The Holland Broadcast Language and the Modeling of Biochemical Networks
The Broadcast Language is a programming formalism devised by Holland in 1975, which aims at improving the efficiency of Genetic Algorithms (GAs) during long-term evolution. The key mechanism of the Broadcast Language is to allow GAs to employ an adaptable problem representation. Fixed problem encoding is commonly used by GAs but may limit their performance in particular cases. This paper describes an implementation of the Broadcast Language and its application to modeling biochemical networks. Holland presented the Broadcast Language in his book “Adaptation in Natural and Artificial Systems” where only a description of the language was provided, without any implementation. Our primary motivation for this work was the fact that there is currently no published implementation of the Broadcast Language available. Secondly, no additional examination of the Broadcast Language and its applications can be found in the literature. Holland proposed that the Broadcast Language would be suitable for the modeling of biochemical models. However, he did not support this belief with any experimental work. In this paper, we propose an implementation of the Broadcast Language which is then applied to the modeling of a signal transduction network. We conclude the paper by proposing that with some refinements it will be possible to use the Broadcast Language to evolve biochemical networks in silico.
KeywordsBroadcast Language adaptable representation biochemical networks modeling
Unable to display preview. Download preview PDF.
- 2.Decraene, J.: The Holland Broadcast Language. Technical Report ALL-06-01, Artificial Life Lab, RINCE, School of Electronic Engineering, Dublin City University (2006)Google Scholar
- 4.Groß, D., McMullin, B.: The creation of novelty in artificial chemistries. In: Proceedings of the eighth international conference on Artificial life. ICAL 2003, pp. 400–409. MIT Press, Cambridge (2003)Google Scholar
- 5.Hallinan, J., Wiles, J.: Evolving genetic regulatory networks using an artificial genome. In: Proceedings of the second conference on Asia-Pacific bioinformatics,-vol 29, pp. 291–296 (2004)Google Scholar
- 6.Holland, J.H.: Adaptation in natural and artificial systems. MIT Press, Cambridge (1992)Google Scholar
- 7.Kauffman, S.A.: The Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, Oxford (1993)Google Scholar
- 8.Taylor, T.: Creativity in evolution: individuals, interactions, and environments, pp. 79–108 (2002)Google Scholar