Issue No. 02 - March-April (2013 vol. 10)
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.101
Qian Gao , Sch. of Inf. Syst., Comput., & Math., Brunel Univ., Uxbridge, UK
David Gilbert , Sch. of Inf. Syst., Comput., & Math., Brunel Univ., Uxbridge, UK
Monika Heiner , Fac. of Math., Natural Sci. & Comput. Sci., Brandenburg Univ. of Technol. Cottbus, Cottbus, Germany
Fei Liu , Control & Simulation Center, Harbin Inst. of Technol. Sci. Park, Harbin, China
Daniele Maccagnola , Dept. of Comput. Sci. (DISCo), Univ. of Milano-Bicocca, Milano, Italy
David Tree , Sch. of Health Sci. & Social Care, Brunel Univ., Uxbridge, UK
Modeling across multiple scales is a current challenge in Systems Biology, especially when applied to multicellular organisms. In this paper, we present an approach to model at different spatial scales, using the new concept of Hierarchically Colored Petri Nets (HCPN). We apply HCPN to model a tissue comprising multiple cells hexagonally packed in a honeycomb formation in order to describe the phenomenon of Planar Cell Polarity (PCP) signaling in Drosophila wing. We have constructed a family of related models, permitting different hypotheses to be explored regarding the mechanisms underlying PCP. In addition our models include the effect of well-studied genetic mutations. We have applied a set of analytical techniques including clustering and model checking over time series of primary and secondary data. Our models support the interpretation of biological observations reported in the literature.
Biological system modeling, Color, Petri nets, Proteins, Mathematical model, Image color analysis, Analytical models
Qian Gao, D. Gilbert, M. Heiner, Fei Liu, D. Maccagnola and D. Tree, "Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 2, pp. 337-351, 2013.