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data structures and software dependability

computer science department

brandenburg university of technology cottbus - senftenberg

International Workshop on Biological Processes & Petri Nets (BioPPN 2011)

A satellite event of Petri Nets 2011 - Newcastle upon Tyne, UK, June 20, 2011

The workshop enjoyed an open-minded and productive atmosphere having 20-25 participants in each session.

See you all next year at BioPPN 2012 in Hamburg.


CEUR Workshop Proceedings Vol. 724

9:00-9:10 Opening address [ slides ]

9:10-10:40 Session A (Modelling)

  • Koichi Kobayashi and Kunihiko Hiraishi
    Optimal Control of Asynchronous Boolean Networks Modeled by Petri Nets [ slides ]
  • Nicolas Sedlmajer, Didier Buchs, Steve Hostettler, Alban Linard, Edmundo Lopez and Alexis Marechal
    GReg : a domain specific language for the modeling of genetic regulatory mechanisms [ slides ]
  • Jetty Kleijn, Maciej Koutny and Grzegorz Rozenberg
    Modelling Reaction Systems with Petri Nets [ slides ]

10:40-11:10 Coffee break

11:10-12:10 Invited talk

12:10-14:00 Lunch

14:00-15:30 Session B (Analysis)

  • Chen Li, Keisuke Kuroyanagi, Masao Nagasaki and Satoru Miyano
    Parameter Estimation of Biological Pathways Using Data Assimilation and Model Checking [ slides ]
  • Louchka Popova-Zeugmann and Elisabeth Pelz
    Studying Steady States in Biochemical Reaction Systems by Time Petri Nets [ slides ]
  • Shota Nakano and Shingo Yamaguchi
    Two modeling methods for signaling pathways with multiple signals using UPPAAL [ slides ]

15:30-16:00 Coffee break

16:00-17:30 Session C (Applications)

  • Paolo Baldan, Nicoletta Cocco, Francesco De Nes, Merce Llabres Segura, Andrea Marin and Marta Simeoni
    MPath2PN - Translating metabolic pathways into Petri nets [ slides ]
  • Mary Ann Blaetke, Sonja Meyer and Wolfgang Marwan
    Pain Signaling - A Case Study of the Modular Petri Net Modeling Concept with Prospect to a Protein-Oriented Modeling Platform [ slides ]
  • Qian Gao, Fei Liu, David Tree and David Gilbert
    Multi-cell Modelling Using Coloured Petri Nets Applied to Planar Cell Polarity [ slides ]

17:30-17:40 Concluding remarks

Invited Talk

Systems Biology in Supercomputing Environment

Satoru Miyano

Human Genome Center, Institute of Medical Science, The University of Tokyo 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan

We developed a software platform XiP (eXtensible integrative Pipeline) that is a flexible, editable and modular environment with a user-friendly interface for systems biology. With XiP, we can build various analysis workflows including simulation, visualization, pathway modeling, etc. Construction of a workflow under XiP follows the intuitive notion of dragging and dropping. XiP already equips with several “ready to use” pipeline flows for the most common analysis and more than 300 statistical/computational analysis components, and XiP also recognizes components written in R (http://www.r-project.org). It runs under multiprocessors environments. The source code is available as open source under the Lesser General Public License (LGPL) (download: http://xip.hgc.jp/wiki/en/).

On the other hand, we have been developing a modeling and simulation tool Cell Illustrator Online 5.0 (CIO, https://cionline.hgc.jp/) that enables us to draw, model, elucidate and simulate complex biological processes and systems such as metabolic pathways, signal transduction cascades, gene regulatory pathways and dynamic interactions of various biological entities. Cell System Ontology (CSO) (http://www.csml.org/) and Cell System Markup Language (CSML) constitute the basis of CIO. CIO uses Hybrid Functional Petri Net with extension (HFPNe) which is defined by enhancing some functions to hybrid Petri net so that various aspects in biological pathways can be intuitively modeled. CIO has been used to build, for example, a simulatable macrophage pathway knowledge base (MACPAK) (http://macpak.csml.org/). A key technology for driving systems biology is a method for automatic parameter estimation for models. For this purpose, we developed a method for HFPNe, namely CIO, by using a technology called data assimilation which "blends" simulation models and observational data "rationally". This data assimilation method requires supercomputer systems.

We are currently creating the next generation supercomputing environment for systems biology on XiP by enrolling CIO, data assimilation, model checking, and various systems biology tools such as SiGN (large-scale gene network estimation software package (http://sign.hgc.jp/) on XiP.

Technical Description

Integrative biology, made possible by the spectacular growth of biological information, intends to decipher essential biological processes that are driven by complex mechanisms, involving miscellaneous interacting molecular compounds. In this context, the need for appropriate mathematical and computational modelling tools is widely advocated.

Since about 15 years 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 fundamental research. Indeed, because of their complexity, size and heterogeneity, biological networks raise distinctive challenges to the modeller.

The goal of this workshop is to provide a platform for researchers aiming at such fundamental research and real life applications.


  • standard Petri nets for qualitative modelling, if kinetics are unknown or deliberately abstracted;
  • discrete quantitative modelling by time Petri nets, or stochastic Petri nets to account for intrinsic noise of molecular fluctuation, and/or sources of extrinsic noise;
  • ordinary differential equations and continuous Petri nets, back and forth;
  • hybrid Petri nets, or how to handle different abstraction and time scales in biological processes;
  • case studies of metabolic, signalling, regulatory, and combined networks, or other biological applications;
  • analysis and simulation techniques, and related tools, including exchange formats, dedicated to biological processes.


This workshop intends to gather students and researchers, especially from Asian countries, 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 activities of Asian countries in Petri net applications on biological processes.

Paper submission

All papers should be in LNCS format, and will have to be submitted via EasyChair. Submitted papers should describe original work that has not been previously published and is not under review for publication elsewhere. There are three categories of papers:

  • Regular papers should not exceed 15 p. in LNCS format.
  • "Work in progress" papers, also up to 15 p. in LNCS format, which have to be indicated as such.
  • Short papers presenting original results should not exceed 6 p. in LNCS format, including figures, tables and references. Short papers may be selected for oral presentation.


Workshop Proceedings

Proceedings will be electronically published with CEUR Workshop Proceedings (http://ceur-ws.org) with five consecutive volume numbers for each workshop allocated with PETRI NET 2011, 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 -- Program Committee

Monika Heiner

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

Hiroshi Matsuno

Graduate School of Science and Engineering, Yamaguchi University, Japan
matsuno (at) sci.yamaguchi-u.ac.jp

Program Committee


  • April 15: Submission of papers.
  • May 15: Notification of acceptance/rejection.
  • June 01: Final version of papers.

… the end …

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