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Authors: Paweł Bednarz and Bartek Wilczyński

Affiliation: University of Warsaw, Poland

Keyword(s): Stochastic Simulation, Cellular Population, Regulatory Network, GPU Computing.

Related Ontology Subjects/Areas/Topics: Biological Systems ; Complex Systems Modeling and Simulation ; Simulation and Modeling

Abstract: We present a new approach to high level stochastic simulations of cell populations. The proposed method employs the Stochastic Logical Network (SLN) method for simulating independent regulatory processes occurring in individual cells allowing for efficient simulations of systems consisting of thousands of cells. The stochastic logical network model is extended to account for not only regulatory control of gene expression but other related processes such as: inter-cellular signaling, cell division and programmed cell death. In the paper, we present the method and several case studies, where the proposed approach is used to provide models of biological phenomena. These examples include community effect in gene expression, the role of negative feedback in growing epithelial cell lineage and the role of asymmetric cell division in cell fate choices. We present also an efficient implementation of the method using GPU computing and show that its performance is significantly better than tha t using CPU. (More)

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Paper citation in several formats:
Bednarz, P. and Wilczyński, B. (2012). Modeling Cell Populations in Development using Individual Stochastic Regulatory Networks. In Proceedings of the 2nd International Conference on Simulation and Modeling Methodologies, Technologies and Applications - SIMULTECH; ISBN 978-989-8565-20-4; ISSN 2184-2841, SciTePress, pages 334-340. DOI: 10.5220/0004060703340340

@conference{simultech12,
author={Paweł Bednarz. and Bartek Wilczyński.},
title={Modeling Cell Populations in Development using Individual Stochastic Regulatory Networks},
booktitle={Proceedings of the 2nd International Conference on Simulation and Modeling Methodologies, Technologies and Applications - SIMULTECH},
year={2012},
pages={334-340},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004060703340340},
isbn={978-989-8565-20-4},
issn={2184-2841},
}

TY - CONF

JO - Proceedings of the 2nd International Conference on Simulation and Modeling Methodologies, Technologies and Applications - SIMULTECH
TI - Modeling Cell Populations in Development using Individual Stochastic Regulatory Networks
SN - 978-989-8565-20-4
IS - 2184-2841
AU - Bednarz, P.
AU - Wilczyński, B.
PY - 2012
SP - 334
EP - 340
DO - 10.5220/0004060703340340
PB - SciTePress

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