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Population dynamics

In recent years there has been a great interest in modeling and simulating various aspects of population dynamics in biological and ecological systems (Wilkinson, 2011; Wilkinson, 2009; Black and McKane, 2012; Hucka et al., 2003). The increasing…
TennessenEAonly
Desktop

TennessenEAonly

Implements the demographic model for the EA population of Tennessen et al.…

Implements the demographic model for the EA population of Tennessen et al. TennessenEAonly was used in a study that explores the impact of genetic model and population growth on distribution of…

BSim
Desktop

BSim

Allows to build and characterize agent based models of bacterial populations.…

Allows to build and characterize agent based models of bacterial populations. BSim permits users to take multiple levels of detail and scale into account throughout modeling and simulation. It can…

Simbiotics
Desktop

Simbiotics

Allows the design, simulation and analysis of multicellular systems. 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…

B-GREAT
Desktop

B-GREAT Bayesian Growth Rate Effect Analysis and Test

Overcomes the limitations of parametric growth modelling. B-GREAT is based on a…

Overcomes the limitations of parametric growth modelling. B-GREAT is based on a Gaussian process (GP) regression model of microbial growth. It is able to model growth curves that deviate from a…

eSTGt
Desktop

eSTGt eSTG tool

Allows researchers to use existing biological knowledge in order to model the…

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…

stpm
Desktop

stpm

Implements the Stochastic Process Model (SPM) methodology. stpm can be used not…

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…

MASTER
Desktop

MASTER Moments and Stochastic Trees from Event Reactions

Simulates and analyses stochastic models of population phylodynamics and…

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…

Reduced-EMT-Model
Desktop

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

A set of mathematical models describing the induction of Epithelial to…

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).…

FeijenEtAl2017
Dataset

FeijenEtAl2017

Gathers a dataset of more than 700 species of land plants for which the…

Gathers a dataset of more than 700 species of land plants for which the mycorrhizal fungi have been identified with molecular methods. The database shows an evolutionary scenario of evolution of…

SodaPop
Desktop

SodaPop

Provides a simulator of large haploid populations. SodaPop intends to furnish…

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…

DirtyGenes
Desktop

DirtyGenes

Highlights differences between bacterial populations. DirtyGenes is useful with…

Highlights differences between bacterial populations. DirtyGenes is useful with different types of data, such as metagenomics data, or quantitative polymerase chain reaction (qPCR) data. This tool is…

iDynoMiCS
Desktop

iDynoMiCS individual-based Dynamics of Microbial Communities Simulator

Provides a common platform for development of all individual-based models of…

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…

SGNS
Desktop

SGNS Stochastic Gene Networks Simulator

An extension of SGNS, the stochastic simulator of SGNSim. SGNS contains all the…

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…

Vortex
Desktop

Vortex

Simulates birth and death processes and the transmission of genes through the…

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…

RuleMonkey
Desktop

RuleMonkey

Implements a network-free method for simulation of rule-based models that is…

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…

BacSim
Desktop

BacSim

Provides an extension of Gecko, an ecological flight simulator. BacSim is both…

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…

Cain
Desktop

Cain

Permits to carry out stochastic and deterministic simulations of chemical…

Permits to carry out stochastic and deterministic simulations of chemical reactions. Cain can spawn multiple simulation processes. It is able to store models, simulation parameters, and simulation…

SimBiology
Desktop

SimBiology

Provides an application and programmatic tools to model, simulate, and analyze…

Provides an application and programmatic tools to model, simulate, and analyze dynamic systems, focusing on pharmacokinetic/pharmacodynamic (PK/PD) and systems biology applications. SimBiology…

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