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Medizinische Bioinformatik
und Systembiologie



German/Russian Network


Sino/German Network

Introduction

OMPetri is a Petri net modeling and simulation environment which is developed in the Bioinformatics group at Bielefeld University.

Requirements

• Java 8 or higher (with JavaFX support i.e. by Oracle)
• OpenModelica 1.12.0 stable release
• OMPetri

Installation

For editing a Petri net, OMPetri is sufficient. If you want to run a simulation, the installation of OpenModelica is required. We support 1.12.0 stable release of OpenModelica. Nightly Builds might be more powerful, but might be also incompatible with OMPetri. The installation path must not contain any whitespaces! During installation process, make sure that you select PNlib as library to install. By default, all third party libraries will be installed. The installation process will also set some environment variables which are needed for OMPetri to detect the OpenModelica installation.

After the installation of OpenModelica finished, start OMPetri, to ensure that OMPetri is started with the updated environment variables of your system.

Downloads and Tutorial

• OMPetri executable JAR
• Tutorial which gives an introduction to OMPetri
• Petri net example which is based on the biological model presented in Hynne
• Simulation results which can be imported and mapped to the Petri net example

Sources

• Github repository of OMPetri
• Scientific paper of the biological example by Hynne et. al. 2001

Contacts

• Philo Reipke: preipke [at] techfak [dot] uni-bielefeld [dot] de
• Christoph Brinkrolf

Scientific publications

List of scientific publications that are related to OMPetri, PNlib and OpenModelica.

2018

• C. Brinkrolf, P. Reipke
  OMPetri - A Software Application for Modeling and Simulation using Extended Hybrid Petri nets by Employing OpenModelica
  V. Khomenko and O. H. Roux (Eds.): PETRI NETS 2018, LNCS 10877, pp. 1-10, 2018. (accepted)

2017

• L. Ochel
  Petri-Netz-basierte Simulation biologischer Prozesse mit OpenModelica
  Dissertation Bielefeld University 2017
  Link

2013

• S. Proß
  Hybrid modeling and optimization of biological processes
  Dissertation Bielefeld University 2013
  Link

2012

• S. Proß, B. Bachmann
  PNlib - An Advanced Petri Net Library for Hybrid Process Modeling
  Proceedings of the 9th International MODELICA Conference; September 3-5; 2012; Munich; Germany
  DOI: 10.3384/ecp1207647
• S. Proß, S. J. Janowski, B. Bachmann, C. Kaltschmidt, B. Kaltschmidt
  PNlib - A Modelica Library for Simulation of Biological Systems Based on Extended Hybrid Petri Nets
  Proceedings Proc. BioPPN 2012, a satellite event of PETRI NET 2012
  PDF