Allows users to model the behavior of complex systems. Mobius offers a variety of existing modeling formalisms, including compositional modeling formalisms, a metric specification formalism that permits for time- and event-based rewards, global model parameterization. The software can be useful for supporting the validation of systems in several application domains such as biological systems.

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A free, open-source, biochemical reaction simulator designed to handle systems that have a large or even infinite number of possible molecular interactions or states. NFsim also has advanced and flexible options for simulating coarse-grained representations of complex nonlinear reaction mechanisms.

Allows communication between heterogeneous application components. SBW is a computational resource sharing framework that allows applications to communicate with each other efficiently and without losing their identity. Applications can be written in several different languages and can run on different operating systems across the internet.

Assists with the analysis of systems modelled in the Bio-PEPA process algebra which is designed for the modelling and the analysis of biochemical networks. Bio-PEPA Workbench is a lightweight modelling tool chain whose primary function is to compile Bio-PEPA models into a variety of formats for analysis. The software uses a range of other analysis tools.

Enables design, qualitative and quantitative analysis of Generalized Stochastic Petri Nets (GSPN) and Stochastic Well-Formed Nets (SWN). GreatSPN is composed of programs that cooperate in the construction and analysis of Petri Nets (PN) models by sharing files. The software supports both GSPN and SWN-based performance evaluation either through discrete event simulation, or through the generation of a Markov chain representing the model behavior in time.

Infers time-evolving networks. TESLA is a machine learning algorithm for recovering the structure of time-varying networks over a fixed set of nodes from time series of nodal attributes. In these networks, an edge between two nodes implies a dependency between their nodal states, such as coactivation in a gene regulatory network. It employs the smooth-evolution property as an explicit penalty in the loss function that can be traded-off with data-fitness.

Enables users to automatically convert networks for analysis with the signaling petri net (SPN) simulator from the standard systems biology markup language. The automation of this step opens the SPN simulator to a far larger user group than has previously been possible.

Provides an alternative way of specifying simulation experiments. SESSL is a domain-specific language developed as binding for ML-Rules and adds an easy-to-use interface for running simulations with the new simulation algorithms. This application allows for efficiently performing simulation studies by exploiting the asynchronous, parallelized simulation interface to execute replications simultaneously. It can also be used for simulation-system agnostic and other simulation systems.

Allows model specification, simulation, formal verification and optimization of large-scale systems and synthetic biology models. Infobiotics Workbench is a platform providing an interface to guide users in their parameter choices when performing simulation, model checking and parameter optimization experiments, and in analyzing the results of these experiments. The software can adjust the simulated behaviour of a model such that it fits time series data.

Simultaneously models biochemical processes within individual cells and the associated motion of cells within a 3D environment. AgentCell is an agent-based model that uses agent-based technology to study the effect of intracellular stochastic fluctuations on the behavior of single cells. The software was tested by modeling the chemotactic response of single E.coli cells to chemoattractant gradients in a 3D environment.

Simulates large-scale rule-based models. DYNSTOC is an opensource software that implements an extension of the StochSim simulation method that uses a set of rules specified in an expressive model-specification language. It assess whether randomly selected molecular components are able to participate in a reaction. This application can be useful for simulating a wide variety of biochemical systems.

Allows users to specify molecular complexes and their interactions as well as the reaction-induced modifications of the molecules through a flexible visual interface. It can take into account the positions of the components of trans-membrane complexes relative to the embedding membranes as well as symmetry aspects affecting the reactions of multimeric molecular structures. Models created with this tool can be simulated using the Simmune Simulator or be exported as SBML code or as files describing the reaction networks as systems of ODEs for import into Matlab.

A Cytoscape plugin that conveniently simulates dynamics related to robustness, and examines structural properties with respect to feedforward/feedback loops. NetDS can evaluate how robustly a network sustains a stable state against mutations by employing a Boolean network model. In addition, the plugin can examine all feedforward/feedback loops appearing in a network and determine whether or not a pair of loops is coupled. Random networks can also be generated to evaluate whether or not an interesting finding in real biological networks is significantly random.

An open-source in-browser tool for simulation and manipulation of Boolean networks. BooleSim can be used specifically for the modeling of gene regulatory or signal transduction networks.

Allows creation and manipulation of SBML format metabolic networks with reactions and compounds defined as in the KEGG LIGAND database. MetNetMaker is an application that uses the KEGG LIGAND compound/reaction naming convention and provides a graphical interface dedicated to flux-balance analysis (FBA)-ready metabolic network creation. The software has two main tabs: (i) Reaction Creator to create custom reactions and add them to the reaction database and, (ii) Reaction Picker to browse the reaction database and select reactions using filters.

Explores the space of alignments looking for ones scoring well according to M (an objective function for alignment quality). SANA is based on a metaheuristic search algorithm with a rich history of successful applications to many optimization problems across a wide variety of domains. It was applied to protein-protein interaction networks using Symmetric Substructure Score (S3) as the topological measure. The tool significantly outperforms all other aligners in S3 score, for every pair of networks tested.

