Discrete Event Multi-level Models for Systems Biology

Author(s):  
Adelinde M. Uhrmacher ◽  
Daniela Degenring ◽  
Bernard Zeigler
2006 ◽  
Vol 48 (3) ◽  
Author(s):  
Adelinde Uhrmacher ◽  
Céline Kuttler

SummaryThe creation of models for heterogeneous and complex cellular networks is a central goal of Systems Biology. When modeling a biological network, one may wish to account for certain aspects in detail, while a bird's eye perspective would seem more appropriate for other parts. Multi-level models combine such overview and detail representations. We illustrate multi-level modeling with gene regulation of the Tryptophan operon in E. coli. We review three discrete event modeling formalisms and discuss model design therein: DEVS, STATECHARTS, and stochastic π-CALCULUS. This introductory presentation already reveals some of their respective virtues and shortcomings.


2010 ◽  
Vol 171-172 ◽  
pp. 596-599
Author(s):  
Zhi Hui Wang ◽  
Shang Fu Hao ◽  
Yuan Qiang Wang

The virtual reality technology is a three-dimensional virtual environment composed by computer hardware, software and various of sensors. It creates an unprecedented wealth of content and more fantastic teaching environment which reflects strong advantage in experiment and practice. In accordance with the needs of experiment teaching, multi-level interrupt virtual experiment environment is studied combining with the characteristics of its principle. The experiment environment is based on Tec-xp test box designed and developed by Tsinghua University computer factory. Microsoft Visual C++6.0 language is adopted for software platform development. Seen from the system needs analysis, object-oriented simulation method is adopted for modeling in this experiment environment. Meanwhile combining with computer system features and the characteristics of Computer Organization Principle teaching, the basic theory and methods of discrete event system simulation are used, which make the operation of virtual environment the same as on real device.


2011 ◽  
Vol 26 (S2) ◽  
pp. 2224-2224
Author(s):  
F. Iris

Psychiatric illnesses remain of unclear etiopathogenesis and a variety of them can coexist, partly mimicking each other while contributing to and distorting symptomatic expressions. To understand the processes involved, it is necessary to unravel signalling pathways, complex interaction networks and metabolic alterations involving a plethora of anatomical components. Hence, whatever the nature of the alterations convincingly detected, these must be associated with their most-likely cellular contexts to then have a chance to reverse engineer the events that could have given rise to the observed alterations and predict their most plausible functional consequences. This requires the utilisation of analytical approaches collectively known as “Systems Biology”.Systems biology explores how parts of biological entities function and interact to give rise to the behaviour of the system as a whole. But having said that, what can we actually do?Two broad approaches to systems biology currently exist: the frequently followed mathematical (Bayesian) procedures and the more rarely encountered heuristic approaches.Heuristic modelling plays the role of an architect (defines the nature, the structure, the functionalities and the contextual constrains of a process) while mathematical modelling plays the role of an engineer (reveals the dynamics and robustness of this process while defining the set of parameters sufficient to give rise to similar or very different phenotypes).This talk will explain, through concrete examples, the approaches whereby one can harness heuristic frameworks to produce multi-level models of complex neurobiological processes that can then be independently tested and biologically validated or refuted.


2012 ◽  
Vol 220-223 ◽  
pp. 2975-2982
Author(s):  
Jie Gao ◽  
Yuan Li ◽  
Yong Gang Wang ◽  
Gang Chen

System-level understanding, which provides specific views on the system of interest focusing both on a macro and on a micro view, has been a recurrent theme in systems biology modeling. However only little work has been done to directly support the micro-macro linking explicitly in a modeling formalism. Multi-resolution discrete event systems specification (MR-DEVS) was introduced to model biology at system-level. MR-DEVS can model upward and downward causation and adapt to represent those systems with emergence and controlling relationship between the micro level and macro level in a biological system. Moreover, MR-DEVS is closed under coupling. And so, it can also model biological process at multiply level hierarchically and modularly.


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