Multiscale modeling for biologists.

Karen Lipkow, Steven S. Andrews, Dennis Bray, Simulated Diffusion of Phosphorylated CheY through the Cytoplasm of Escherichia coli Journal of Bacteriology. ,vol. 187, pp. 45- 53 ,(2005) , 10.1128/JB.187.1.45-53.2005

Kurt W. Kohn, Mirit I. Aladjem, John N. Weinstein, Yves Pommier, Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Molecular Biology of the Cell. ,vol. 17, pp. 1- 13 ,(2005) , 10.1091/MBC.E05-09-0824

Michael Hucka, Andrew Finney, Herbert M Sauro, Hamid Bolouri, John C Doyle, Hiroaki Kitano, Adam P Arkin, Benjamin J Bornstein, Dennis Bray, Athel Cornish-Bowden, Autumn A Cuellar, Serge Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, II Goryanin, WJ Hedley, T Charles Hodgman, J-H Hofmeyr, Peter J Hunter, Nick S. Juty, JL Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, D Lucio, Pedro Mendes, Eric Minch, ED Mjolsness, Yoichi Nakayama, MR Nelson, PF Nielsen, T Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas Simon Shimizu, Hugh D. Spence, Jörg Stelling, Koichi Takahashi, Masaru Tomita, J Wagner, J Wang, None, The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. ,vol. 19, pp. 524- 531 ,(2003) , 10.1093/BIOINFORMATICS/BTG015

E. M. Izhikevich, G. M. Edelman, Large-scale model of mammalian thalamocortical systems Proceedings of the National Academy of Sciences of the United States of America. ,vol. 105, pp. 3593- 3598 ,(2008) , 10.1073/PNAS.0712231105

Kanae Oda, Hiroaki Kitano, A comprehensive map of the toll-like receptor signaling network Molecular Systems Biology. ,vol. 2, ,(2006) , 10.1038/MSB4100057

Hiroshi Watanabe, Seiryo Sugiura, Toshiaki Hisada, The looped heart does not save energy by maintaining the momentum of blood flowing in the ventricle. American Journal of Physiology-heart and Circulatory Physiology. ,vol. 294, ,(2008) , 10.1152/AJPHEART.00041.2008

Boris N. Kholodenko, Cell-signalling dynamics in time and space Nature Reviews Molecular Cell Biology. ,vol. 7, pp. 165- 176 ,(2006) , 10.1038/NRM1838

Denis Noble, Computational Models of the Heart and Their Use in Assessing the Actions of Drugs Journal of Pharmacological Sciences. ,vol. 107, pp. 107- 117 ,(2008) , 10.1254/JPHS.CR0070042

Alan Garny, David P Nickerson, Jonathan Cooper, Rodrigo Weber dos Santos, Andrew K Miller, Steve McKeever, Poul M.F Nielsen, Peter J Hunter, CellML and associated tools and techniques. Philosophical Transactions of the Royal Society A. ,vol. 366, pp. 3017- 3043 ,(2008) , 10.1098/RSTA.2008.0094

M. L. Blinov, J. R. Faeder, B. Goldstein, W. S. Hlavacek, BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains Bioinformatics. ,vol. 20, pp. 3289- 3291 ,(2004) , 10.1093/BIOINFORMATICS/BTH378