Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA

Brinkrolf C, Henke NA, Ochel L, Pucker B, Kruse O, Lutter P (2018)
Journal of Integrative Bioinformatics 15(3): 20180018.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
In this work we present new concepts of VANESA, a tool for modeling and simulation in systems biology. We provide a convenient way to handle mathematical expressions and take physical units into account. Simulation and result management has been improved, and syntax and consistency checks, based on physical units, reduce modeling errors. As a proof of concept, essential components of the aerobic carbon metabolism of the green microalga Chlamydomonas reinhardtii are modeled and simulated. The modeling process is based on xHPN Petri net formalism and simulation is performed with OpenModelica, a powerful environment and compiler for Modelica. VANESA, as well as OpenModelica, is open source, free-of-charge for non-commercial use, and is available at: http://agbi.techfak.uni-bielefeld.de/vanesa.
Erscheinungsjahr
Zeitschriftentitel
Journal of Integrative Bioinformatics
Band
15
Zeitschriftennummer
3
Artikelnummer
20180018
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Brinkrolf C, Henke NA, Ochel L, Pucker B, Kruse O, Lutter P. Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. Journal of Integrative Bioinformatics. 2018;15(3): 20180018.
Brinkrolf, C., Henke, N. A., Ochel, L., Pucker, B., Kruse, O., & Lutter, P. (2018). Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. Journal of Integrative Bioinformatics, 15(3), 20180018. doi:10.1515/jib-2018-0018
Brinkrolf, C., Henke, N. A., Ochel, L., Pucker, B., Kruse, O., and Lutter, P. (2018). Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. Journal of Integrative Bioinformatics 15:20180018.
Brinkrolf, C., et al., 2018. Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. Journal of Integrative Bioinformatics, 15(3): 20180018.
C. Brinkrolf, et al., “Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA”, Journal of Integrative Bioinformatics, vol. 15, 2018, : 20180018.
Brinkrolf, C., Henke, N.A., Ochel, L., Pucker, B., Kruse, O., Lutter, P.: Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. Journal of Integrative Bioinformatics. 15, : 20180018 (2018).
Brinkrolf, Christoph, Henke, Nadja Alina, Ochel, Lennart, Pucker, Boas, Kruse, Olaf, and Lutter, Petra. “Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA”. Journal of Integrative Bioinformatics 15.3 (2018): 20180018.
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