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Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA
Bielefeld University, Faculty of Technology, Bioinformatics Department, Bielefeld, Germany.
Bielefeld University, Faculty of Biology and CeBiTec, Genetics of Prokaryotes, Bielefeld, Germany.
Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, Faculty of Science & Engineering. Bielefeld University, Faculty of Technology, Bioinformatics Department, Bielefeld, Germany.
Bielefeld University, Faculty of Biology and CeBiTec, Genome Research, Bielefeld, Germany; University of Cambridge, Department of PlantSciences, Evolution and Diversity, Cambridge, UK.
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2018 (English)In: Journal of integrative bioinformatics, ISSN 1613-4516, Vol. 15, no 3Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
De Gruyter Open, 2018. Vol. 15, no 3
Keywords [en]
Chlamydomonas reinhardtii; OpenModelica; metabolic network; systems biology; xHPN
National Category
Computer Sciences
Identifiers
URN: urn:nbn:se:liu:diva-156014DOI: 10.1515/jib-2018-0018PubMedID: 30218605OAI: oai:DiVA.org:liu-156014DiVA, id: diva2:1301600
Available from: 2019-04-02 Created: 2019-04-02 Last updated: 2019-04-02

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