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RESEARCH ARTICLE
Contents Vol 35(10)

The rule-based language XL and the modelling environment GroIMP illustrated with simulated tree competition

Reinhard Hemmerling A D , Ole Kniemeyer A B , Dirk Lanwert B , Winfried Kurth A and Gerhard Buck-Sorlin C
+ Author Affiliations
- Author Affiliations

A Brandenburg University of Technology at Cottbus, PO Box 10 13 44, 03013 Cottbus, Germany.

B University of Göttingen, Ecoinformatics, Biometrics and Forest Growth, Büsgenweg 4, 37077 Göttingen, Germany.

C Wageningen UR, Centre for Crop Systems Analysis, Haarweg 333, 6709 RZ Wageningen, The Netherlands.

D Corresponding author. Email: rhemmerl@informatik.tu-cottbus.de

This paper originates from a presentation at the 5th International Workshop on Functional–Structural Plant Models, Napier, New Zealand, November 2007.

Functional Plant Biology 35(10) 739-750 https://doi.org/10.1071/FP08052
Submitted: 7 March 2008  Accepted: 30 September 2008   Published: 11 November 2008

Abstract

The programming language XL (‘eXtended L-system language’) is an extension of Java, which supports the specification and execution of relational growth grammars, a variant of parallel graph grammars. XL is a powerful generalisation of the well-known L-system approach to functional–structural plant modelling. Some features of XL are discussed that are particularly useful for combining structure and function and for querying plant architectural data, and an exemplary functional–structural plant model of young beech trees is presented that is implemented in XL and includes PAR distribution, assimilate allocation and morphological plasticity. Together with a simpler model of spruce trees, this beech model is included in a virtual landscape with a mixed-species forest stand where competition for light occurs. The open-source platform GroIMP was used for the complete model development process and for visualising the results.

Additional keywords: Fagus sylvatica L., forest, L-systems, Picea abies (L.) Karst., radiation model.


Acknowledgements

This research was funded in part by the Deutsche Forschungsgemeinschaft (DFG) under grant Ku 847/6-1. O. Kniemeyer thanks Branislav Sloboda (University of Göttingen) for the opportunity to work as a guest in his department. Special thanks go to Andreas Hotho and Jörn Dreyer from the Knowledge and Data Engineering Group of the University of Kassel for providing us with a high-performance machine for the landscape simulation. We thank SourceForge for hosting GroIMP.


References


Batz GV , Kroll M , Geiß R (2008) First experimental evaluation of search plan driven graph pattern matching. In ‘Applications of graph transformation with industrial relevance – AGTIVE 2007.’ (Eds A Schürr, M Nagel, A Zündorf) pp. 468–483. (Springer: Berlin)

Buck-Sorlin G, Kniemeyer O, Kurth W (2005) Barley morphology, genetics and hormonal regulation of internode elongation modelled by a relational growth grammar. The New Phytologist 166(3), 859–867.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Buck-Sorlin G, Hemmerling R, Kniemeyer O, Burema B, Kurth W (2008) A rule-based model of barley morphogenesis, with special respect to shading and gibberellic acid signal transduction. Annals of Botany 101(8), 1109–1123.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Chelle M, Andrieu B (1998) The nested radiosity model for the distribution of light within plant canopies. Ecological Modelling 111, 75–91.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Chelle M, Andrieu B (1999) Radiative models for architectural modeling. Agronomie 19, 225–240.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Chelle M , Hanan J , Autret H (2004) Lighting virtual crops: the CARIBU solution for open L-systems. In ‘Proceedings of the 4th International Workshop on Functional–Structural Plant Models (FSPM04), Montpellier, France’. (Eds C Godin, J Hanan, W Kurth, et al.) (UMR AMAP: Montpellier, France)

de Reffye P , Houllier F , Blaise F , Fourcaud T (1997) Essai sur les relations entre l’architecture d’un arbre et la grosseur de ses axes végétatifs. In: ‘Modélisation et Simulation de l’Architecture des Végétaux.’ pp. 255–423. (Eds J Bouchon, P de Reffye, D Barthélémy) (Science Update, INRA: Paris)

Dufrêne E, Davi H, François C, le Maire G, le Dantec V, Granier A (2005) Modelling carbon and water cycles in a beech forest. Part I: model description and uncertainty analysis on modelled NEE. Ecological Modelling 185, 407–436.
| Crossref |
open url image1

Foley JD , van Dam A , Feiner SK , Hughes JF (1995) ‘Computer graphics: principles and practice in C, 2nd edn.’ (Addison-Wesley Professional: Amsterdam)

Gautier H, Měch R, Prusinkiewicz P, Varlet-Grancher C (2000) 3D architectural modelling of aerial photomorphogenesis in white clover (Trifolium repens L.) using L-systems. Annals of Botany 85, 359–370.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Godin C, Sinoquet H (2005) Functional–structural plant modelling. The New Phytologist 166, 705–708.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Godin C , Guédon Y , Costes E , Caraglio Y (1997) Measuring and analysing plants with the AMAPmod software. In ‘Plants to ecosystems: advances in computational life sciences’. (Ed. M Michalewicz) pp. 53–84. (CSIRO Australia: Melbourne)

Kang MZ , de Reffye P (2007) A mathematical approach estimating source and sink functioning of competing organs. In ‘Functional–structural plant modelling in crop production, volume 22’. (Eds J Vos, LFM Marcelis, PHB de Visser, PC Struik, JB Evers) pp. 65–74. (Springer-Verlag: New York)

Karwowski R (2002) Improving the Process of Plant Modeling: the L+C Modeling Language. PhD Thesis, University of Calgary.

