Population dynamics software tools | Mathematical modeling

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 genetic variance across the allele frequency spectrum underlying risk for a complex disease. This package has been implemented in Python and is available for local use.

Permits to automate the selection of a partitioning scheme given a set of user-defined data blocks as input. PartitionFinder can be used to compare millions of partitioning schemes in a single run and to select good and often optimal partitioning schemes for a large range of DNA data sets. It was developed to simplify the selection of partitioning schemes and lead to concomitant improvements in phylogenetic analyses.

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.

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 sigmoid form. This tool was applied to yeast population growth data under diverse stress conditions and genetic backgrounds. It can recapitulate known differential growth phenotypes and enables discovery of novel phenotypes.

Proposes an autoregressive model using queries made through Google to evaluate influenza-like illnesses (ILI) activity. ARGO is a flu-tracking model that considers flu-related Google search frequencies, electronic health records and historical flu of multiple Google Flu Trends (GFT) engines. This application can be used to study the dynamics of various events with modulable parameters of space and time.

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 predict the consequences of competition between the induced and uninduced sub-populations of bacteria. The tool allows for historic models to readily make use of improved knowledge and can be customized by users.

Performs semi-automatic spike sorting on large extra-cellular recordings. SpyKING CIRCUS is a method that assists in overlapping spikes. It works in two main steps: a clustering followed by a template matching step. First, spikes are detected as threshold crossings and then, the algorithm isolated the extracellular waveforms for a number of randomly chosen spike times.

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.

Provides algorithms for the analysis of ecological networks. enaR uses a branch of network ecology: Ecosystem Network Analysis (ENA). ENA is a set of algorithms developed to analyze network models of energy or matter movement in ecosystems. This R package gathers workflow management functions and is customizable to support individual needs. It permits users to address relational questions at the core of ecology.

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.

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.

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.

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.

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.

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 useful for computation number of samples needed in experiments.

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.

Plots and animates three-strategy evolutionary games on a triangular simplex. egtplot is a package for displaying both static and animated dynamics with the game space. The software provides two functions: “plot_static” for plotting static simplex figures and “plot_animated” for generating simplex animations. It permits users to build phase portraits of 3-strategy games. egtplot also allows the creation of animated simplices.

Consists of a simulator of crypt evolution. Cryptsim’s model includes several constituents: a clone tree, a two-dimensional spatial model, and an agent-based model that describes the evolution of crypts through time. This software is based on Barrett’s esophagus (BE) and implements a series of strategies to limit its computational burden.

Evaluates state-level flu activity. ARGONet proposes an approach merging two tracking techniques. This application combines: (i) ARGO, that gathers data derived from flu-related Google search frequencies, electronic health records and historical flu to deduce flu activity; and (ii) Net, that integrates structural spatio-temporal synchronicities in flu activity to refine the previous estimates made by ARGO.

Offers a method for analyzing mRNA and protein abundances. This pipeline contains four machine learning algorithms: linear and radial support vector machine (SVM) models, sigmoidal kernels, and random forest models. It consists of three distinct phases (i) data preparation, (ii) training and prediction, and (iii) model tuning with the aim of selecting the best model that can be employed for the predictions.

Provides a platform for collaborative monitoring on the specialization of infectious diseases of wildlife. SISS-Geo is built on four modules: (i) the first stores georeferenced field observation records of animals, their physical conditions and their surrounding environment; (ii) the second analyzes data and create alert models that take account several information; (iii) the third focuses on the machine learning feature and wildlife health and (iv) finally the last one assists to apprehend relationships from trained models.

Allows users to distinct biological and technical variation in artificial time-series. MALLARD is a framework dedicated to the analysis of microbiota time-series data. This program is based on generalized dynamic linear models and is able to split targeted time-series into features related with both technical and biological sources of variation. It intends to assist user in exploring patterns and time-scales into microbiota variations.

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.

Identifies the presence of bacterial growth in well plates. AMyGDA analyzes well plate images and marks graphically the bacterial growth with an estimation of the drug and concentration. This software reads images up to 96 wells. It aims to complement human-based plate reading with a combination of plate-based MIC measurements. It can also high-throughput culture-based drug susceptibility testing for tuberculosis.

Performs common tasks related to species’ potential distribution modelling based on correlative approach. openModeller follows a generic design that may allow other areas such as archaeological research and geological prospecting to make use of it. It can run different algorithms, read and write different data formats, and be used by different types of interfaces. The result can then be post-processed by other tools.

Enables users to extend and share data, methods or procedures to reproduce them by other users. sdm is an object-oriented reproducible and extensible framework for species distribution modelling. It permits to perform the entire modelling process within the same environment using different approaches. It can handle spatial and temporal data for single or multiple species and uses high performance computing solutions to speed up modelling and simulations.

Offers a set of scripts dedicated to the analysis of data derived from microscopy investigation. The application attributes a status of either dark and bright to pixels and then juxtaposes them to detect cells. Besides, it also integrates a detection algorithm to identify cell boundaries, features microcolonies and centroid position as well facilities allowing users to calculate and determine the distribution of growth rates.

Provides trait data and scripts of mycorrhizal symbiosis in land plant diversification. The package includes a dataset of more than 700 species of land plants, some conversion scripts for phylogenetic analysis and comparative analysis and supporting documentation. It also provides data about full or partial chloroplast genomes for over 140 species.

Mimics the trajectory of the epidemic according to a specific compartmental model based on Gillespie’s stochastic simulation algorithms. This tool employs variants for simulating sampled transmission tree from an epidemiological trajectory using the coalescent approach. It was used to feign epidemics using either a simple susceptible-infected-recovered (SIR) model or a detailed model describing HIV spread in a heterogeneous population.

Provides an application and programmatic tools to model, simulate, and analyze dynamic systems, focusing on pharmacokinetic/pharmacodynamic (PK/PD) and systems biology applications. SimBiology provides a block diagram editor for building models, or you can create models programmatically using the MATLAB language. SimBiology includes a library of common PK models, which you can customize and integrate with mechanistic systems biology models.

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 results. The tool contains different solvers: Gillespie's direct method, Gillespie's first reaction method, Gibson and Bruck's next reaction method, Tau-leaping, Hybrid direct/tau-leaping, Ordinary Differential Equation (ODE) integration.

Provides a set of tools that assists to support AquaMaps, a model-based large-scale predictor of natural occurrences of marine species. raquamaps is an R package that helps in licensing issues.

Simulates the movement of mosquito across landscapes. MoNeT defines transition probabilities using the distances between resources points in a spatial plane. It is based on a clustering algorithm that takes into account both: mosquito movement, and geographical constraints. This tool can serve for the comprehension of the factors that would promote more efficient mosquito-control campaigns.

Reproduces and describes microbiome data. SparseDOSSA is a model-based Bayesian method intending to assist users in comparing statistical metagenomics methods in order to choose the most adapted one. This program is able to handle known feature-feature and feature-metadata correlation structures and can be used to set microbes and communities within reference microbial datasets or to mimic synthetic datasets with specific population structure.

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.

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.