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Understanding of the links between coral reef ecosystems, the goods and services they provide to people, and the wellbeing of human societies.


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Examining the multi-scale dynamics of reefs, from population dynamics to macroevolution


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Coral Reef Studies

From 2005 to 2022, the main node of the ARC Centre of Excellence for Coral Reef Studies was headquartered at James Cook University in Townsville, Queensland (Australia)

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Computational modelling of corals: from genes to colony


Wednesday 22 August 2007,  3.00pm

ARC Centre of Excellence for Coral Reef Studies Conference Room, JCU – to be video-linked to Centre for Marine Studies, UQ
A/Prof Jaap A. Kaandorp, University of Amsterdam

Jaap A. Kaandorp received his MS, with distinction, in biology (main subject marine biology) in 1985 and a PhD (subject modelling growth and form of marine organisms) in computer science and mathematics in 1992, both from the University of Amsterdam. He has worked from 1985 -1987 as a researcher at the Centre of Computer Science and Mathematics in Amsterdam. In 1992 he did research as a postdoctoral fellow, on a Government of Canada Award, at the Department of Computer Science of the University of Calgary in Canada. Currently he works as an associate professor at the Section Computational Science of the Faculty of Mathematics, Computer Science, Physics & Astronomy of the University of Amsterdam. His research interests are: morphogenesis, marine sessile organisms, evolutionary processes, modelling and simulation of developmental regulatory networks and metabolic pathways, modelling and simulation of growth and form, and biomechanics. Jaap has done some groundbreaking work on modelling the growth of coral colonies, and has written two books: “Fractal modelling growth and form in biology” (Springer, 1994) and “The algorithmic beauty of seaweeds, sponges and corals” (Springer, 2001). Jaap’s work is both unique and biologically relevant, and he is an expert in presenting his work to largely non-mathematical audiences.


Within the metazoans, sponges and cnidarians represent the phyla with the simplest body plan and a relatively simple regulatory network controlling the development. This makes these organisms an excellent case study for understanding morphogenesis and the physical translation of the genetic information into a growth form, using a combination of biomechanical models of growth and form and a model of the spatial and temporal expression of developmental genes. During this talk we will give an overview of the ongoing work at the Section Computational Science on modelling and simulation of growth and form in scleractinian corals. For modelling growth and form of corals it is required to combine models at very different spatio-temporal scales: gene regulation and cellular level, calcification, physiology (respiration and photosynthesis), growth of the coral skeleton and the impact of the physical environment (water movement and availability of light). We will briefly discuss:

  • Modelling spatio-temporal gene expression patterns and cell movement in early  development  of  the cnidarians Nematostella vectensis  and Acropora millepora and methods for inferring gene networks from gene expression data based on mathematical models of early development in Drosophila melanogaster
  • Some preliminary results on modelling genetic regulation of calcification in Acropora millepora and the analysis of micro-Computer Tomography scans of corallites of Madracis sp.
  • Modelling of calcification (calcium and carbonate physiology, photosynthesis)(If time permits: ) Modelling accretive growth of Madracis sp colonies and the impact of the physical environment (advection-diffusion and light), methods for the morphological analysis and comparison of three-dimensional images of coral colonies obtained with Computer Tomography scanning and simulated morphologies and methods for the genetic comparison of different coral colonies.


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