[CEUR Workshop Proceedings] Vol-724
urn:nbn:de:0074-724-4

Copyright © 2011 for the individual papers by the papers' authors. Copying permitted only for private and academic purposes. This volume is published and copyrighted by its editors.

BioPPN-2011
International Workshop on Biological Processes & Petri Nets


Proceedings of the International Workshop on Biological Processes & Petri Nets

Newcastle upon Tyne, United Kingdom, June 20, 2011.


Edited by

Monika Heiner *
Hiroshi Matsuno **

* Brandenburg University of Technology at Cottbus, Faculty of Mathematics, Natural Sciences and Computer Science, D-03013 Cottbus, Germany
** Yamaguchi University, Graduate School of Science and Engineering, 753-8512 Yamaguchi, Japan




Table of Contents

    Invited Talk

  1. Systems Biology in Supercomputing Environment 6
    Satoru Miyano

    2. Session A: Modelling

  2. Optimal Control of Asynchronous Boolean Networks Modeled by Petri Nets 7-20
    Koichi Kobayashi, Kunihiko Hiraishi
  3. GReg : a Domain Specific Language for the Modeling of Genetic Regulatory Mechanisms 21-35
    Nicolas Sedlmajer, Didier Buchs, Steve Hostettler, Alban Linard, Edmundo Lopez, Alexis Marechal
  4. Modelling Reaction Systems with Petri Nets 36-52
    Jetty Kleijn, Maciej Koutny, Grzegorz Rozenberg

    5. Session B: Analysis

  5. Parameter Estimation of Biological Pathways Using Data Assimilation and Model Checking 53-70
    Chen Li, Keisuke Kuroyanagi, Masao Nagasaki, Satoru Miyano
  6. Studying Steady States in Biochemical Reaction Systems by Time Petri Nets 71-86
    Louchka Popova-Zeugmann, Elisabeth Pelz
  7. Two Modeling Methods for Signaling Pathways with Multiple Signals using UPPAAL 87-101
    Shota Nakano, Shingo Yamaguchi

    8. Session C: Applications

  8. MPath2PN - Translating Metabolic Pathways into Petri Nets 102-116
    Paolo Baldan, Nicoletta Cocco, Francesco De Nes, Merce Llabres Segura, Andrea Marin, Marta Simeoni
  9. Pain Signaling - A Case Study of the Modular Petri Net Modeling Concept with Prospect to a Protein-Oriented Modeling Platform 117-134
    Mary Ann Blaetke, Sonja Meyer, Wolfgang Marwan
  10. Multi-cell Modelling Using Coloured Petri Nets Applied to Planar Cell Polarity 135-150
    Qian Gao, Fei Liu, David Tree, David Gilbert

The whole proceedings can also be downloaded as a single file (PDF, including title pages, preface, and table of contents).

09-Jun-2011: submitted by Hiroshi Matsuno
11-Jun-2011: published on CEUR-WS.org