Re: biological ABM modelling publications

[Mark H. Butler]

Hi Trey

> Hi all,
>       I'm a grad student trying to convince potential advisor(s) of the
utility
> of agent based modeling systems in obtaining a better understanding how
> intricate patterns of gene expression are formed in developing tissues of
> embryos.  They (quite understanably) want to see publications in "the
> field".  Can somebody please help me?  

Tissue modelling is my area of study - unfortunately there doesn't seem to
be a lot of agent based work on it. In my experience people are
concentrating on neural stuff or pde based models of development. Here are
some ideas:

1. "Cellular automata approaches to biological modelling", Bard Ermentrout
and Leah Edelstein-Keshet, Journal Of Theoretical Biology, 1993, vol.160,
97-133. This reviews some other papers on developmental biology, CA models
for shell patterning, fibroblast aggregation and occular dominance columns.

2. Pankaj Agarwal has written a language called CPL for simulation of cell
behaviour. He's used this to do some create some developmental models of
tissues. I think he's got some more information on his web page:

http://www.ibc.wustl.edu/~agarwal/cpl/
http://www.ibc.wustl.edu/~agarwal
His email address is address@hidden

3. Narenda S. Goel and Richard L. Thompson at Department of Systems
Science, Binghamton Washington have been working on this area but their
computer simulations aren't necessarily agent based. A review of their work
can be found in Pankaj Agarwal's PhD thesis.  A good paper is:
"Organization of biological systems: some principles and models",
International Review of Cytology, Vol. 103, 1986 p.1-88

4. Moshe Sipper (I think he's at Lausanne in Switzerland - try querying
Altavista with "moshe sipper" host:.ch) has done some work on heterogeneous
cellular automata for tissue models. He's got the paper on his webpage, but
the reference is "Studying Artificial Life Using a Simple General Cellular
Model", Artificial Life Journal, Volume 2, Number 1, pages 1-35, 1995

5. Richard Stark (address@hidden) contributed a chapter to my
supervisor's book: "Artificial Tissue Models" in "Computing With Biological
Models", Edited by Ray Paton, Chapman and Hall 1994. His work is network /
graph based but he does consider some development biology.

6. "Generalised Context-Sensitive Cell Systems" by Maria Lantin and David
Fracchia, Proceedings of IPCAT'95 looks at L-system / CA models of
development biology. Try emailing address@hidden as I don't know if this
made it in to the published proceedings - if it did it will be in
Computation in cellular and Molecular Biological Systems, Edited by R
Cuthbertson, M. Holcombe and R. Paton, World Scientific

7."On topological simulations in developmental biology", Sharon
Duvdevani-Bar and Lee Segel, Journal of Theorertical Biology 1994, vol.166
p.33-50. This is computer based rather than agent based. 

8."Coupled maps lattices as theoretical models for gene-network dynamics",
Franco Bignone looks at the relation between gene and cell-cell
interactions. This was presented at IPCAT'95 but didn't make it into the
published proceedings. Try emailing address@hidden

9. "Tissue Automat: An A-Life form with feedback", G. Zajicek, email
address@hidden, presented at IPCAT'95 (see 6 for published
reference). This work is looking at models of self-regeneration in tissues
in order to consider pathologies e.g. cancer, cirrhosis etc.

10. Michael A. Arbib, "Automata theory in the context of theoretical
embryology", in Foundations of Mathematical biology, Edited by Robert
Rosen, volume 2, pages 141-215, Academic Press 1972

11. Brian C. Goodwin, "Developing organsims as self-organizing fields", in
Self-organising systems: The emergence of order, edited by F. Eugene Yates,
Plenum press 1987 pp.167-180

12. Ray C. Paton et al, "Computing at the tissue / organ level", in Towards
a Practice of Autonomous systems editied by F. J. Varela and P.Bourgine,
MIT Press 1992.

It might also be worth looking at my 1st year report (on my web page) for
more references. More details of IPCAT can be found on the Liverpool
Biocomputation Group web site.

Hope this helps and I would be interested to hear any suggestions anyone
else might have.

Mark H. Butler
address@hidden
http://www.csc.liv.ac.uk/~mhb
Liverpool Biocomputation Group  http://www.csc.liv.ac.uk/~biocomp


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