in ordinary differential equation (ODE) models. BioPARKIN is a renewed version of the former codes LARKIN and PARKIN. The software combines a basis of…

DEDiscover
Desktop

DEDiscover

Offers simulation, parameter estimation and statistical analysis to solve…

Offers simulation, parameter estimation and statistical analysis to solve differential equations. DEDiscover fixes equations in a special syntax which resembles to ones provided in a research…

ByoDyn
Web
Desktop

ByoDyn

Allows analysis of biochemical networks. ByoDyn is compatible with SBML format.

Allows analysis of biochemical networks. ByoDyn is compatible with SBML format.

XPP-Aut
Desktop
Mobile

XPP-Aut X-windows PhasePlane plus Auto

Provides an ordinary differential equations (ODE) solver. XPP-AUT is an…

Provides an ordinary differential equations (ODE) solver. XPP-AUT is an application that solves differential equations, difference equations, delay equations, functional equations, boundary value…

DuMux
Desktop

DuMux

Flows and transports processes in porous media. DuMux is a simulator for…

Flows and transports processes in porous media. DuMux is a simulator for includes several standard models of varying complexity, ranging from stationary isothermal single-phase single-component flow…

CellML Compiler
Desktop

CellML Compiler

Generates executable codes for several CellML models using a number of ordinary…

Generates executable codes for several CellML models using a number of ordinary differential equation (ODE) numerical solutions. CellML compliler is a two-stage designed approach where the system…

Simbody
Desktop

Simbody

Uses an advanced Featherstone-style formulation of rigid body mechanics to…

Uses an advanced Featherstone-style formulation of rigid body mechanics to provide results in Order(n) time for any set of n generalized coordinates. Simbody can be used for internal coordinate…

APM
Desktop

APM Automatic state Partitioning for Multi-body systems

Constructs Markov state models (MSMs) to elucidate conformational dynamics of…

Constructs Markov state models (MSMs) to elucidate conformational dynamics of multi-body systems. The APM algorithm effectively addresses different timescales in the multi-body systems by directly…

SBML-SAT
Desktop

SBML-SAT Systems Biology Markup Language based Sensitivity Analysis Tool

Automates sensitivity analysis for different types of systems biology models.…

Automates sensitivity analysis for different types of systems biology models. SBML-SAT allows users to represent and exchange models of biochemical reaction networks. It can run simulation, steady…

GetBonNie
Web

GetBonNie

A web-based application for building, analyzing and sharing rule-based models…

A web-based application for building, analyzing and sharing rule-based models encoded in the BioNetGen language (BNGL). Tools accessible within the GetBonNie environment include (i) an applet for…

WebCell
Web

WebCell

An integrated simulation environment for managing quantitative and qualitative…

An integrated simulation environment for managing quantitative and qualitative information on cellular networks, and for interactively exploring their steady-state and dynamic behaviors over the web.…

acslXtreme
Desktop

acslXtreme

Provides commercial modelling environment that uses a script language called…

Provides commercial modelling environment that uses a script language called CSL. acslXtreme is an execution and analysis environment for continuous dynamic systems and processes. This application…

PyBioS
Web

PyBioS

An integrated, web-based software platform for the design, modeling and…

An integrated, web-based software platform for the design, modeling and simulation of cellular systems. PyBioS can function as a model repository and supports the construction of biological models…

SobolHDMR
Desktop

SobolHDMR Sobol High Dimensional Model Representation

A metamodeling software to reduce the complexity of mathematical models, such…

A metamodeling software to reduce the complexity of mathematical models, such as those for metabolic networks and other biological pathways, yielding simpler descriptions that retain the features of…

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