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data structures and software dependability

computer science department

brandenburg university of technology cottbus - senftenberg

Indian Summer School 2010 - Petri Net Modeling in Systems Biology


Magdeburg Centre for Systems Biology (MaCS)


3.10. - 5.10.2010

Picture of participants

you find here


Petri nets provide a powerful graphically and intuitively understandable unifying modeling framework for qualitative, stochastic and continuous analysis & simulation as well as reverse engineering. The course specifically addresses both dry-lab and mathematically naive wet-lab systems biologists and exemplifies the specific benefits of Petri nets for the research of both groups. The course is also open for graduate and PhD students.


Monika Heiner

Brandenburg University of Technology at Cottbus, Computer Science Institute, Germany
monika.heiner (at) informatik.tu-cottbus.de

Wolfgang Marwan

Otto von Guericke University Magdeburg, Germany
marwan (at) mpi-magdeburg.mpg.de


All talks are in English.

day 1 evening welcome dinner
day 2 morning basics of Petri net theory + practical part
  afternoon stochastic Petri nets and colored Petri nets + practical part
day 3 morning analysis and model checking + practical part
  afternoon network reconstruction + practical part

Detailed Information abou the scientific programme

Reconstructing networks from experimental data - A.K. Wagler, M. Durzinsky

The first lectures of the summer school focus on modeling biological systems in terms of Petri nets and analyzing processes within this framework. The last part of the summer school is dedicated to the challenging task of reconstructing such models from experimental data.

The current state of the art approach tries to cope with the reconstruction problem by cycling through several phases: forming hypothesis, model construction, model-based analysis/simulation, and wet-lab validation of the findings. This approach is hypothesis-driven and yields potentially incomplete information, as e.g. no certificate can be given that no suitable model alternatives exist.

Our group developed an exact mathematical approach that is exclusively data-driven and generates the complete list of all minimal place/transition Petri nets fitting the experimental data. Hereby, the set of biological species considered to be crucial for the observed phenomenon is part of the input and will form the set of places in each of the reconstructed networks. The task is to find all minimal sets of transitions which are able to reproduce the experimentally observed time-dependent mass or signal flux in the system.

In this course, we present the main features and main steps of the reconstruction algorithm:

1. The input: Which type and quality of data is suitable

2. The core routine of the algorithm: How to analyze the experimentally observed state changes of the system in order to determine suitable transition sets of the networks

3. When the algorithm returns no solution: How to detect and resolve infeasibility by extending the network

4. When the algorithm returns too many solutions: How to exclude unsuitable solution alternatives by considering advanced dynamic aspects or by designing new experiments

The course will be accompanied by a practical part, including exercises to step-by-step reconstruct Petri nets from given experimental data and a demonstration how to run the algorithm on some biological examples.

Further information concerning the scientific programme, the list of referents as well as an overview for the planned social activities are following.


  • Registration Fee: approx. 100 €
  • Registration Fee for OvGU-students: approx. 50 € (optional: + 25 € for the welcome dinner)
  • Please ask Matthias Jach (see below) for possible travel scholarships


  1. Registration deadline: 26 September 2010, number of places is limited
  2. Send an E-mail to Matthias Jach (summerschool-macs (at) ovgu.de) with the subject "Registration: Petri Net Summer School at MACS" containing the following information:
    • Name:
    • Institution:
    • Email address:
    • Address:
    • Telephone number:
    • Background (biolgist, theoretician etc.):
    • OvGU-student(Yes/No):
  3. You will get in return a mail containing banking information (bank account number etc.).
  4. As soon as you have paid the fee the registration is valid.
    • OvGU-students also have to send their certificate of matriculation.

Contact and Further Information

summerschool-macs (at) ovgu.de

this website: http://www-dssz.informatik.tu-cottbus.de/BME/ISS-BioPN2010

Otto-von-Guericke University Magdeburg: http://www.uni-magdeburg.de/

Max Planck Institute for Dynamics of Complex Technical Systems: http://www.mpi-magdeburg.mpg.de/

Magdeburg: http://www.magdeburg.de/


flyer Indian Summer School 2010


If you need a hotel booking please contact Janine Stierwald stierwald (at) mpi-magdeburg.mpg.de.

… the end …

Any comments or questions are welcome. Please direct them to monika.heiner@b-tu.de