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…

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 experimental data, that specify initial species concentrations and kinetic rate constants. Once calibrated, a model should be analyzed for its sensitivity and predictive power over ranges of parameter values (Fisher and Henzinger, 2007). Both model calibration and analysis can require thousands to millions of model simulations for statistical convergence and significance (Eydgahi et al., 2013; Gutenkunst et al., 2007). In many cases, the computational expense of simulation at this scale makes detailed model analysis infeasible.

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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,…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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.

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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.…

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…

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.…

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…

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…

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.…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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.…

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…

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…

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…