SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks

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.

Approximating intrinsic noise in continuous multispecies models

“…Several powerful numerical methods have been developed to generate stochastic simulation of the reaction-transport master equation (Ander et al 2004;Elf & Ehrenberg 2004;Lampoudi et al 2009). Nonetheless, for a systematic mapping of parameter space, simulation methods rapidly become prohibitively timeconsuming, even for reasonably simple models.…”

Space as the final frontier in stochastic simulations of biological systems

“…We attempt in this review to present the stateof-the-art of such general-purpose software, describing the modeling methodology, highlighting the approximations inherent to modeling objects of such complex nature, and presenting perspectives of refinement. References are made to the following actively developed and freely available programs: Virtual Cell [7], E-Cell [8], MCell [9], Smoldyn [10], MesoRD [11], and STOCHSIM [12] as well as SmartCell [13], developed in our lab as a tool to analyze stochastic spatially relevant biological processes (see Table 1). …”

Modeling Three-Dimensional Spatial Regulation of Bacterial Cell Division (Dissertation)

“…Elf and Ehrenberg (2004) on the other hand, extended the fast version of the Gillespie's algorithm, the Next Reaction (NR) method (Gibson and Bruck, 2000), to be used in subvolumes. The SmartCell (Ander et al, 2004) and GMP (Rodríguez et al, 2006) simulators also implemented a similar scheme. The subvolume sizes, as shown in (Figure 1.2D), are determined such that all reactive molecular species, represented as point particles, are almost uniformly distributed in each subvolume's space.…”