Integrated biological systems modeling: challenges and opportunities

doi:10.1007/s11704-007-0011-9

Front Comput Sci Chin

2009, Vol. 3

Issue (1) : 92-100 https://doi.org/10.1007/s11704-007-0011-9

RESEARCH ARTICLE

Integrated biological systems modeling: challenges and opportunities

Jialiang WU¹, Eberhard VOIT^2,3(

)

1. Department of Mathematics, Bioinformatics Program, Georgia Institute of Technology, Atlanta, GA 0332, USA; 2. Integrative BioSystems Institute, Georgia Institute of Technology, Atlanta, GA 30332, USA; 3. The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, tlanta, GA 30332, USA

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Abstract

Most biological systems are by nature hybrids consist of interacting discrete and continuous components, which may even operate on different time scales. Therefore, it is desirable to establish modeling frameworks that are capable of combining deterministic and stochastic, discrete and continuous, as well as multi-timescale features. In the context of molecular systems biology, an example for the need of such a combination is the investigation of integrated biological pathways that contain gene regulatory, metabolic and signaling components, which may operate on different time scales and involve on-off switches as well as stochastic effects. The implementation of integrated hybrid systems is not trivial because most software is limited to one or the other of the dichotomies above. In this study, we first review the motivation for hybrid modeling. Secondly, by using the example of a toggle switch model, we illustrate a recently developed modeling framework that is based on the combination of biochemical systems theory (BST) and hybrid functional Petri nets (HFPN). Finally, we discuss remaining challenges and future opportunities.

Keywords biochemical systems theory Petri net hybrid modeling hybrid functional Petri net toggle switch canonical modeling stochastic delay

Corresponding Author(s): VOIT Eberhard,Email:gtg337v@mail.gatech. edu, eberhard. voit@bme.gatech.edu

Issue Date: 05 March 2009

Cite this article:

Jialiang WU,Eberhard VOIT. Integrated biological systems modeling: challenges and opportunities[J]. Front Comput Sci Chin, 2009, 3(1): 92-100.

URL:

https://academic.hep.com.cn/fcs/EN/10.1007/s11704-007-0011-9
https://academic.hep.com.cn/fcs/EN/Y2009/V3/I1/92

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