Mathematical modeling and computer simulation software tools | Systems biology

Mathematical modeling steps

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 and computer simulation software tools | Systems biology

Web app
Simulation Experiment… Simulation Experiment Description Markup Language…

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…

Desktop app
Variational… Variational Bayes-Double Chain Markov Model

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…

Desktop app
Bayesian Network… Bayesian Network Structure Learning from Data…

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…

Desktop app
Physics-based… Physics-based multiCellular simulator

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…

Desktop app
Dynetica Dynetica

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…

Desktop app
Cellware Cellware

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…

Desktop app
Validation… Validation Discriminant Analysis

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…

Desktop app
Gene Inactivation… Gene Inactivation Moderated by Metabolism…

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…

Desktop app
C-elegans C-elegans

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…

Desktop app
LimitsExptDesign LimitsExptDesign

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…

Desktop app
Data2Dynamics Data2Dynamics

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…

Desktop app
REduced Dimension… REduced Dimension Ensemble Modeling and Parameter…

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…

LibSBMLSim LibSBMLSim

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…

Desktop app
Python Simulator for… Python Simulator for Cellular Systems

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…

Desktop app
SBML ODE Solver… SBML ODE Solver Library

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…

libRoadRunner libRoadRunner

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…

Desktop app
BioJazz BioJazz

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…

Desktop app
Web app
WholeCellViz WholeCellViz

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…

Desktop app
Web app
SensA SensA

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…

Desktop app
Biocellion Biocellion

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…

Desktop app
EPISIM EPISIM

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…

Desktop app
Morpheus Morpheus

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…

Web app
JWS Online JWS Online

JWS Online

A systems biology tool for the construction, modification and simulation of…

A systems biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models. You can build a model from scratch using a simple interface. Models…

Web app
SYCAMORE SYCAMORE

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…

Desktop app
Virtual Cell Virtual Cell

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…

Desktop app
Antimony Antimony

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…

Desktop app
CellDesigner CellDesigner

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…

Desktop app
COPASI COPASI

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…

Desktop app
DNA Artificial… DNA Artificial Circuit Computer Assisted Design

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…

Web app
WebCell WebCell

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.…

Web app
GetBonNie Deprecated GetBonNie

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…

Web app
PyBioS Deprecated PyBioS

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…

Desktop app
Sobol High… Deprecated Sobol High Dimensional Model Representation

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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