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data structures and software dependability

computer science department

brandenburg university of technology cottbus - senftenberg

4th International Workshop on Biological Processes & Petri Nets (BioPPN 2013)

latest update: July 03, 2013, at 08:56 PM

Basic facts


See you all next year at BioPPN 2014 in Tunis.



CEUR Workshop Proceedings Vol. 988

9:00 joint opening for all workshops

9.15 - 10.15 Invited Talk (joined session with PNSE/ModBE)

session chair: Gianfranco Balbo

30' coffee break

10.45 - 11.45 Session A - Qualitative Modelling and Analysis

session chair: Hiroshi Matsuno

  • Paolo Baldan, Martina Bocci, Nicoletta Cocco and Marta Simeoni
    Comparing metabolic pathways through potential fluxes: a selective opening approach [ slides ]
  • Luboš Brim, Vilém Dĕd, David Šafránek
    Qualitative modelling and analysis of Photosystem II [ slides ]

5' break

11.50 - 12.50 Session B - New Net Classes and their Application

session chair: Wolfgang Marwan

  • Marco Nobile, Daniela Besozzi, Paolo Cazzaniga and Giancarlo Mauri
    The foundation of Evolutionary Petri Nets [ slides ]
  • Marie C.F. Favre and Annegret Wagler
    Reconstructing X’-deterministic extended Petri nets from experimental time-series data X’ [ slides ]

12.50 - 14.00 lunch

14:00 - 15.00 Invited Talk (joined session with PNSE/ModBE)

  • Ernesto Damiani and Paolo Ceravolo
    Knowledge and Business Intelligence Technologies in Cross-Enterprise Environments for Italian Advanced Mechanical Industry

15:00 - 15:30 Posters presentation and demos PNSE

30' coffee break

16:00 - 17:30 Session C - Quantitative Modelling and Analysis

session chair: Chen Li

  • Jure Bordon, Miha Moškon and Miha Mraz
    Quantitative modelling of biological systems with extended Fuzzy Petri Nets [ slides ]
  • Nimet İlke Çetin, Rza Bashirov, Şükrü Tüzmen
    Petri net based modelling and simulation of p16-Cdk4/6-Rb pathway [ slides ]
  • Zhongyuan Tian, Adrien Fauré, Hirotada Mori and Hiroshi Matsuno
    Identification of key regulators in glycogen utilization in E. coli based on the simulations from a Hybrid Functional Petri Net model [ slides ]

17.30 - 17.45 Closing Discussion

17:45 - The End

Invited Talk

Raffaele Calogero
Department of Molecular Biotechnologies and Life Sciences, University of Torino, Italy

Dreaming about models: a biologist’s perspective

The last 15 years revolutionized biology moving from gene centric to genome centric views of biological mechanisms. Technology has been one of the main driving forces of this revolution which involves analyzing, storing and mining huge data sets and which challenges the researchers to integrate data coming from many data sources to obtain a global vision of complex systems and phenomena. However, technology improvement represents only the tip of the iceberg in biology. Mathematical models, built and tuned from experimental data, can offer both a precise representation of the interactions of biological systems and a way of studying their dynamics to reveal new knowledge.

This talk focuses on the biologist view of experiments and the implication of such a view on the use of biological data in model definition.

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, an abstract can 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 2013, 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

Gianfranco Balbo

Universita degli Studi di Torino, Dipartimento di Informatica, Italy
balbo (at) di.unito.it

Monika Heiner

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

Program Committee


  • April, 15th 2013: Submission of papers.
  • May, 15th 2013: Notification of acceptance/rejection.
  • June, 1st 2013: Final version of papers.


Registration is handled by the hosting conference website PETRI NET 2013

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