Analysis and Prototyping of Biological Systems: the Abstract Biological Process Model
The aim of a biological model is to understand the
integrated structure and behavior of complex biological systems as a
function of the underlying molecular networks to achieve simulation
and forecast of their operation. Although several approaches have
been introduced to take into account structural and environment
related features, relatively little attention has been given to represent
the behavior of biological systems. The Abstract Biological Process
(ABP) model illustrated in this paper is an object-oriented model
based on UML (the standard object-oriented language). Its main
objective is to bring into focus the functional aspects of the
biological system under analysis.
[1] Stein, L. "Integrating biological databases" Nat. Rev. Genet., 4, 337-
345, 2003.
[2] P. E. Midford "Ontologies for Behavior" BIOINFORMATICS, Vol. 20
no. 18, 2004, pp. 3700-3701.
[3] Rumbaugh, J., Jacobson, I. and Booch, G.: "The Unified Modeling
Language Reference Manual"; Addison Wesley, 1999.
[4] D.Shegogue and W.J. Zheng "Object-oriented modeling of the SARS
coronavirus" BIOINFORMATICS, Vol. 21 no. 10, 2005, pages 2502-
2509.
[5] B.P. Zeigler, H. Praehofer, T.G. Kim Theory of Modeling and
Simulation, 2nd Ed., Academic press, 2000.
[6] Chang, Liang-Cheng and Yi-Ming Tu "Attempt to Integrate System
Dynamics and UML in Business Process Modeling" Proceedings
The 23rd International Conference of the System Dynamics Society
July 17-21, 2005 Boston.
[7] Sterman, J. Business Dynamics: Systems Thinking and Modeling for a
Complex World, McGraw Hill, 2000.
[1] Stein, L. "Integrating biological databases" Nat. Rev. Genet., 4, 337-
345, 2003.
[2] P. E. Midford "Ontologies for Behavior" BIOINFORMATICS, Vol. 20
no. 18, 2004, pp. 3700-3701.
[3] Rumbaugh, J., Jacobson, I. and Booch, G.: "The Unified Modeling
Language Reference Manual"; Addison Wesley, 1999.
[4] D.Shegogue and W.J. Zheng "Object-oriented modeling of the SARS
coronavirus" BIOINFORMATICS, Vol. 21 no. 10, 2005, pages 2502-
2509.
[5] B.P. Zeigler, H. Praehofer, T.G. Kim Theory of Modeling and
Simulation, 2nd Ed., Academic press, 2000.
[6] Chang, Liang-Cheng and Yi-Ming Tu "Attempt to Integrate System
Dynamics and UML in Business Process Modeling" Proceedings
The 23rd International Conference of the System Dynamics Society
July 17-21, 2005 Boston.
[7] Sterman, J. Business Dynamics: Systems Thinking and Modeling for a
Complex World, McGraw Hill, 2000.
@article{"International Journal of Biological, Life and Agricultural Sciences:61323", author = "Antonio Di Leva and Roberto Berchi and Gianpiero Pescarmona and Michele Sonnessa", title = "Analysis and Prototyping of Biological Systems: the Abstract Biological Process Model", abstract = "The aim of a biological model is to understand the
integrated structure and behavior of complex biological systems as a
function of the underlying molecular networks to achieve simulation
and forecast of their operation. Although several approaches have
been introduced to take into account structural and environment
related features, relatively little attention has been given to represent
the behavior of biological systems. The Abstract Biological Process
(ABP) model illustrated in this paper is an object-oriented model
based on UML (the standard object-oriented language). Its main
objective is to bring into focus the functional aspects of the
biological system under analysis.", keywords = "Biological processes, system dynamics, systemmodeling, UML.", volume = "1", number = "10", pages = "126-6", }