A state-of-the-art problem in Computational Systems Biology is to provide suitable tools to model and predict the behaviour of multicellular systems (tissues, embryos) where biological interactions occur both inside and between cells (or compartments in general). Starting from existing computational models and languages such as stochastic pi-calculus, Petri Nets, mobile ambients, and membrane computing, we developed a new computational framework based on (i) a compositional model for biological compartments, and (ii) an enhanced model of chemical rules addressing also biomechanical actions such as substances diffusion across membranes or compartments splitting. We tested a fragment of the framework using a case study based on spatial pattern formation in embryogenesis, where the interplay between cells' internal dynamics and cell-to-cell interactions has a central role
A computational framework for modelling multicellular biochemistry / S. Montagna; M. Viroli. - STAMPA. - (2009), pp. 2223-2240. (Intervento presentato al convegno IEEE Congress on Evolutionary Computation, 2009. CEC '09. tenutosi a Trondheim, Norway nel 18-21 May 2009) [10.1109/CEC.2009.4983218].
A computational framework for modelling multicellular biochemistry
MONTAGNA, SARA;VIROLI, MIRKO
2009
Abstract
A state-of-the-art problem in Computational Systems Biology is to provide suitable tools to model and predict the behaviour of multicellular systems (tissues, embryos) where biological interactions occur both inside and between cells (or compartments in general). Starting from existing computational models and languages such as stochastic pi-calculus, Petri Nets, mobile ambients, and membrane computing, we developed a new computational framework based on (i) a compositional model for biological compartments, and (ii) an enhanced model of chemical rules addressing also biomechanical actions such as substances diffusion across membranes or compartments splitting. We tested a fragment of the framework using a case study based on spatial pattern formation in embryogenesis, where the interplay between cells' internal dynamics and cell-to-cell interactions has a central roleI documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
