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data structures and software dependability

computer science department

brandenburg university of technology cottbus - senftenberg

3rd International Workshop on Biological Processes & Petri Nets (BioPPN 2012)

A satellite event of Petri Nets 2012 & ACSD 2012 - Hamburg, Germany, June 25, 2012

The workshop attracted 18 participants, who enjoyed an open-minded and productive atmosphere. Excellent idea of the local organisers to join the invited talks of the workshops running in parallel.

See you all next year at BioPPN 2013 in Milano.


Programme (tentative)

CEUR Workshop Proceedings Vol. 852

8:45 joint opening for all workshops

9.00-10.00 Invited Talk (joined session with PNSE, LAM)

15' coffee break

10.15 - 11.15 Session A (Analysis Techniques)

session chair: Gianfranco Balbo

  • Paolo Baldan, Nicoletta Cocco, Marta Simeoni
    Comparison of Metabolic Pathways by Considering Potential Fluxes [ slides ]
  • Christian Rohr
    Simulative Model Checking of Steady-State and Time-Unbounded Temporal Operators [ slides ]

15' coffee break

11.30 - 12.30 Session B (Hybrid Petri Nets)

session chair: Hiroshi Matsuno

  • Sabrina Proß, Sebastian Jan Janowski, Bernhard Bachmann, Christian Kaltschmidt, Barbara Kaltschmidt
    PNlib – A Modelica Library for Simulation of Biological Systems Based on Extended Hybrid Petri Nets
  • Mostafa Herajy, Martin Schwarick
    A Hybrid Petri Net Model of the Eukaryotic Cell Cycle [ slides ]

12.30 -13.30 lunch

13.30 - 14.30 Session C (Applications)

session chair: Wolfgang Marwan

  • Nicholas Stoy, Sophie Chen, Andrzej Kierzek
    Studying prostate cancer as a network disease by qualitative computer simulation with Petri Nets [ slides ]
  • Marta Ewa Polak
    Modelling Atopic Dermatitis using Petri Nets [ slides ]

30' coffee break

15.00 - 16.00 Session D (Tools)

session chair: Monika Heiner

  • Anja Hartmann, Hendrik Rohn, Kevin Pucknat, Falk Schreiber
    Petri-nets in VANTED: Simulation of Barley Seed Metabolism
  • Mary Ann Blaetke, Wolfgang Marwan
    A Database-supported Modular Modelling Platform for Systems and Synthetic Biology [ slides ]

16.00 - 16.15 Closing Discussion

30' coffee break

16.45 Invited Talk (joined session with PNSE, LAM)

17:45 - The End

Invited Talk

Wolfgang Marwan, D

Petri Nets - an Integrative Framework for Advanced Biomodel Engineering

Petri nets are employed as a multifunctional integrative framework for biomodel engineering. We describe the general concept of a modular modelling approach that consideres the functional coupling of components of genome, transcriptome, and proteome with complex cellular phenotypes. For this purpose, the effects of genes and their mutated alleles on downstream components are modeled by composable, metadata-containing Petri net models organized in a database with version control, accessible through a web interface. Gene modules are coupled to protein modules through mRNA modules by specific interfaces designed for the automatic, database-assisted composition. Automatically assembled executable models may then consider cell type-specific gene expression patterns and take the resulting protein concentrations into account. With a sufficient number of protein modules in the database, the composed Petri nets can predict complex effects of gene mutations or uncover complex genotype/phenotype relationships. In this context, forward and reverse engineered modules are fully compatible.

Technical Description

The goal of this workshop is to provide a platform for researchers aiming at fundamental research and real life applications of Petri nets in Systems and Synthetic Biology.

Systems and Synthetic Biology are full of challenges and open issues, with adequate modelling and analysis techniques being one of them.

Petri nets offer a family of related models, which can be used as a kind of umbrella formalism — models may share the network structure, but vary in their kinetic details (quantitative information). This clearly contributes to bridging the gap between different formalisms, and helps to unify diversity.

Topics of interest include, but are not limited to:

  • standard Petri nets for qualitative modelling and analysis, if kinetics are unknown or deliberately abstracted away;
  • discrete quantitative modelling by time(d) Petri nets;
  • stochastic Petri nets to account for intrinsic noise of molecular fluctuation, and/or sources of extrinsic noise;
  • continuous Petri nets (and thus Ordinary Differential Equations), back and forth;
  • hybrid Petri nets, or how to handle different abstraction and time scales in biological processes;
  • dedicated support of multi-scale issues;
  • case studies of metabolic, signalling, regulatory, and combined networks, or other biological applications;
  • dedicated analysis and simulation techniques;
  • related tool debvelopment, including exchange formats, dedicated to biological processes;

Case studies in systems and synthetic biology demonstrating the specific power by the combined use of different Petri net classes are especially encouraged.


This workshop intends to gather students and researchers, who have interests in the application of Petri nets for biological processes. Its main goal will be to demonstrate that Petri net can be an effective technique to tackle the issues which reside in many biological problems. The workshop also promotes discussions between advanced researchers and beginners, which may enhance the world-wide activities in Petri net applications on biological processes.

Paper Submission

Submitted papers should describe original work that has not been previously published and is not under review for publication elsewhere. All papers should be in LNCS format, and have to be submitted via EasyChair. The page limit given below includes figures, tables and references.

There are the following categories of submissions.

  • Regular papers should not exceed 15 p. in LNCS format.
  • "Work in progress" papers should not exceed 15 p. in LNCS format.
  • Short papers should not exceed 6 p. in LNCS format.
  • Posters up to A0 format.

A submission should be clearly assigned to one category.

Based on the review process, a submission may be accepted as is, accepted with minor changes, rejected or selected for oral presentation only. In the latter case, a 1-page abstract will be published.


Workshop Proceedings

Proceedings will be electronically published with CEUR Workshop Proceedings (http://ceur-ws.org) with consecutive volume numbers for each workshop allocated with PETRI NET 2012, as well as local proceedings distributed via USB Memory Sticks.

Special Issue

Best papers will be proposed to be invited for the follow-up publication in Transactions on Petri Nets and other models of Concurrency (ToPNoC).

Organizers -- Programme Committee

Monika Heiner

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

Ralf Hofestädt

Bielefeld University, Faculty of Technology, Bioinformatics Department, Germany
ralf.hofestaedt (at) uni-bielefeld.de

Program Committee


  • April, 15th: Submission of papers.
  • May, 13th: Notification of acceptance/rejection.
  • June, 1st: Final version of papers.


Registration is handled by the hosting conference website. Early registration fees (workshop only): 100 € for students, 130 € else; early registration ends May 23, 2012.

… the end …

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