Ole Kniemeyer

Relational growth grammars – a graph rewriting approach to dynamical systems with a dynamical structure

Relational growth grammars (RGG) are a graph rewriting formalism which extends the notations and semantics of Lindenmayer systems and which allows the specification of dynamical processes on dynamical structures, particularly in biological and chemical applications. RGG were embedded in the language XL, combining rule-based and conventional object-oriented constructions. Key features of RGG and of the software GroIMP (Growth grammar related Interactive Modelling Platform) are listed. Five simple examples are shown which demonstrate the essential ideas and possibilities of RGG: signal propagation in a network, cellular automata, globally-sensitive growth of a plant, a chemical prime number generator, and a polymerisation model using a simple mass-spring kinetics.

The Modelling Platform GroIMP and the Programming Language XL

We present the open-source modelling platform GroIMP and the rule-based programming language XL. The underlying representation of data within GroIMP is a graph, which can be transformed by rules specified in XL. The principal field of application is modelling of virtual plants, but the system can also be used for a lot of other applications.

Relational Growth Grammars --- A Parallel Graph Transformation Approach with Applications in Biology and Architecture

We present the formalism of relational growth grammars. They are a variant of graph grammars with a principal application for plant modelling, where they extend the well-established, but limited formalism of L-systems. The main property is the application of rules in parallel, motivated by the fact that life is fundamentally parallel. A further speciality is the dynamic creation of right-hand sides on rule application. Relational growth grammars have been successfully used not only for plant modelling, but also to model general 3D structures or systems of Artificial Life. We illustrate these applications at several examples, all being implemented using our programming language XL which extends Java and provides an implementation of relational growth grammars.

Representation of Genotype and Phenotype in a Coherent Framework Based on Extended L-Systems

A formal language approach for the specification of ALife models is presented. “Relational Growth Grammars” incorporate rule-based, procedural and object-oriented concepts. By enabling parametric Lindenmayer systems to rewrite multiscaled graphs, it becomes possible to represent genes, plant organs and populations as well as developmental aspects of these entities in a common formal framework. Genetic operators (mutation, crossing-over, selection) take the form of simple graph rewrite rules. This is illustrated using Richard Dawkins’ “biomorphs”, whereas other applications are briefly sketched. The formalism is implemented as part of an interactive software platform.

XL4C4D - Adding the Graph Transformation Language XL to CINEMA 4D

A plug-in for the 3D modeling application CINEMA 4D is presented which allows to use the graph transformation language XL to transform the 3D scene graph of CINEMA 4D. XL extends Java by graph query and rewrite facilities via a data model interface, the default rewrite mechanism is that of relational growth grammars which are based on parallel single-pushout derivations. We illustrate the plug-in at several examples, some of which make use of advanced 3D features.

FOREST STRUCTURE, COMPETITION AND PLANT-HERBIVORE INTERACTION MODELLED WITH RELATIONAL GROWTH GRAMMARS

Relačne rastove gramatiky su systemy prepisovacich pravidiel (grafove gramatiky) s grafickou interpretaciou. Umožňuju spatnu vazbu z vytvorenych virtualnych 3D štruktur do ďalšieho procesu aplikacie pravidiel. Ich použitim je možne kombinovať morfologicke (geneticky viazane) rastove pravidla s environmentalnym vplyvom a s funkciami hodnotiacimi konkurenčnu situaciu jednotlivych rastlin. Relačne rastove gramatiky su preto idealnym nastrojom na presnu špecifikaciu funkčno-štrukturalnych modelov rastu a architektury rastlin. Dynamika vyvoja porastu v takychto modeloch vyplyva z čisto lokalnej aplikacie pravidiel. Predbežne vysledky su ukazane na troch aplikaciach modelovania lesneho ekosystemu: (a) Tvorba nepravidelnych porastovych štruktur, (b) simulacia vplyvov konkurencie na vyvoj polomeru koruny a vyslednu dynamiku porastu a (c) modelovanie interakcie medzi stromami a herbivormi, založene na energetickych narokoch individualnych rastlin a živočichov. Posledny model zahŕňa geneticky prenos a evoluciu potravnej strategie živočichov. Softverovy system GroIMP (Growthgrammar related Interactive Modelling Platform), open source projekt pristupny na www.grogra.de, bol navrhnuty na interpretaciu relačnych rastovych gramatik v objektovo orientovanom ramci. Tiež služi na vizualizaciu vyslednych priestorovych štruktur. Kod, spustiteľny v GroIMPe, je pre vyššie spomenute modely kompletne dokumentovany a vysvetleny. Dufame, že uvedenymi prikladmi budeme motivovať čitateľov k použivaniu na pravidlach založenych štrukturalnych modelov v ekologii lesa. Relational Growth Grammars are systems of rewriting rules (graph grammars) with graphical interpretation. They allow a feedback from the created virtual 3-d structures to the subsequent ruleapplication process. Using them it is possible to combine morphological (genetically fixed) growth rules with environmental impact and with functions evaluating the competitive situation of individual plants. Relational Growth Grammars are thus an ideal tool for precise specification of functional-structural models of plant growth and architecture. The dynamics of stand development in such models results from purely local rule application. Preliminary results are shown for three applications in forest-ecosystem modelling: (a) Creation of irregular stand structures, (b) simulation of competitive effects on crown radius development and resulting stand dynamics, and (c) modelling the interaction between trees and herbivores, based on the energy budgets of the individual plants and animals. The latter model includes genetical transfer and evolution of the foraging strategy of the animals. The software system GroIMP (Growth-grammar related Interactive Modelling Platform), an open source project available under www. grogra.de, was designed to interpret Relational Growth Grammars in an object-oriented framework. It also serves to visualize the resulting spatial structures. The code, executable by GroIMP, for the abovementioned models is completely documented and explained. By our examples, we hope to motivate the readers to use rule-based structural models in forest ecology.