Related Experiment Video
Updated: Aug 3, 2026

Recapitulating Suckling-to-Weaning Transition In Vitro using Fetal Intestinal Organoids
Published on: November 15, 2019
VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology
Christoph Brinkrolf1, Lennart Ochel2, Ralf Hofestädt1
1Bioinformatics Department, Faculty of Technology, Bielefeld University, 33501 Bielefeld, Germany.
Abstract:
Petri nets are a common method for modeling and simulation of systems biology application cases. Usually different Petri net concepts (e.g. discrete, hybrid, functional) are demanded depending on the purpose of the application cases. Modeling complex application cases requires a unification of those concepts, e.g. hybrid functional Petri nets (HFPN) and extended hybrid Petri nets (xHPN). Existing tools have certain limitations which motivated the extension of VANESA, an existing open-source editor for biological networks. The extension can be used to model, simulate, and visualize Petri nets based on the xHPN formalism. Moreover, it comprises additional functionality to support and help the user. Complex (kinetic) functions are syntactically analyzed and mathematically rendered. Based on syntax and given physical unit information, modeling errors are revealed. The numerical simulation is seamlessly integrated and executed in the background by the open-source simulation environment OpenModelica utilizing the Modelica library PNlib. Visualization of simulation results for places, transitions, and arcs are useful to investigate and understand the model and its dynamic behavior. The impact of single parameters can be revealed by comparing multiple simulation results. Simulation results, charts, and entire specification of the Petri net model as Latex file can be exported. All these features are shown in the demonstration case. The utilized Petri net formalism xHPN is fully specified and implemented in PNlib. This assures transparency, reliability, and comprehensible simulation results. Thus, the combination of VANESA and OpenModelica shape a unique open-source Petri net environment focusing on systems biology application cases. VANESA is available at: http://agbi.techfak.uni-bielefeld.de/vanesa.
More Related Videos
11:25Identification and Quantification of Decomposition Mechanisms in Lithium-Ion Batteries; Input to Heat Flow Simulation for Modeling Thermal Runaway
Published on: March 7, 2022
14:45Analyzing the Parkinson's Disease Mouse Model Induced by Adeno-associated Viral Vectors Encoding Human α-Synuclein
Published on: July 29, 2022
Related Concept Videos
Molecular Models
Synthetic Biology
Golden rice
Golden rice is a genetically modified...
Open and closed-loop control systems
An open-loop control system operates without feedback from the output. It consists of two primary elements: the controller and the controlled process. The controller receives an input signal and...
Two-Compartment Open Model: Overview
The...
Three-Compartment Open Model
Modeling with Differential Equations