Generating database representations of L-systems in virtual plant applications
Yi‐Ping Phoebe Chen · The University of Queensland · 2000
This research covers an aspect of biological informatics, that is the marriage of information technology and biology, involving the study of real world phenomena using virtual plants derived from L-systems simulation. L-systems were introduced in 1968 by Aristid Lindenmayer as a mathematical model of multicellular organisms. Not much consideration has been given to the problem of persistent storage for simulations of such systems. Current approaches to querying data generated by L-systems for scientific experiments, simulations, and measurements, are also inadequate. To address these problems the research in this thesis presents a generic approach towards data modelling providing tools (L-DBM) for L-systems. These tools will exploit one of the major strengths of the relational model, its ability to express complex operations relativity straight-forwardly. In particular, this thesis shows how database schemata for L-system productions can be automatically derived, and how their populations can be computed from L-systems strings. This thesis further describes the idea of pre-computing derived attributes capturing recursive structures in the original L-systems using compiler techniques. This simplifies the formalism of complex queries considerately. A. method for establishing a correspondence between biologists' terms and compiler generated terms is supplied, thus contributing to a biologist-friendly computing environment. This environment also includes a visual query interface. The approach chosen is generic. Once an L-DBM gets a specific L-systems production and its declarations, it can generate the specific schema for both simple correspondence terminology and also complex recursive attributes and relationships. The same correspondence applies to any L-systems using the same vocabulary. Once established it can be used to support an entire research program. Hence, this research provides a generic solution for all kinds of L-systems.