Modeling a Bacterium's Life: a Petri-net Library in Modelica
نویسندگان
چکیده
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.
منابع مشابه
An Advanced Environment for Hybrid Modeling of Biological Systems Based on Modelica
Biological systems are often very complex so that an appropriate formalism is needed for modeling their behavior. Hybrid Petri Nets, consisting of time-discrete Petri Net elements as well as continuous ones, have proven to be ideal for this task. Therefore, a new Petri Net library was implemented based on the object-oriented modeling language Modelica which allows the modeling of discrete, stoc...
متن کاملPNlib - An Advanced Petri Net Library for Hybrid Process Modeling
A new Petri net library, called PNlib, is presented to enable graphical hierarchical modeling, hybrid simulation, and animation of processes in life sciences, technical applications, among others. In order to model these most different processes, a new powerful and universally usable mathematical modeling concept – xHPN (extended Hybrid Petri Net) – has been established. This formalism is used ...
متن کاملHybrid Modelling and Process Optimization of Biological Systems
An environment has been developed which comprises mathematical methods, concepts, and tools to enable the processing of experimental data to usable new insights about biological systems. Therefore, a mathematical modelling concept Hybrid Petri-Nets for biological applications (HPNbio) – has been defined which is properly adapted to the demands of biological process. This concept has been implem...
متن کاملPNlib – A Modelica Library for Simulation of Biological Systems Based on Extended Hybrid Petri Nets
We present a new Petri net simulation environment to enable the processing of experimental data to gain usable new insights about biological systems. Therefore, a powerful mathematical modeling concept – xHPNbio (extended Hybrid Petri Nets for biological applications) – has been defined which is properly adapted to the demands of biological processes. This specification is used for the PNlib (P...
متن کاملModelica Library for Hybrid Simulation of Mass Flow in Process Plants
Operation, control and maintenance of large process plants can be very energy and cost intensive. Optimization of the involved technical, organizational and dependent economic aspects is a non-trivial, multicriteria problem; solving it can be supported by dynamic plant modeling. First principles, constitutive and empirical relations are used to derive quasi-steady-state mathematical models of f...
متن کامل