Population dynamics software tools | Mathematical modeling

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.

Allows users to study microbial communities. DEMIC can infer the relative distances of contigs from the replication origin and compare bacterial growth rates between samples. It was used to estimate the growth rates in over 120 species-experiment combinations. This tool performs growth estimation based on principal component analysis (PCA) of contig coverages in multiple samples.

Allows users to model, simulate and analyze complex, heterogeneous and multi-scale systems like a cell. E-Cell is a generic software package for cell simulation, based on structured Substance–Reactor Model (SRM), an object-oriented modeling theory. The software accepts multi-algorithms, multi-timescales and multi-spatial-representations as its central feature. It includes ordinary differential equations, Gillespie algorithm (the direct method), and spatial Gillespie algorithm.

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.

Offers a modeling environment for simulating complex phenomena. NetLogo is available through both a standalone software and a web application coupled to a homepage that displays a library of models and extensions. The software encompasses a large model application area including spread of disease, fractals, cellular automata or crystallization. Additionally, the program includes a feature for saving models as Java applets, for facilitating the publication of the simulations from the tool to a Web page.

Performs mathematical modeling for cell organisms. SimBio is an open source biological simulation platform that consists of five modules – two databases related to three different items for instantiation, calculation and steering – which have been developed independently for being adjusted to user needs. This program aims to ease the conception of models composed of functional modules and their complete or partly sharing.

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.