On the use of organisation modelling techniques to address biological organisation

Abstract

This paper explores how the dynamics of complex biological processes can be modelled and simulated as an organisation of multiple agents. This modelling perspective identifies organisational structure occurring in complex decentralised processes and handles complexity of the analysis of the dynamics by structuring these dynamics according to an organisational structure. More specifically, dynamic properties at different levels of aggregation in the organisational structure are identified, and related to each other according to the organisational structure. The applicability of this organisational modelling approach to address complexity in biological context is illustrated by two case studies: the organisation of intracellular processes and the organisation of the circulatory system.

Past–future separation and normal forms in temporal predicate logic specifications

“…Often such a phenomenon can be conceptualised at different aggregation levels that can be identified. For example, for bacterial behaviour, the level of the bacterium as a whole, the level of its two main subprocesses control and metabolism, the level of subprocesses of these, transcription and translation, respectively, and catabolism, anabolism and transport, and the level of specific chemical reactions within such subprocesses; e.g., (Bosse, Jonker, and Treur, 2007). Modelling such phenomena according to different aggregation levels means that their dynamics is described by specifications at these different levels, connected by logical interlevel relations expressing, for example, that a certain specification at one aggregation level is entailed by a specification at the next lower level; e.g., .…”

Agent-oriented modeling of the dynamics of biological organisms

“…This question is directed to the relationship between the descriptions of dynamics at two different aggregation levels (agent-internal and externally observable agent behaviour). For the multi-agent case, addressed in [4] also for the different levels of aggregation in a multi-agent organisation, comparable interlevel relationships can be identified.…”