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https://ceur-ws.org/Vol-1373/preface.pdf
Monika Heiner, Annegret K. Wagler (Eds.)
Biological Processes & Petri Nets
6th International Workshop BioPPN 2015
Brussels, 22 June 2015
Proceedings
CEUR Workshop Proceedings
Volume 1373
Editors:
Monika Heiner
Brandenburg University of Technology Cottbus-Senftenberg
Computer Science Institute
Data Structures and Software Dependability
03013 Cottbus, Germany
monika.heiner@b-tu.de
Annegret K. Wagler
University Blaise Pascal (Clermont-Ferrand II)
Faculty of Sciences and Technology
ISIMA - LIMOS - CNRS
BP 10125, 63173 Aubiére, France
wagler@isima.fr
Online available as CEUR Workshop Proceedings (ISSN 1613-0073), Volume 1373
http://CEUR-WS.org/Vol-1373/
BibTEX entry:
@proceedings{bioppn2015,
editor = {Monika Heiner, Annegret K. Wagler},
title = {Proceedings of the 6th International Workshop on
Biological Processes \& Petri Nets (BioPPN 2015),
satellite event of Petri Nets 2015, Brussels, Belgium, June 22, 2015},
booktitle = {Biological Processes \& Petri Nets},
location = {Brussels, Belgium},
publisher = {CEUR-WS.org},
series = {CEUR Workshop Proceedings},
volume = {Vol-1373},
year = {2015},
url = {http://CEUR-WS.org/Vol-1373/}
}
Copyright c 2015 for the individual papers by the papers’ authors. Copying permitted
for private and academic purposes. This volume is published and copyrighted by its ed-
itors. Re-publication of material from this volume requires permission by the copyright
owners.
Preface
This volume contains the peer-reviewed papers presented at BioPPN 2015 – the
6th International Workshop on Biological Processes & Petri Nets held on June
22, 2015 in Brussels as satellite event of PETRI NETS 2015 and ACSD 2015.
The workshop had been organised to provide a platform for researchers aim-
ing at fundamental research and real life applications of Petri nets and other
concurrency models in Systems and Synthetic Biology. Systems and Synthetic
Biology are full of challenges and open issues, with adequate modelling and anal-
ysis techniques being one of them. The need for appropriate mathematical and
computational modelling tools is widely acknowledged.
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 undoubtedly contributes
to bridging the gap between different formalisms, and helps to unify diversity.
Thus, Petri nets have proved their usefulness for the modelling, analysis, and
simulation of a diversity of biological networks, covering qualitative, stochastic,
continuous and hybrid models. The deployment of Petri nets to study biological
applications has not only generated original models, but has also motivated
research of formal foundations.
In this context, the invited talk on A compact modeling approach for de-
terministic biological systems given by Luis M. Torres from Centro de Mod-
elización Matemática (ModeMat)/Escuela Politécnica Nacional Quito, Ecuador,
addressed the problem of extending Petri nets in such a way to obtain a compact
model for the dynamics of certain discrete deterministic systems.
In addition, there is a position paper presented by Hugues Bersini on State-
transition diagrams for biological modelling: A few cases to initiate a discussion
on advantages and drawbacks of different modeling frameworks (Petri nets versus
state-transition diagrams) for biological modelling.
Each submission was reviewed by five to six program committee members
assisted by one external reviewer. The list of reviewers comprises 18 professionals
of the field coming from 11 different countries and writing in total 28 reviews,
most of them of substantial length. The programme committees decided finally
to accept five papers, involving 14 authors coming from four different countries.
In summary, the workshop proceedings enclose theoretical contributions and
biological applications, demonstrating the interdisciplinary nature of the topic.
For more details see the workshop’s website
http://www-dssz.informatik.tu- cottbus.de/BME/BioPPN2015.
We acknowledge substantial support by the EasyChair management system,
see http://www.easychair.org, during the reviewing process and the production
of these proceedings.
June 16, 2015 Monika Heiner
Cottbus Annegret K. Wagler
i
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ii
Table of Contents
The dynamics of deterministic systems – A survey (invited talk) . . . . . . . . 1
Luis M. Torres and Annegret K. Wagler
Petri nets for modelling and analysing trophic networks . . . . . . . . . . . . . . . . 21
Paolo Baldan, Martina Bocci, Daniele Brigolin, Nicoletta Cocco and
Marta Simeoni
A Colored Petri net approach for spatial Biomodel Engineering based
on the modular model composition framework Biomodelkit . . . . . . . . . . . . . 37
Mary Ann Blaetke and Christian Rohr
On Modeling internal organs and meridian system based on traditional
Chinese medicine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Qi-Wei Ge, Ren Wu and Mitsuru Nakata
Full structural model refinement as type refinement of colored Petri nets . 70
Diana-Elena Gratie and Ion Petre
Dependent shrink for Petri net models of signaling pathways . . . . . . . . . . . 85
Atsushi Mizuta, Qi-Wei Ge and Hiroshi Matsuno
iii
Program Committee
Gianfranco Balbo University of Torino, Computer Science Depart-
ment, Italy
Marco Becutti University of Torino, Computer Science Depart-
ment, Italy
Rainer Breitling University of Manchester, Manchester Institute of
Biotechnology, UK
Ming Chen Zhejiang University, College of Life Sciences,
Department of Bioinformatics, China
David Gilbert Brunel University, Centre for Systems and Synthetic
Biology, UK
Simon Hardy Université Laval, Institut universitaire en santé men-
tale de Québec, Canada
Monika Heiner Brandenburg University of Technology Cottbus-
Senftenberg, Computer Science Institute, Germany
Mostafa Herajy Port Said University, Mathematics and Computer
Science Department, Egypt
David R.C. Hill Universite Blaise Pascal, Faculty of Sciences and
Technology
Peter Kemper College of William and Mary, Department of Com-
puter Science, USA
Sriram Krishnamachari Indraprastha Institute of Information Technology
(IIIT), India
Chen Li Zhejiang University, School of Medicine, Center for
Genetic & Genomic Medicine, China
Fei Liu Harbin Institute of Technology, Control and Simu-
lation Center, China
Wolfgang Marwan Otto von Guericke University Magdeburg & Magde-
burg Centre for Systems Biology, Germany
Hiroshi Matsuno Yamaguchi University, Graduate School of Science
and Engineering, Japan
P.S. Thiagarajan National University of Singapore, School of Comput-
ing, Department of Computer Science, Singapore
Annegret K. Wagler Université Blaise Pascal (Clermont-Ferrand II), Fac-
ulty of Sciences and Technology
iv
Additional Reviewers
C
Cordero, Francesca
v