Abstract
Cellular signalling is a vital process in living organisms for coordinating highly diverse responses to various stimuli. Particle-based modelling excels in its ability to model complex features of cellular signalling pathways including stochasticity, spatial effects, and heterogeneity, thus improving our understanding of critical decision processes in biology. Yet, particle-based modelling is computationally prohibitive to implement. We recently developed FaST (FLAME-accelerated signalling tool), a software tool that harnesses the power of high-performance computation to reduce the computational burden of particle-based modelling. In particular, employing the unique massively parallel architecture of graphic processing units (GPUs) provided extreme speed ups of simulations by >650-fold. In this chapter, we provide a step-by-step walkthrough of how to use FaST to create GPU-accelerated simulations of a simple cellular signalling network. We further explore how the flexibility of FaST can be used to implement entirely customized simulations while still including the intrinsic speed up advantages of GPU-based parallelization.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Chuang H-Y, Hofree M, Ideker T (2010) A decade of systems biology. Annu Rev Cell Dev Biol 26:721–744
Ideker T, Galitski T, Hood L (2001) A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet 2:343–372
Bray SSA, Bray D (2004) Stochastic simulation of chemical reactions with spatial resolution and single molecule detail. Phys Biol 1:137–151
Andrews SS (2017) Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface. Bioinformatics 33:710–717
Slepoy SJP, Slepoy A (2005) Microbial cell modeling via reacting diffusive particles. J Phys Conf Ser 16:305–309
Kerr R, Bartol T, Kaminsky B et al (2008) Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces. SIAM J Sci Comput 30:3126–3149
Pogson M, Holcombe M, Smallwood R, Qwarnstrom E (2008) Introducing spatial information into predictive NF-kappa B modelling – an agent-based approach. PLoS One 3:e2367
Klann MT, Lapin A, Reuss M (2011) Agent-based simulation of reactions in the crowded and structured intracellular environment: Influence of mobility and location of the reactants. BMC Syst Biol 5(1):1–14
Fullstone G, Guttà C, Beyer A, Rehm M (2020) The FLAME-accelerated signalling tool (FaST) for facile parallelisation of flexible agent-based models of cell signalling. NPJ Syst Biol Appl 6:10
Nenninger A, Mastroianni G, Mullineaux CW (2010) Size dependence of protein diffusion in the cytoplasm of Escherichia coli. J Bacteriol 192:4535–4540
Schavemaker PE, Boersma AJ, Poolman B (2018) How important is protein diffusion in prokaryotes? Front Mol Biosci 5:93
Kalwarczyk T, Kwapiszewska K, Szczepanski K et al (2017) Apparent anomalous diffusion in the cytoplasm of human cells: the effect of probesn polydispersity. J Phys Chem B 121:9831–9837
Ramadurai S, Holt A, Krasnikov V et al (2009) Lateral diffusion of membrane proteins. J Am Chem Soc 131:12650–12656
Weiß K, Neef A, Van Q et al (2013) Quantifying the diffusion of membrane proteins and peptides in black lipid membranes with 2-focus fluorescence correlation spectroscopy. Biophys J 105:455–462
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Fullstone, G. (2023). Rapid Particle-Based Simulations of Cellular Signalling with the FLAME-Accelerated Signalling Tool (FaST) and GPUs. In: Nguyen, L.K. (eds) Computational Modeling of Signaling Networks. Methods in Molecular Biology, vol 2634. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3008-2_9
Download citation
DOI: https://doi.org/10.1007/978-1-0716-3008-2_9
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-3007-5
Online ISBN: 978-1-0716-3008-2
eBook Packages: Springer Protocols