Modeling Cell Populations in Development using Individual Stochastic Regulatory Networks

Paweł Bednarz, Bartek Wilczyński

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 that using CPU.

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Paper Citation


in Harvard Style

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 - Volume 1: SIMULTECH, ISBN 978-989-8565-20-4, pages 334-340. DOI: 10.5220/0004060703340340


in Bibtex Style

@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 - Volume 1: SIMULTECH,},
year={2012},
pages={334-340},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004060703340340},
isbn={978-989-8565-20-4},
}


in EndNote Style

TY - CONF
JO - Proceedings of the 2nd International Conference on Simulation and Modeling Methodologies, Technologies and Applications - Volume 1: SIMULTECH,
TI - Modeling Cell Populations in Development using Individual Stochastic Regulatory Networks
SN - 978-989-8565-20-4
AU - Bednarz P.
AU - Wilczyński B.
PY - 2012
SP - 334
EP - 340
DO - 10.5220/0004060703340340