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Stochastic Simulation of Biological Systems with Dynamical Compartment Structure [chapter]

Cristian Versari, Nadia Busi
Lecture Notes in Computer Science  
In this paper we introduce an extended formalisation of the above algorithm which preserves the original model but allows the stochastic simulation in presence of multiple compartments with dynamical structure  ...  Despite of its conservativeness, Sπ@ is showed to allow flexible modelling of multiple compartments with dynamical structure and to provide increased biological faithfulness.  ...  This approximation can be tolerated until very few molecules walk through during the time of the simulation, but becomes unreasonable when the aim is the modelling of compartments with dynamical structure  ... 
doi:10.1007/978-3-540-75140-3_6 fatcat:up4l5k2u7vfxjjdxpbaqxcg6p4

Simulation techniques for the calculus of wrapped compartments

Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Elena Grassi, Eva Sciacca, Salvatore Spinella, Angelo Troina
2012 Theoretical Computer Science  
In this paper we define a hybrid simulation method, combining the stochastic approach with ODEs, for systems described in the Calculus of Wrapped Compartments (CWC), a calculus on which we can express  ...  entities whose compartmentalised structure evolves dynamically.  ...  We thank Marco Aldinucci for the useful discussions on the simulator implementation issues and for providing us computing resources (Intel workstations with 2 quad-core Xeon).  ... 
doi:10.1016/j.tcs.2011.12.063 fatcat:je3an2rqu5gp7pvgzswy5iz5hy

Hybrid Calculus of Wrapped Compartments

Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Elena Grassi, Eva Sciacca, Salvatore Spinella, Angelo Troina
2010 Electronic Proceedings in Theoretical Computer Science  
entities whose compartmentalised structure evolves dynamically.  ...  In this paper we define a hybrid simulation method, combining the stochastic approach with ODEs, for systems described in CWC, a calculus on which we can express the compartmentalisation of a biological  ...  system has a fixed compartment structure.  ... 
doi:10.4204/eptcs.40.8 fatcat:qyahhvlayfcpzlvrv5qy4x2q4m

Editorial: Special Issue on Stochastic Modelling of Reaction–Diffusion Processes in Biology

Radek Erban, Hans G. Othmer
2014 Bulletin of Mathematical Biology  
or for densities of individuals, and stochastic models in which individual events of reaction or diffusion are followed.  ...  For instance, chemical reactions occur in discrete steps at the molecular level, the processes are inherently stochastic, and the inherent "irreproducibility" in these dynamics has been demonstrated experimentally  ...  In this Special Issue, the compartment size selection is discussed by Hu et al. (2013) , who also present a stochastic simulation algorithm for compartmentalized systems in which reactions are aggregated  ... 
doi:10.1007/s11538-013-9929-z pmid:24402472 pmcid:PMC3997611 fatcat:gwvp34yr45hr3jgej7s6saqzbe

Space as the final frontier in stochastic simulations of biological systems

Caroline Lemerle, Barbara Di Ventura, Luis Serrano
2005 FEBS Letters  
Recent technological and theoretical advances are only now allowing the simulation of detailed kinetic models of biological systems that reflect the stochastic movement and reactivity of individual molecules  ...  Modeling choices, current limitations and perspectives of improvement of current general-purpose modeling/simulation platforms for biological systems are discussed.  ...  (b) Compartmental geometry: space is subdivided into containers, corresponding to cellular compartments, with no geometrical properties.  ... 
doi:10.1016/j.febslet.2005.02.009 pmid:15763553 fatcat:mxtg3s2ggrcmbhmeo2bwrks2aq

Coarse-graining and hybrid methods for efficient simulation of stochastic multi-scale models of tumour growth

Roberto de la Cruz, Pilar Guerrero, Juan Calvo, Tomás Alarcón
2017 Journal of Computational Physics  
This implies that, in addition to the issues that arise in stochastic-reaction diffusion systems, we need to account for the age-structure of the population when attempting to couple both descriptions.  ...  intracellular dynamics.  ...  Such systems of gene regulation are often modelled as non-linear, high-dimensional dynamical systems whose structure has been moulded in the course of biological evolution.  ... 
doi:10.1016/ pmid:29200499 pmcid:PMC5656096 fatcat:u24vnvkswfbwlgm43ctdro7bxa

A deterministic-stochastic crossover algorithm for simulation of complex biochemical systems

Guoxing Fu, Amit Sabnis, Robert W. Harrison
2013 2013 IEEE 3rd International Conference on Computational Advances in Bio and medical Sciences (ICCABS)  
Our group has developed a deterministic-stochastic crossover algorithm for simulating biological networks. This method features with XML-based model representation, multiple compartments and events.  ...  The ability of revealing the stochastic property with high efficiency makes our new algorithm useful for researches and applications based on systems biology.  ...  Further, the added features of compartment and event made the simulation of biological systems become more realistic.  ... 
doi:10.1109/iccabs.2013.6629194 dblp:conf/iccabs/FuSH13 fatcat:4d6k236r5rdezk7fuwlygznlve

Efficient Stochastic Simulation of Biological Systems with Multiple Variable Volumes

