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

J Integr Bioinform. 2018 Sep 15;15(3):20180018. doi: 10.1515/jib-2018-0018.

Abstract

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.

Keywords: Chlamydomonas reinhardtii; OpenModelica; metabolic network; systems biology; xHPN.

MeSH terms

  • Algorithms
  • Carbon / metabolism*
  • Chlamydomonas reinhardtii / metabolism*
  • Computer Simulation*
  • Metabolic Networks and Pathways*
  • Models, Biological
  • Software*
  • Workflow

Substances

  • Carbon