Karwowski R , Prusinkiewicz P (2004) The L-system-based plant-modeling environment L-studio 4.0. In ‘Proceedings of the 4th International Workshop on Functional–Structural Plant Models (FSPM04), Montpellier, France’. (Eds C Godin, J Hanan, W Kurth, et al.) (UMR AMAP: Montpellier, France)

Kniemeyer O (2008) Design and implementation of a graph grammar based language for functional–structural plant modelling. PhD Thesis, BTU Cottbus. Available at http://www.grogra.de

Kniemeyer O, Buck-Sorlin G, Kurth W (2004) A graph-grammar approach to artificial life. Artificial Life 10, 413–431.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Kniemeyer O , Buck-Sorlin G , Kurth W (2007) GroIMP as a platform for functional–structural modelling of plants. In ‘Functional–structural plant modelling in crop production, volume 22’. (Eds J Vos, LFM Marcelis, PHB de Visser, PC Struik, JB Evers) pp. 43–52. (Springer-Verlag: New York)

Kniemeyer O , Barczik G , Hemmerling R , Kurth W (2008) Relational growth grammars – a parallel graph transformation approach with applications in biology and architecture. In ‘Applications of graph transformation with industrial relevance – AGTIVE 2007’. (Eds A Schürr, M Nagel, A Zündorf) (Springer: Berlin)

Kurth W (1994) Growth Grammar Interpreter GROGRA 2.4 – A software tool for the 3-dimensional interpretation of stochastic, sensitive growth grammars in the context of plant modelling – Introduction and Reference Manual, vol. 38 of Berichte des FZW. (Forschungszentrum Waldökosysteme der Universität Göttingen: Göttingen)

Kurth W (1999) ‘Die Simulation der Baumarchitektur mit Wachstumsgrammatiken.’ (Wissenschaftlicher Verlag: Berlin)

Kurth W , Anzola‐Jürgenson GA (1997) Triebwachstum und Verzweigung junger Fichten in Abhängigkeit von den beiden Einflußgrößen Beschattung und Wuchsdichte: Datenaufbereitung und analyse mit GROGRA. In ‘Deutscher Verband Forstlicher Forschungsanstalten, Sektion Forstliche Biometrie und Informatik, 10. Tagung Freiburg i. Br. 1997’. (pp. 89–108). (Biotechnische Fakultät: Ljubljana)

Měch R , Prusinkiewicz P (1996) Visual models of plants interacting with their environment. In ‘Proceedings of SIGGRAPH’. pp. 397–410. (ACM: New York)

Pradal C , Dufour-Kowalski S (2007) OpenAlea – visual programming and component based software for plant modeling. In ‘Proceedings of EuroPython, Vilnius, Lithuania’.

Pradal C, Dufour-Kowalski S, Boudon F, Fournier C, Godin C (2008) OpenAlea: a visual programming and component-based software platform for plant modeling. Functional Plant Biology 35, 751–760. open url image1

Preetham AJ , Shirley P , Smits B (1999) A practical model for daylight. In ‘Proceedings of SIGGRAPH’. pp. 397–410. (ACM Press/Addison-Wesley Publishing: New York)

Prioul JL, Chartier P (1977) Partitioning of transfer and carboxylation components of intracellular resistance to photosynthetic CO2 fixation: a critical analysis of the methods used. Annals of Botany 41, 789–800. open url image1

Prusinkiewicz P , Lindenmayer A (1990) The algorithmic beauty of plants. (Springer-Verlag: Berlin)

Prusinkiewicz P , Hammel M , Hanan J , Měch R (1997) Visual models of plant development. In ‘Handbook of formal languages, vol. 3.’ (Eds G Rozenberg, A Salomaa) pp. 535–597. (Springer-Verlag: Berlin)

Smith C , Prusinkiewicz P , Samavati FF (2003) Local specification of surface subdivision algorithms. AGTIVE 2003, vol. 3062 of Lecture Notes in Computer Science, pp. 313–327. (Springer-Verlag: Berlin)

Steilmann M (1996) Morphologische Untersuchungen zur Modellierung des Wachstums in Abhängigkeit von den Licht- und Konkurrenzverhältnissen von Jungbuchen. Diploma Thesis, University of Göttingen.

Strobel J (2004) Die Atmung der verholzten Organe von Altbuchen (Fagus sylvativa L.) in einem Kalk- und einem Sauerhumusbuchenwald. PhD Thesis, University of Göttingen.

Taentzer G , Biermann E , Bisztray D , Bohnet B , Boneva I , et al . (2008) Generation of Sierpinski triangles: a case study for graph transformation tools. In ‘Applications of graph transformation with industrial relevance – AGTIVE 2007’. (Eds A Schürr, M Nagel, A Zündorf) (Springer: Berlin)

Veach E (1998) Robust Monte Carlo Methods for Light Transport Simulation. PhD Thesis, Stanford University.