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Issue No. 01 - January/February (2006 vol. 8)
ISSN: 1521-9615
pp: 61-72
Roeland M.H. Merks , University of Amsterdam
Alfons G. Hoekstra , University of Amsterdam
Jaap A. Kaandorp , University of Amsterdam
Peter M.A. Sloot , University of Amsterdam
Paulien Hogeweg , Utrecht University
Simulation is becoming an important tool to understand developmental mechanisms. In this article we discuss two prototypical problem solving environments (PSEs) for biological development. The first PSE implements a three-dimensional model of coral growth and enables marine biologists to construct and analyze simulations with high-level concepts. The second PSE helps explore the interplay between genetic information and physical mechanisms during embryonic development of multicellular organisms and its evolution. The two PSEs have contrasting demands. A single simulation of a coral and its environment is very expensive. Thus the PSE manages single simulation set-ups and streamlines analysis of single simulations. The study of biological evolution requires high simulation throughput, and for this reason we use a simple, efficient two-dimensional model of biological development. The modular architecture of the PSEs gives advanced users full control, while keeping them accessible to the computationally unskilled.
modeling morphogenesis, coral growth, developmental biology, computational biology, problem solving environment

J. A. Kaandorp, P. Hogeweg, P. M. Sloot, R. M. Merks and A. G. Hoekstra, "Problem-Solving Environments for Biological Morphogenesis," in Computing in Science & Engineering, vol. 8, no. , pp. 61-72, 2006.
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