Publications

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Here is a list of publications related to BioSimWare and to its application to the study of biological systems.

Reference to BioSimWare in literature

D. Besozzi, P. Cazzaniga, G. Mauri, D. Pescini.
BioSimWare: a software for the modeling, simulation and analysis of biological systems.
Membrane Computing, 11th International Conference, CMC 2010, Jena, Germany, August 24-27, 2010. Revised Selected Papers, (M. Gheorghe, T. Hinze, G. Păun, G. Rozenberg, A. Salomaa, eds.), LNCS 6501, 119-143, 2010.

Published research papers which use BioSimWare

D. Besozzi, P. Cazzaniga, D. Pescini, G. Mauri.
An analysis on the influence of network topologies on local and global dynamics of metapopulation systems.
Applications of Membrane Computing, Concurrency and Agent-based Modelling in Population Biology (AMCA-POP 2010) (P. Milazzo, M.J. Pérez-Jiménez, eds.), EPTCS 33, 1–17, 2010.

D. Besozzi, P. Cazzaniga, M. Dugo, D. Pescini, G. Mauri.
A study on the combined interplay between stochastic fluctuations and the number of flagella in bacterial chemotaxis.
Proceedings of CompMod2009 – 2nd International Workshop on Computational Models for Cell Processes (R.J. Back, I. Petre, E. de Vink, eds.), EPTCS 6, 47–62, 2009.

D. Besozzi, P. Cazzaniga, G.Mauri, D. Pescini, L. Vanneschi.
A comparison of genetic algorithms and particle swarm optimization for parameter estimation in stochastic biochemical systems.
EvoBIO 2009, (C. Pizzuti, M.D. Ritchie, M. Giacobini, eds.), LNCS 5483, 116–127, 2009.

P. Cazzaniga, D. Pescini, D. Besozzi, G. Mauri, S. Colombo, E. Martegani.
Modeling and stochastic simulation of the Ras/cAMP/PKA pathway in the yeast Saccharomyces cerevisiae evidences a key regulatory function for intracellular guanine nucleotides pools.
Journal of Biotechnology, Vol. 133, Issue 3, 377-385, 2008.

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