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…

Mathematical modeling steps

Mathematical modeling and computer simulation software tools | Systems biology

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…

IraPPA
Web

IraPPA Integrative Ranking of Protein Protein Assemblies

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…

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…

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…

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…

VB-DCMM
Desktop

VB-DCMM Variational Bayes-Double Chain Markov Model

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…

FIT
Desktop

FIT

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

ExPASy
Dataset

ExPASy Expert Protein Analysis System

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…

VDA
Desktop

VDA Validation Discriminant Analysis

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…

IRECS
Desktop

IRECS iterative REduction of Conformational Space

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.…

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…

ARP/wARP
Web
Desktop

ARP/wARP

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…

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…

SCWRL
Desktop

SCWRL

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,…

DACCAD
Desktop

DACCAD DNA Artificial Circuit Computer Assisted Design

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…

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…

OPUS-Rota
Desktop

OPUS-Rota

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…

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…

HilbertVisGUI
Desktop

HilbertVisGUI

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…

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…

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…

BASILISK
Desktop
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…

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…

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…

MapReduce
Desktop

MapReduce

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…

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.…

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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