A generic simulation framework for BioPAX. BioASF explicitly separates the execution model from the model structure as provided by BioPAX, with the advantage that the modelling process becomes more reproducible and intrinsically more modular; this ensures natural biological constraints are satisfied upon execution. The framework is based on the principles of discrete event systems and multi-agent systems, and is capable of automatically generating a hierarchical multi-agent system for a given BioPAX model.

Proposes a neural mass model to simulate brain activity that consists of a Wilson-Cowan model coupled to inhibitory synaptic plasticity (ISP). The application is composed of three main features: (i) “TimeSeries” that supplies an assortment of methods for handling time series including a mean to calculate amplitude or to introduce an orthogonal routine; (ii) “Model” that allows users to simulate networked oscillators; and (iii) “Network” to generate graphs or networks representing brain regions.

Supplies simulation and analysis tools. PyDSTool provides high-level compositional model-building tools involving symbolic expressions and modular component templates for improving users construct large models. Besides, the software supports simulations of ordinary differential equations (ODEs), differential-algebraic equations (DAEs), and discrete mappings and allows users to specify dynamics using evolution equations or explicit functions of time or state.

Provides a theoretical model of the bee lobula orientation-sensitive neurons. BeeLobulaModel is a very simple neural network models based directly on the neural circuitry of honeybees. It just uses four large-field lobula orientation-sensitive neurons from each eye, which sparsely connect to a single layer of interneurons within the bee brain learning centres, are able to discriminate complex achromatic patterns often used in bee behavioural experiments, without the need for an internal image representation. This model allows replication of the twenty-six discrimination & generalization visual stimuli experiments simulated taken from four published honeybee behaviour papers.

Analyzes metabolic pathways, principally by using Flux Balance Analysis (FBA) and Open Dynamics Engine (ODE) simulation. Pathway Analyzer performs report on gene deletions and flux values from Systems Biology Markup Language (SBML) files by using modifiers to detect gene–reaction associations.

A tool for modeling biological networks and simulating their discrete-time dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network that enables researchers to construct, set the parameters, and observe network behavior under various conditions. To construct a network instance in BioNSi, only partial, qualitative biological data suffices. The tool is aimed for use by experimental biologists and requires no prior computational or mathematical expertise.

A visualization system for the integrated visualization, modeling and simulation of rule-based intracellular biochemistry. RuleBender has been adopted as both an educational and a research tool. A development cycle that includes close interaction with expert users allows RuleBender to better serve the needs of the systems biology community.

Serves for stochastic simulation and analysis of chemical reaction networks. FERN is a Java framework for modeling and simulating biological systems which provides accurate and state-of-the-art simulation algorithms. This tool can serve for biochemical network analysis or the development of new analysis methods or applications.

Designed to efficiently rewire large bipartite networks. BiRewire3 is a one-stop tool to rewire in a meaningful way any type of unweighted networks (undirected, directed, and signed) currently used to model different datasets and relations in computational biology (including presence-absence matrices, genomics datasets, pathways and signaling networks) in an computationally efficient way. It represents a significant and formally demonstrated advance with respect to its previous version, whose applicability was restricted to presence/absence matrices and undirected bipartite networks.

Models and simulates reaction-diffusion systems. Meredys allows for the simulation of multi-component, multi-feature state molecular species in two and three dimensions. The software employs a Brownian dynamics engine to simulate reaction-diffusion systems at the reactive particle level, based on compartment properties, complex structure, and hydro-dynamic radii. Zeroth-, first-, and second order reactions are supported. The tool provides a powerful and versatile way to run accurate simulations of molecular and subcellular systems, that complement existing multi-agent simulation systems.

Reproduces neural systems from biochemical signaling to complex models including single neurons, circuits, and larges networks. Moose classifies biological concepts into classes and dispatch them into instances connected by messages and then generates the corresponding model. The software supports a wide range of format and supplies many functionalities as well as data representations, solvers, a scripting interface and graphical displays.

Permits to study the dynamical features of gene regulatory circuits without the requirement of detailed kinetic parameters. RACIPE uses a self-consistent scheme to randomize all kinetic parameters for each mathematical model instead of relying on a particular set of parameters. In addition, this application can unbiasedly generate an ensemble of mathematical models providing a unique set of parameters for each of them.

Allows user to analyze biochemical networks. xCellerator is useful for deterministic simulations in Mathematica.

Allows users to conduct stochastic and deterministic simulations of the dynamics of complex networks of biochemical reactions. Dizzy has a modular design in which a simulator is a plug-in that conforms to a well-defined software interface, which allows for a variety of simulation techniques to be applied to a single model description, and for the clean separation of the simulation method from the model description. The software is suitable for modeling the dynamics of integrated large-scale genetic, metabolic, and signaling networks.

