The algorithmic beauty of seaweeds, sponges, and corals
The algorithmic beauty of seaweeds, sponges, and corals
From Scientific Software Libraries to Problem-Solving Environments
IEEE Computational Science & Engineering
Applying the Lattice Boltzmann Equation to Multiscale Fluid Problems
Computing in Science and Engineering
A Framework for Three-Dimensional Simulation of Morphogenesis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development
Computing in Science and Engineering
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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.