what kind of Automata I can use to design Biological Network is it cellular Automata,finite Automata. How can I use them in designing and analysis of network designing. I am using ANIMO a cytoscape tool for designing network using Grammar and Automata does i am in right track and UPPAL checker for analysis. Please brief me as knowing as biologist because very less information is available in tutorials.
Cellular automata and lattice gas automata might provide the kind of support you need if the targeted biological network is of a lattice structure. If the phenomena you seek to model are not well disposed to arrangement upon a lattice, then I suggest you pursue instead network automata, such as Generative Network Automata.
William R. Buckley can you elaborate some of it and how can i use them in modelling Pathways for eg Map kinase pathways.
I recommend 3 fairly "introductory-level" references (links also provided):
With regards to biological network, not really sure what you mean but perhaps a boolean network- cellular automata hybrid? Consider the Chapter 5 of
1. A NEW KIND OF SCIENCE- Stephen Wolfram (2002) [good to also consult the notes at the end of the HARDCOPY book, for more technical aspects]
Lattice gas automata of a kind similar to that suggested by William R. Buckley can be found in:
2. MODELING NATURE WITH CELLULAR AUTOMATA - Gaylord and Nishidate (1996), pp 77-78.
Also another good overview on the potential of cellular automata is Schif's (2007)
3. CELLULAR AUTOMATA- A DISCRETE VIEW OF THE WORLD
http://www.wolframscience.com/nksonline/page-936g-text
https://books.google.com.my/books?id=uXJC2C2sRbIC&lpg=PA237&ots=53BIYnsyri&dq=Modeling%20Nature%20Gaylord%20and%20Nishidate%20%20lattice%20gas&pg=PP1#v=onepage&q=Modeling%20Nature%20Gaylord%20and%20Nishidate%20%20lattice%20gas&f=true
For more specific answers, I believe you need to specify more exactly what you want to model, and especially what aspects of the network the model should simulate. The best automaton model depends very much on these factors.
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