The Cell Programming Language

In developmental biology, modeling and simulation play an important role in understanding cellular behavior. This article includes a review of the general models of development that are based on cellular interaction. Inspired by these models, we suggest a simple language, the Cell Programming Language (CPL), to write computer programs to describe this developmental behavior. These programs are an estimate of the minimal information needed to model realistically such developmental systems. Using these programs, it is possible to simulate and visualize cell behavior. We have employed CPL to model the following: aggregation in cellular slime mold in response to a chemotactic agent, cellular segregation and engulfment due to differential adhesion, and precartilage formation in vertebrate limbs. We believe CPL is a useful tool for developing, understanding, and checking biological models.

[1]  D R Soll,et al.  Behavior of Dictyostelium amoebae is regulated primarily by the temporal dynamic of the natural cAMP wave. , 1992, Cell motility and the cytoskeleton.

[2]  D. A. Ede,et al.  A model generating the pattern of cartilage skeletal elements in the embryonic chick limb. , 1975, Journal of theoretical biology.

[3]  G B Ermentrout,et al.  Cellular automata approaches to biological modeling. , 1993, Journal of theoretical biology.

[4]  H. Swinney,et al.  Transition from a uniform state to hexagonal and striped Turing patterns , 1991, Nature.

[5]  Tommaso Toffoli,et al.  Cellular automata machines - a new environment for modeling , 1987, MIT Press series in scientific computation.

[6]  Robert Ransom.  Computers and embryos: Models in developmental biology , 1981 .

[7]  H. V. Wilson.  On some phenomena of coalescence and regeneration in sponges , 1907 .

[8]  J. Dana Eckart,et al.  A cellular automata simulation system , 1991, SIGP.

[9]  David H. Sharp,et al.  A connectionist model of development. , 1991, Journal of theoretical biology.

[10]  M S Steinberg.  Cell-cell recognition in multicellular assembly: levels of specificity. , 1978, Symposia of the Society for Experimental Biology.

[11]  P Agarwal.  Cellular segregation and engulfment simulations using the cell programming language. , 1995, Journal of theoretical biology.

[12]  L. Wolpert.  Developmental Biology , 1968, Nature.

[13]  J. Davies,et al.  Molecular Biology of the Cell , 1983, Bristol Medico-Chirurgical Journal.

[14]  Kessler,et al.  Pattern formation in Dictyostelium via the dynamics of cooperative biological entities. , 1993, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[15]  F. Alcântara,et al.  Signal propagation during aggregation in the slime mould Dictyostelium discoideum. , 1974, Journal of general microbiology.

[16]  Malcolm S. Steinberg,et al.  Reconstruction of Tissues by Dissociated Cells , 1963 .

[17]  P. Agarwal,et al.  Cell-based Computer Models in Developmental Biology , 1993 .

[18]  H. Meinhardt.  Models of biological pattern formation , 1982 .

[19]  P. Alberch,et al.  The mechanical basis of morphogenesis. I. Epithelial folding and invagination. , 1981, Developmental biology.

[20]  Y. J. Tejwani,et al.  Robot vision , 1989, IEEE International Symposium on Circuits and Systems,.

[21]  Stuart A. Newman,et al.  Role of transforming growth factor-β in chondrogenic pattern formation in the embryonic limb: Stimulation of mesenchymal condensation and fibronectin gene expression by exogenenous TGF-β and evidence for endogenous TGF-β-like activity , 1991 .

[22]  P. Devreotes,et al.  Adenosine 3',5'-monophosphate waves in Dictyostelium discoideum: a demonstration by isotope dilution--fluorography. , 1981, Science.

[23]  Pankaj Agarwal,et al.  Simulation of aggregation in Dictyostelium using the Cell Programming Language , 1994, Comput. Appl. Biosci..

[24]  M. S. Steinberg,et al.  Does differential adhesion govern self-assembly processes in histogenesis? Equilibrium configurations and the emergence of a hierarchy among populations of embryonic cells. , 1970, The Journal of experimental zoology.

[25]  Hans B. Sieburg,et al.  The Cellular Device Machine Development System for Modeling Biology on the Computer , 1991, Complex Syst..

[26]  H L Frisch,et al.  Dynamics of skeletal pattern formation in developing chick limb. , 1979, Science.

[27]  S A Newman,et al.  The mechanism of precartilage mesenchymal condensation: a major role for interaction of the cell surface with the amino-terminal heparin-binding domain of fibronectin. , 1989, Developmental biology.

[28]  R Gordon.  On stochastic growth and form. , 1966, Proceedings of the National Academy of Sciences of the United States of America.

[29]  George D. Mostow,et al.  Mathematical models for cell rearrangement , 1975 .

[30]  A. M. Turing,et al.  The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.

[31]  C. Waddington,et al.  Principles of development and differentiation , 1956 .

[32]  M. Sussman,et al.  Cellular Slime Molds , 1974 .

[33]  S A Newman,et al.  Lineage and pattern in the developing vertebrate limb. , 1988, Trends in genetics : TIG.

[34]  S A Newman,et al.  Morphogenetic differences between fore and hind limb precartilage mesenchyme: relation to mechanisms of skeletal pattern formation. , 1994, Developmental biology.

[35]  Przemyslaw Prusinkiewicz,et al.  The Algorithmic Beauty of Plants , 1990, The Virtual Laboratory.

[36]  Przemyslaw Prusinkiewicz,et al.  Visual Models of Morphogenesis , 1993, Artificial Life.

[37]  Bjarne Stroustrup,et al.  C++ Programming Language , 1986, IEEE Softw..

[38]  D'arcy W. Thompson,et al.  On Growth and Form , 1917, Nature.

[39]  N S Goel,et al.  Computer simulation of engulfment and other movements of embryonic tissues. , 1978, Journal of theoretical biology.

[40]  S. A. MacKay.  Computer simulation of aggregation in Dictyostelium discoideum. , 1978, Journal of cell science.

[41]  N. Rashevsky,et al.  Mathematical biology , 1961, Connecticut medicine.