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Simmune
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.
NetDS
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.
MetNetMaker
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.
SESSL
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.
SANA / Simulated Annealing Network Aligner
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.
BioASF / BioPAX-based Agent-oriented Simulation Framework
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.
BeeLobulaModel
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.
AbeysuriyaEtAl2018
New
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.
BioNSi / Biological Networks Simulator
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.
BiRewire3
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.
Meredys / MEsoscopic REaction DYnamics Simulator
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.
Moose / Multiscale Object-Oriented Simulation environment
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.
Dizzy
New
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.
BAM / BioAmbient Machine
New
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.
MetaPlab
New
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.
TimeNET / Timed Net Evaluation Tool
New
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.
RuleMonkey
Implements a network-free method for simulation of rule-based models that is similar to Gillespie's method. The method is suitable for rule-based models that can be encoded in BNGL, including models with rules that have global application conditions, such as rules for intramolecular association reactions. In addition, the method is rejection free, unlike other network-free methods that introduce null events, i.e., steps in the simulation procedure that do not change the state of the reaction system being simulated.
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