Modelling a Bacterimss Life: A Petrin-Net Library in Modelica

Sabrina Pross
University of Applied Sciences, Germany

Bernhard Bachmann
University of Applied Sciences, Germany

Ralf Hofestädt
Bielefeld University, Germany

Karsten Niehaus
Bielefeld University, Germany

Rainer Ueckerdt
University of Applied Sciences, Germany

Frank-Jörg Vorhölter
Bielefeld University, Germany

Petra Lutter
Bielefeld University, Germany

Ladda ner artikelhttp://dx.doi.org/10.3384/ecp09430015

Ingår i: Proceedings of the 7th International Modelica Conference; Como; Italy; 20-22 September 2009

Linköping Electronic Conference Proceedings 43:51, s. 463-472

Visa mer +

Publicerad: 2009-12-29

ISBN: 978-91-7393-513-5

ISSN: 1650-3686 (tryckt), 1650-3740 (online)


For modeling biological systems the already existing Petri Net Libraries were further developed with OpenModelica using the SimForge graphical user interface (GUI). The Petri Nets elements were wrapped into models for different reaction types to simplify the modeling process. Additionally; a database connection was implemented for integrating kinetic data. The application of this new Reaction Library is demonstrated by the xanthan production of the bacterium Xanthomonas campestris pv. campestris. A mathematical model is introduced to predict growth and xanthan production; given an initial glucose concentration. The parameters of this model are estimated with the aid of the Optimization Toolbox in MATLAB.


Inga nyckelord är tillgängliga


[1] Garcia-Ochoa; F.; et al. Xanthan gum: production; recovery; and properties. Biotechnology Advances. 2000; 18; pp. 549-579. doi: 10.1016/S0734-9750(00)00050-1.

[2] Vorhölter; Frank-Jörg; et al. The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis. Journal of Biotechnology. 2008; pp. 33-45. doi: 10.1016/j.jbiotec.2007.12.013.

[3] Garcia-Ochoa; F.; Santos; V. E. and Alcon; A. Structured kinetic model for Xanthomonas campestris growth. Enzyme and Microbial Technology. 2004; pp. 583-594. doi: 10.1016/j.enzmictec.2004.01.005.

[4] Monod; Jacques. The Growth of Bacterial Cultures. Annual Review of Microbiology. 1949; pp. 371-394. doi: 10.1146/annurev.mi.03.100149.002103

[5] Quinlan; Alician V. Kinetics of Secondary Metabolite Synthesis in Batch Cultures When Two Different Substrates Limit Cell Growth and Metabolite Production: Xanthan Synthesis by Xanthomonas campestris. Biochemical Eng. 469; 1986; pp. 259-269.

[6] Proß; Sabrina and Bachmann; Bernhard. A Petri Net Library for Modeling Hybrid Systems in OpenModelica. submitted (Modelica Conference 2009). 2009.

[7] Reddy; Venkatramana N.; Liebman; Michael N. and Mavrovouniotis; Michael L. Qualitative Analysis of Biochemical Reaction Systems. Compu. Biol. Med. 1996; pp. 9-24.

[8] Hofestädt; R. and Thelen; S. Quantitative Modeling of Biochemical Networks. In Silico Biology. 1998; 1; pp. 39-53.

[9] Doi; Atsushi; et al. Constructing biological pathway models with hybrid functional Petri nets. In Silico Biology. 2004.

[10] Berg; Jeremy M.; Tymoczko; John L. and Stryer; Lubert. Biochemistry. New York : W. H: Freeman; 2006.

[11] Gompertz; Benjamin. On the nature of the function expressive of the law of human mortality; and on a new mode of determining the value of life contingencies. Phil. Trans. R. Soc. Lond. 115; pp. 513-585.

[12] Friesen; Rafael. Petrinets in systems biology: Modelling cell communication with petri nets. Bielefeld; 2009.

[13] Watt; Tony. private communication. Bielefeld; 2009.

Citeringar i Crossref