Problem-solving environments for biological morphogenesis

Simulation is an important tool for understanding developmental mechanisms, but the technology is often too complex for biologists lacking higher computational skills. Using a tiered architecture, the developers of these problem-solving environment (PSE) prototypes ensure accessibility for users at all skill levels.

[1]  Peter M. A. Sloot,et al.  Implementation aspects of 3d lattice-bgk: Boundaries, accuracy and a new fast relaxation method , 1999 .

[2]  Roeland M. H. Merks,et al.  Polyp oriented modelling of coral growth. , 2004, Journal of theoretical biology.

[3]  G. R. Mcghee,et al.  Theoretical Morphology: The Concept and Its Applications , 1998 .

[4]  S. Kauffman.  Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.

[5]  P. Hogeweg,et al.  Evolving mechanisms of morphogenesis: on the interplay between differential adhesion and cell differentiation. , 2000, Journal of theoretical biology.

[6]  Jesús A. Izaguirre,et al.  A framework for three-dimensional simulation of morphogenesis , 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[7]  Peter M. A. Sloot,et al.  Implementation Aspects of 3D Lattice-BGK: Boundaries, Accuracy, and a New Fast Relaxation Method , 1999 .

[8]  James R. Rice,et al.  From Scientific Software Libraries to Problem Solving Environments John R. Rice , 1996 .

[9]  P. Hogeweg,et al.  How amoeboids self-organize into a fruiting body: Multicellular coordination in Dictyostelium discoideum , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Roeland M. H. Merks,et al.  A cell-centered approach to developmental biology , 2005 .

[11]  Jaap A. Kaandorp,et al.  The Algorithmic Beauty of Seaweeds, Sponges and Corals , 2001, The Virtual Laboratory.

[12]  Sauro Succi,et al.  Applying the lattice Boltzmann equation to multiscale fluid problems , 2001, Comput. Sci. Eng..

[13]  Roeland M. H. Merks,et al.  Morphogenesis of the branching reef coral Madracis mirabilis , 2005, Proceedings of the Royal Society B: Biological Sciences.

[14]  L. Sander.  Diffusion-limited aggregation: A kinetic critical phenomenon? , 2000 .

[15]  Paulien Hogeweg,et al.  Computing an organism: on the interface between informatic and dynamic processes. , 2002, Bio Systems.

[16]  Peter M. A. Sloot,et al.  The moment propagation method for advection-diffusion in the lattice Boltzmann method: validation and péclet number limits , 2002 .

[17]  L. Segel,et al.  Computing an organism , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Roeland M. H. Merks,et al.  Models of coral growth: spontaneous branching, compactification and the Laplacian growth assumption. , 2003, Journal of theoretical biology.