Mathematical Biology and Bioinformatics. 2014, Vol. 9, No. 2, pp. 585-596 [full text]

HEC 2.0: improved simulation of the evolution of prokaryotic communities

Lashin S.A., Klimenko A.I., Mustafin Z.S., Kolchanov N.A., Matushkin Yu.G.

Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia; Faculty of Natural Science, Novosibirsk State University, Novosibirsk, Russia, e-mail: lashin[_at_]bionet.nsc.ru

Abstract

Modeling and simulation of prokaryotes and prokaryotic communities are important for the development of modern fundamental, medical and biotechnological researches. Previously, we had developed a software package “Haploid evolutionary constructor”, which models simultaneously describe several layers of biological organization: genetic, metabolic, population, ecological. Here
we present a new version of the program, which includes the following major improvements: graphic user interface, parallel version of the computational core, and support of user-defined plugins. Plugins describe either changes of prokaryotic population size or cellular metabolism (gene networks). The graphic user interface components for the “Haploid evolutionary constructor” provide convenient visualization of data, model construction, setting up and control. High-performance versions of our software have been implemented using OpenMP and MPI technologies, and can be run at both desktops and MPI clusters. The software is available at the website http://evol-constructor.bionet.nsc.ru/ along with documentation and example models. The “Haploid evolutionary constructor” provides researchers the convenient tool for simulation of bacterial communities’ evolution. The models of prokaryotic communities constructed with this software
may be used for studying the fundamental principles of evolution, connecting various levels of biological organization, from genetic to ecological ones. It may also be used as an educational tool for the illustration of fundamental biological laws.

Keywords: simulation software, bacterial evolution, prokaryotic community.

Bibliography link: Lashin S.A., Klimenko A.I., Mustafin Z.S., Kolchanov N.A., Matushkin Yu.G. HEC 2.0: IMPROVED SIMULATION OF THE EVOLUTION OF PROKARYOTIC COMMUNITIES // Math. Biology & Bioinformatics, 2014, Vol. 9, No. 2, pp. 585-596.