SmartCell: a framework to simulate cellular processes that combines stichastic approximation with diffusion and localization: analysis of simple gene networks

Maria Ander, Pedro Beltrao, Barbara Ventura, Jesper Ferkinghoff-Borg, Mathilde Foglierini, Anders Kaplan, Caroline Lemerle, Isabelle Tomas-Oliveira, Luis Serrano

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

SmartCell has been developed to be a general framework for modelling and simulation of diffusion-reaction networks in a whole-cell context. It supports localisation and diffusion by using a mesoscopic stochastic reaction model. The SmartCell package can handle any cell geometry, considers different cell compartments, allows localisation of species, supports DNA transcription and translation, membrane diffusion and multistep reactions, as well as cell growth. Moreover, different temporal and spatial constraints can be applied to the model. A GUI interface that facilitates model making is also available. In this work we discuss limitations and advantages arising from the approach used in SmartCell and determine the impact of localisation on the behaviour of simple well-defined networks, previously analysed with differential equations. Our results show that this factor might play an important role in the response of networks and cannot be neglected in cell simulations.
Original languageEnglish
JournalIEE Proceedings - Systems Biology
Volume1
Issue number1
Pages (from-to)129-138
ISSN1741-2471
Publication statusPublished - 2004
Externally publishedYes

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