Simulates the behaviour of the stochastic BioAmbients according to the Gillespie algorithm. BAM implements a superset language of the Stochastic Ambient Calculus, making it viable for simulation of large distributed mobile systems. The software is composed of a GUI interface that feeds into a parser, which translates the syntax of BioAmbients into machine terms. It can assist users in studying multiple interconnections between components in bioregulatory networks.

Permits to model regulatory network systems. transsys (1) integrates several methods for modelling gene regulatory systems, (2) facilitates interfacing with models of growth processes and (3) allows formulation of concise and expressive models to facilitate scientific communication. It provides a suitable format for representing and exchanging regulatory networks. The tool is capable of modelling the effects of mutations.

Allows simulation large reaction networks. KINSOLVER is a simulator that can solve reaction networks of arbitrary size, topology, rate constants, and initial conditions by 5 standard methods. It also can predict cell activity. It allows calculation of the concentration of different reactions over time. This tool is available through a desktop and a web version.

Enables creation and analysis of Generalized Stochastic Petri Nets (GSPNs). PIPE is an open source, platform-independent tool that offers a full suite of analysis modules to check behavioral properties, produce performance statistics, and some less common features such as PNs comparison and classification.

A biological network topology simulator in which module structures of different type and size are replicated at different level of network organization and interconnected, so to obtain the desired degree distribution, e.g., scale free, and a clustering coefficient constant with the number of nodes in the network, a typical characteristic of biological networks.

Assists biologists to understand internal mechanisms of biological systems and to forecast, in silico, their response to external stimuli, environmental condition alterations and structural changes. MetaPlab consists of a plugin-based architecture that transforms the software MPsim from a simulator to a virtual laboratory. The software is composed of a core module for designing and managing biological models and a set of plugins for generating, optimizing, simulating and analyzing Metabolic P (MP) models.

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Provides a modeling package for the VMD software. CGTools is a module that permits users to transform structures between coarse grained and all-atom representations. It supports two approaches to create a coarse-grained (CG) model: (i) a residue-based method, in which two or more particles from an all atom representation map onto a single bead and (ii) a shape-based method, where a neural network learning algorithm is used to determine the placement of neurons (or CG beads).

Assists in modelling and simulation of biological processes. PNK uses Stochastic Petri Nets(SPNs) and a graphical representation of Markov Jump Processes to work.

Allows modeling and performability evaluation with several variants of stochastic Petri nets. TimeNET supports evaluation of models combining exponential and deterministic as well as more general non-exponentially distributed firing delays. The software also supports colored stochastic Petri nets as well as rare-event simulation algorithms for these model classes. It provides several performance evaluation and structural analysis algorithms, as well as an interactive token game.

Provides library and tools to support the SBML Layout and Rendering Extension. SBML Layout is a web-server that allows users to layout and render SBML files. It provides a unified interface to a variety of controlled vocabularies like SBO, ChEBI, KEGG, GO. This library also supports CellDesigner and JDesigner annotations. Exporters using the library are available and produce PNG, BMP as well as PDF files.

Allows user to work on chemical reaction systems. Trelis simulation tool permitting the modeling of the time evolution of chemical reaction systems.

Simulates exploration of basic neural networks. cartoon_network allows users to examine the scalability of neurons and the complexity of their behaviors via an interface. This software can be connected to a FINCH robot.

Allows users to investigate place/transition nets (Petri Nets) and coloured petri nets. INA provides a textual editor for constructing and editing nets. It can serve for verifying boundedness and coverability of a graph that can be calculated using either the Karp-Miller algorithm or Finkel's method. This tool computes symmetries of a given net to minimize the size of the reachability graph.

Detects rate constants in molecular network models. PET can be used as a regulatory network models’ builder or for making comparison between models and results from experimentation. It allows customized models parameters, exported plots and models’ simulation. Besides, the software can store several sets of parameters and initial conditions.

Allows users to model and simulate spatio-temporal processes in living cells. Bio-SPICE is a framework and software toolkit that consists of (i) the Dashboard, (ii) data analysis tools, (iii) database tools, (iv) model analysis tools, (v) model composition and visualization tools and, (vi) and simulator tools.

Allows user to perform simulation and reachability test of System Biology Markup Language (SBML) models.

Allows description and simulation of multi model. BioRica contains specific notation to create simulators.

Provides a module to facilitate the programming of an access to files, resulting from the Mascot software, into an application. Mascot Parser is a free program, available in five programming languages (Java, Perl, Python, C++ and C#), containing object libraries, binary executables, header files as well as support material. The program allows users to avoid an update of the created code at each Mascot’s release.

Provides a Matlab toolbox. RMBNToolbox generates random models for biochemical networks.

Provides a Boolean-based representations of Biological Systems. ccBooleanAnalysis is a modeling system that can visualize biological networks as logic gate circuits, and vice-versa.

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