Cristian Versari, Nadia Busi
2008 Electronical Notes in Theoretical Computer Science  
systems with dynamical structure even in presence of computationally expensive phenomena like diffusion.  ...  While the original algorithm considers only one fixed-volume compartment, the simulation of biological systems often requires multi-compartment semantics.  ...  The algorithm can be used for an improved implementation of the Sπ@ calculus [24] which constitutes an elegant candidate for the representation of systems with dynamical compartment structure and varying  ... 
doi:10.1016/j.entcs.2007.12.012 fatcat:4tgv7rk7hzg5fggatp5ji3hho4

Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes

S. Sedwards, T. Mazza
2007 Bioinformatics  
Discrete stochastic simulation of molecular kinetics potentially offers the most accurate representation of cell dynamics.  ...  It is possible to represent compartments and membrane proteins in a nominal way with many mathematical formalisms used in systems biology, however few explicitly model the topology of the membranes themselves  ...  Such reduction may be a necessity if the structure of the system is unknown, or may be used to gain efficiency when the structure is unimportant.  ... 
doi:10.1093/bioinformatics/btm416 pmid:17855418 fatcat:o2cxrvkw2be5hoz4dacjlm6via

Stochastic P systems and the simulation of biochemical processes with dynamic compartments

Antoine Spicher, Olivier Michel, Mikolaj Cieslak, Jean-Louis Giavitto, Przemyslaw Prusinkiewicz
2008 Biosystems (Amsterdam. Print)  
We introduce a sequential rewriting strategy for P systems based on Gillespie's stochastic simulation algorithm, and show that the resulting formalism of stochastic P systems makes it possible to simulate  ...  biochemical processes in dynamically changing, nested compartments.  ...  The support of the Centre National de la Recherche Scientifique ACI grant "NANOPROG" to O.M., and the Natural Sciences and Engineering Research Council of Canada Discovery Grant RGP 130084 to P.P. is gratefully  ... 
doi:10.1016/j.biosystems.2006.12.009 pmid:17728055 fatcat:mr2ksee3rrhmhp23u5z5flzefm

Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology [chapter]

Jonathan Blakes, Jamie Twycross, Savas Konur, Francisco Jose Romero-Campero, Natalio Krasnogor, Marian Gheorghe
2013 Emergence, Complexity and Computation  
Its capability for building, analysing and optimising large spatially discrete and stochastic models of multicellular systems makes it a useful, coherent and comprehensive in silico tool in systems and  ...  This chapter gives an overview of an integrated software suite, the Infobiotics Workbench, which is based on a novel spatial discrete-stochastic P systems modelling framework.  ...  Some parts of this paper are based on the first authors PhD thesis [13] .  ... 
doi:10.1007/978-3-319-03191-0_1 fatcat:vz4edynpzbglxiyg23evljxeqi

On Parallelizing On-Line Statistics for Stochastic Biological Simulations [chapter]

Marco Aldinucci, Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Eva Sciacca, Salvatore Spinella, Massimo Torquati, Angelo Troina
2012 Lecture Notes in Computer Science  
This work concerns a general technique to enrich parallel version of stochastic simulators for biological systems with tools for online statistical analysis of the results.  ...  The simulator and the on-line analysis were validated on large multi-core platforms and representative proof-of-concept biological systems.  ...  biological simulations.  ... 
doi:10.1007/978-3-642-29740-3_2 fatcat:mkwlyv5xjvbnbpjijgnn23s4w4

Experimenting the Simulation Strategy of Membrane Computing with Gillespie Algorithm by Using Two Biological Case Studies

2010 Journal of Computer Science  
Conclusion: The simulation strategy of membrane computing with Gillespie algorithm able to preserve the stochastic behavior of biological systems that absent in the deterministic approach of ordinary differential  ...  With Gillespie simulation of membrane computing model of TGF-β, the movement of objects from one compartment to another and the changes of concentration of objects in the specific compartments at each  ...  This is because the Gillespie simulator only able to capture the basic structure of biological systems.  ... 
doi:10.3844/jcssp.2010.525.535 fatcat:6vauwl6p5zfqzobwcupwx7uo54

Ecological Modelling with the Calculus of Wrapped Compartments [article]

Pablo Ramon, Angelo Troina
2015 arXiv   pre-print
The Calculus of Wrapped Compartments is a framework based on stochastic multiset rewriting in a compartmentalised setting originally developed for the modelling and analysis of biological interactions.  ...  In this paper, we propose to use this calculus for the description of ecological systems and we provide the modelling guidelines to encode within the calculus some of the main interactions leading ecosystems  ...  Namely, CWC is able to model and simulate: (i) multilevel systems, (ii) stochastic dynamics, (iii) explicit spatial systems.  ... 
arXiv:1505.01985v1 fatcat:ot5kj5md6rcuvbju74riboipeu

Spatial modeling in cell biology at multiple levels

Arne T. Bittig, Adelinde M. Uhrmacher
2010 Proceedings of the 2010 Winter Simulation Conference  
As modeling is concerned with abstraction, multi-level modeling touches at the core of modeling and simulation.  ...  of the system.  ...  Approaches that allow representation of at least compartmental space include cBNGL and the Language for Biological Systems (LBS).  ... 
doi:10.1109/wsc.2010.5679125 dblp:conf/wsc/BittigU10 fatcat:kiytb3a2r5cfncxsbh75ftnpwq
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