HIGH-PERFORMANCE SIMULATIONS OF POPULATION-GENETIC PROCESSES IN BACTERIAL COMMUNITIES USING THE HAPLOID EVOLUTIONARY CONSTRUCTOR SOFTWARE

Полный текст:


Аннотация

Three high-performance versions of the Haploid Evolutionary Constructor program are presented (http://evol-constructor.bionet.nsc.ru). The software was designed for simulating the functioning and evolution of microbial communities. These high-performance versions are to be run on systems with shared and distributed memory, using CPU and/or GPU. Almost linear acceleration has been achieved on clusters and multi-core CPU. On GPU systems, the simulation time was reduced to several minutes (dozens of hours on CPU).


Об авторах

Z. S. Mustafin
The Federal research center Institute of cytology and genetics the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
Россия


Yu. G. Matushkin
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk National Research State University, Novosibirsk, Russia
Россия


S. A. Lashin
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk National Research State University, Novosibirsk, Russia
Россия


Список литературы

1. Ashlock D., McEachern A. A simulation of bacterial communities // IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE. 2011. P. 1–8.

2. Ayton G.S., Noid W.G., Voth G.A. Multiscale modeling of biomolecular systems: in serial and in parallel // Curr. Opin. Struct. Biol. 2007. V. 17. No. 2. P. 192–198.

3. Beardmore R.E., Gudelj I., Lipson D.A., Hurst L.D. Metabolic trade–offs and the maintenance of the fi ttest and the fl attest // Nature. 2011. V. 472. No. 7343. P. 342–346.

4. Bihary D., Kerenyi A., Gelencser Z. et al. Simulation of communication and cooperation in multispecies bacterial communities with an agent based model // Scalable Comput. Pract. Exp. 2012. V. 13. No. 1. P. 21–28.

5. DeAngelis D.L., Mooij W.M. Individual-based modeling of ecological and evolutionary processes // Annu. Rev. Ecol. Evol. Syst. 2005. V. 36. No. 1. P. 147–168.

6. Esteban P.G., Rodríguez-Patón A. Simulating a Rock – Scissors – Paper Bacterial Game with a Discrete Cellular Automaton // New Challenges on Bioinspired Applications, Lecture Notes in Computer Science / Eds. Ferrández J.M., Álvarez Sánchez J.R., De la Paz F., Toledo F.J. Berlin Heidelberg: Springer, 2011. P. 363–370.

7. Kutalik Z., Razaz M., Baranyi J. Connection between stochastic and deterministic modelling of microbial growth // J. Theor. Biol. 2005. V. 232. No. 2. P. 285–299.

8. Lashin S.A., Matushkin Y.G. Haploid evolutionary constructor: new features and further challenges // In Silico Biol. 2012. V. 11. No. 3–4. P. 125–135.

9. Lashin S.A., Matushkin Y.G., Suslov V. V., Kolchanov N.A. Evolutionary trends in the prokaryotic community and prokaryotic community-phage systems // Russ. J. Genet. 2011. V. 47. No. 12. P. 1487–1495.

10. Lashin S.A., Suslov V.V., Matushkin Yu.G. Comparative modeling of coevolution in communities of unicellular organisms: adaptability and biodiversity // J. Bioinform. Comput. Biol. 2010. V. 8. No. 3. P. 627–643.

11. Martins M.L., Ferreira S.C., Vilela M.J. Multiscale models for biological systems // Curr. Opin. Colloid Interface Sci. 2010. V. 15. No. 1–2. P. 18–23.

12. Mustafi n Z.S., Matushkin Y.G., Lashin S.A. Haploid Evolutionary Constructor: parallelization and high performance simulations of evolution of prokaryotic communities // Russ. J. Genet. Appl. Res. 2012. V. 16. No. 4/1. P. 825–829.


Дополнительные файлы

Просмотров: 205

Обратные ссылки

  • Обратные ссылки не определены.


Creative Commons License
Контент доступен под лицензией Creative Commons Attribution 4.0 License.


ISSN 2500-0462 (Print)
ISSN 2500-3259 (Online)