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Simbiotics

Allows the design, simulation and analysis of multicellular systems. Simbiotics is focused on modelling of bacterial populations, cellular species with individual behaviour and interactions with their environment can be defined. It permits the simulation of large populations of multispecies communities. This tool provides a standard modelling library of processes typical to bacteria, such as growth, motility, gene regulation, metabolic activity and cell-surface appendages such as receptors and adhesins.

eSTGt / eSTG tool

Allows researchers to use existing biological knowledge in order to model the dynamics of a developmental process and analyze its behavior throughout the historical events. Simulated lineage trees can be used to validate various hypotheses in silico and to predict the behavior of dynamical systems under various conditions. Written under MATLAB environment, the tool also enables to easily integrate the output data within the user’s downstream analysis. eSTGt is an environment-dependent Stochastic Tree Grammars (eSTG) programming and simulation environment. When executing a program, the tool generates the corresponding lineage trees as well as the internal states values, which can then be analyzed either through the tool’s GUI or using MATLAB’s command-line environment.

stpm

Implements the Stochastic Process Model (SPM) methodology. stpm can be used not only for stochastic modeling of probabilities of endpoints but in many other applied areas, e.g., life science applications including biologically based modeling. The package was validated through simulation studies. The stpm R package can be extended by including: (i) SPM with several health states, (ii) SPM with hidden heterogeneity, (iii) SPM with competing risks, and (iv) SPM for partially observed covariates.

MASTER / Moments and Stochastic Trees from Event Reactions

Simulates and analyses stochastic models of population phylodynamics and chemical kinetics. MASTER supports the simulation of inheritance trees and networks under these same models. It allows user to specify a stochastic model in terms of a collection of individual reactions of this form, using a simple syntax. The tool can generate phylogenetic trees or networks alongside the histories they correspond to. It enables investigations into the interplay between genealogies and population dynamics.

Reduced-EMT-Model / Reduced-Epithelial-to-Mesenchymal-Transition-Model

A set of mathematical models describing the induction of Epithelial to Mesenchymal Transition (EMT) by TGF-β isoforms in the presence or absence of vascular endothelial growth factor-A (VEGF-A). Reduced-EMT-Model allows the description of complex regulatory interactions in the absence of specific mechanistic information, it also allowed to build a predictive yet compact model. It also reveals a signaling axis, which possibly regulates carcinoma progression through an EMT versus tubulogenesis response.

SodaPop

Provides a simulator of large haploid populations. SodaPop intends to furnish an open source software for inquiring evolutionary dynamics of large-scale asexual populations with explicit genomic sequences, including in the context of antibiotic resistance, viral evolution and cancer. It authorizes many calculations such as complex metabolic pathways with multiple gene products. In addition, the software includes supplementary tools for analyzing and visualizing the obtained results.

iDynoMiCS / individual-based Dynamics of Microbial Communities Simulator

Provides a common platform for development of all individual-based models of microbial biofilms and such like. The iDynoMiCS software simulates the growth of microbial communities. iDynoMiCS is written in Java, and uses XML protocol files that allow one to specify easily many different types of simulations. iDynoMiCS writes plain-text XML files as output, and these may be processed using any number of software tools (though we provide some general post-processing routines that run in Matlab and R). In addition to XML files, iDynoMiCS also writes files for POV-Ray, which is used to render 3-D images of the simulation.

SGNS / Stochastic Gene Networks Simulator

An extension of SGNS, the stochastic simulator of SGNSim. SGNS contains all the features of SGNS, such as reactions with multi-delayed events. The two key additions in SGNS2 are (i) it supports dynamic, interlinked, hierarchical compartments and (ii) it supports multiple molecule and compartment partitioning schemes, applicable on a per-molecule-type basis. The novel features considerably extend the class of models that can be simulated. SGNS2 enables the modeling of stochastic processes in live cells that require compartmentalization, multi-delayed complex processes and complex stochastic partitioning schemes at a per-molecule type in cell division. These features are necessary to study in silico, among other phenomena, phenotypic diversity in cell populations.

Vortex

Simulates birth and death processes and the transmission of genes through the generations by generating random numbers. Vortex determines whether each animal lives or dies, the number of progeny produced by each female each year, and determines which of the two alleles at a genetic locus are transmitted from each parent to each offspring. The tool allows the user to supplement or harvest the population, and multiple subpopulations can be tracked, with user-specified migration among the units.

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.

BacSim

Obsolete
Provides an extension of Gecko, an ecological flight simulator. BacSim is both a model of Complex Adaptive Systems (microbial communities) and a Complex Adaptive System itself. Its co-evolution with Gecko started in 1997 with the original Objective-C colony model via the biofilm and biofilm with EPS production model to the current Java version of the latter. The step from colony to biofilm model was major heart surgery as a more efficient diffusion-reaction algorithm was implemented. This was made possible by decoupling growth and diffusion on the basis of the different timescales of these processes. This resulted in a tremendous speed-up of model runs, by about 500 times. In addition, the model was extended to multi-species, multi-substrate systems with biofilm geometry (inert substratum at the bottom and bulk liquid at the top of the vertical dimension, periodic boundaries in the other two dimensions), and the bacteria are now living in a 3D space. BacSim is available as a standalone version for download. A demo version is also available online.