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data structures and software dependability

computer science department

brandenburg university of technology cottbus - senftenberg

5th International Workshop on Biological Processes & Petri Nets (BioPPN 2014)

latest update: June 23, 2015, at 09:41 AM

Basic facts


See you all next year at BioPPN 2015 in Brussels.



CEUR Workshop Proceedings Vol-1159

8:30 – 09:30 Registration

9:45 BioPPN opening

10.00 - 11.00 Session 1 - Invited Talk

session chair: Monika Heiner

30' coffee break

11.30 - 13.00 Session 2 - Regular Papers

session chair: Annegret Wagler

  • Rafael V. Carvalho, Jetty Kleijn and Fons Verbeek
    A multi-scale extensive Petri net model of the bacterial–macrophage interaction [ slides ]
  • Jure Bordon, Miha Moškon and Miha Mraz
    Overcoming unknown kinetic data for quantitative modelling of biological systems using fuzzy logic and Petri nets [ slides ]
  • Mostafa Herajy, Fei Liu and Christian Rohr
    Coloured hybrid Petri nets for systems biology [ slides ]

1.30' lunch break

14.30 - 15.30 Session 3 - Regular Papers

session chair: Jetty Kleijn

  • Marie C.F. Favre, Wolfgang Marwan and Annegret Wagler
    Integrating a priori knowledge in automatic network reconstruction [ slides ]
  • Cinzia Di Giusto, Hanna Klaudel and Franck Delaplace
    Systemic approach for toxicity analysis [ slides ]

15:30 - Closing Remarks and Discussion

16.00-16.30 Coffee Break

Invited Talk

Marco Beccuti
Universitŕ degli Studi di Torino, Dipartimento di Informatica

Mathematical models on cancer progression

The Cancer Stem Cell (CSC) involvement into tumor progression, tumor recurrence, and therapy resistance is one of the most studied subject of current cancer research. Nevertheless, due to the complex dynamics characterizing the CSC tumor, a comprehensive theory has not been established yet. To this end, some advises can be obtained combining mathematical modeling and experimental data. Indeed, mathematical modeling is a powerful instrument which may drive the comprehension of a biological system, providing a clear description of its essential dynamics.

The aim of this talk is hence to show how the CSC tumor growth could be described/studied through the application of mathematical models. In details two different modeling approaches are presented: the former one consists in a multilevel/multiscale model, which details both molecular and cellular aspects. By means of this framework we were able to reproduce the tumor growth trend observed in mice, highlighting the strong connection existing between cellular events and cell population dynamics. We were also able to reproduce molecular vaccinations, correctly miming the in vivo vaccinations in animals. However, this detailed approach can engender difficulties in the parameter estimation process when only few kinetic information is available.

The second contribution was designed really to address this complexity issue. We defined a new compartmental mathematical framework only focusing on the cell subpopulation dynamics. Indeed, the aim of this work was to describe CSC tumor progression trying to identify its essential mechanisms at population level. Through a quantitative and qualitative analysis of our model was hence possible to define rules controlling the breast cancer progression.

Lastly, we point out that the CSC theory is applicable to several other human cancers. Therefore, being our two model based on the key dynamics of the CSC theory, they can be further adapted for the study of many other tumor cases too.

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 NETS 2014, 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

Alia Benkahla

Institut Pasteur de Tunis, Tunisia
alia.benkahl (at) pasteur.rns.tn

Monika Heiner

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

Program Committee


  • April, 27 2014: Submission of papers.
  • May, 25 2014: Notification of acceptance/rejection.
  • June, 15 2014: Final version of papers.


Registration is handled by the hosting conference website PETRI NETS 2014

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