Mathematical modeling and computer simulation software tools | Systems biology

Modelling and simulation techniques are valuable tools for the understanding of complex biological systems. The design of a computer model necessarily has many diverse inputs, such as information on the model topology, reaction kinetics and experimental data, derived either from…

Modelling and simulation techniques are valuable tools for the understanding of complex biological systems. The design of a computer model necessarily has many diverse inputs, such as information on the model topology, reaction kinetics and experimental data, derived either from the literature, databases or direct experimental investigation.

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…

Enhances the identification of near-native structures when applied to four…

Enhances the identification of near-native structures when applied to four docking methods. IraPPA is based on methods developed for Internet search ranking and electoral voting to solve the problem…

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…

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…

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…

Analyzes single molecule time trajectories that display dynamic disorder.…

Analyzes single molecule time trajectories that display dynamic disorder. VB-DCMM allows to detect the presence of dynamic disorder, if any, in each trajectory, identify the number of internal…

Offers functions for parameter optimization and transcriptome prediction. FIT…

Offers functions for parameter optimization and transcriptome prediction. FIT achieves comparable or better prediction performance within a shorter computational time than the previous method. It…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

Provides a comprehensive list of resources in different domains, such as…

Provides a comprehensive list of resources in different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics and transcriptomics. ExPASy is the Swiss…

Minimizes the number of validation experiments necessary for reliable…

Minimizes the number of validation experiments necessary for reliable performance estimation and fair comparison between algorithms through a cost-efficient method. VDA is a method for designing a…

Predicts the conformation of protein side chains. IRECS ranks all side-chain…

Predicts the conformation of protein side chains. IRECS ranks all side-chain rotamers of a protein according to the probability with which each side chain adopts the respective rotamer conformation.…

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…

Builds a protein model into an electron density map. ARP/wARP facilitates model…

Builds a protein model into an electron density map. ARP/wARP facilitates model building by initially interpreting a density map with free atoms of unknown chemical identity; all structural…

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…

Determinates side-chain conformations. SCWRL uses a backbone-dependent rotamer…

Determinates side-chain conformations. SCWRL uses a backbone-dependent rotamer library, a simple energy function based on the library rotamer frequencies and a purely repulsive steric energy term,…

A computer-assisted design software that supports the construction of systems…

A computer-assisted design software that supports the construction of systems for the DNA toolbox. DACCAD is ultimately aimed to design actual in vitro implementations, which is made possible by…

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…

Models side-chain conformation. OPUS-Rota uses simulated annealing by heat bath…

Models side-chain conformation. OPUS-Rota uses simulated annealing by heat bath Monte Carlo as a sampling method, which is able to rapidly identify near-native conformations when combined with…

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…

Visualizes long vectors of integer data by means of Hilbert curves.…

Visualizes long vectors of integer data by means of Hilbert curves. HilbertVisGUI allows to display very long data vectors in a space-efficient manner, allowing the user to visually judge the…

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…

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…

Formulates a probabilistic model of the conformational space of amino acid side…

Formulates a probabilistic model of the conformational space of amino acid side chains. BASILISK can be used for rigorous, unbiased sampling with a physical force field. It improves side chain…

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…

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…

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…

Processes and generates large datasets. MapReduce is a programming model and an…

Processes and generates large datasets. MapReduce is a programming model and an associated implementation that is amenable to a broad variety of real-world tasks. Users specify the computation in…

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.…

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…