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Volume 9   Issue 2   Year 2014
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, Novosibirsk, 630090, Russia
Faculty of Natural Science, Novosibirsk State University, Novosibirsk, 630090, Russia 

 
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.
 
Key words: simulation software, bacterial evolution, prokaryotic community.
Table of Contents Original Article
Math. Biol. Bioinf.
2014;9(2):585-596
doi: 10.17537/2014.9.585
published in English

Abstract (eng.)
Abstract (rus.)
Full text (eng., pdf)
References
Supplementary data

 

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