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data structures and software dependability

computer science department

brandenburg university of technology cottbus - senftenberg

6th International Workshop on Biological Processes & Petri Nets (BioPPN 2015)

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

Basic facts

Output

See you all next year at BioPPN 2016 in Torun.

Index

Programme

CEUR Workshop Proceedings Vol. 1373

Location: Forum Building

invited talks (joined sessions): Auditorium F
BioPPN workshop sessions: Room OF2072

lunch:

UAE (Alumni association) on the roof of the Forum building

8:30 – 09:00 Registration

9.00 - 10.00 Invited Talk - joined session

10.00 - 10.30 Session 1 - Regular Papers

session chair: Monika Heiner

  • Atsushi Mizuta, Qi-Wei Ge, and Hiroshi Matsuno
    Dependent shrink for Petri net models of signaling pathways [ slides ]

30' coffee break

11.00 - 12.30 Session 2 - Regular Papers

session chair: Hiroshi Matsuno

  • Paolo Baldan, Martina Bocci, Daniele Brigolin, Nicoletta Cocco, Marta Simeoni
    Petri nets for modelling and analysing trophic networks [ slides ]
  • Diana-Elena Gratie and Ion Petre
    Full structural model refinement as type refinement of colored Petri nets [ slides ]
  • Mary Ann Blätke and Christian Rohr
    A coloured Petri net approach for spatial Biomodel Engineering based on the modular model composition framework Biomodelkit [ slides ]

90' lunch break

14.00 - 15.00 Invited Talk - joined session

session chair: Annegret Wagler

30' coffee break

15.30 - 16.30 Session 3 - Position Paper and Discussion

session chair: Monika Heiner

  • Hugues Bersini
    State-transition diagrams for biological modelling: A few cases
  • Discussion and Closing Remarks

Invited Talk

Luis M. Torres
Centro de Modelización Matemática / Escuela Politécnica Nacional

A compact modeling approach for deterministic biological systems

Petri nets (an their extensions) have become a sound framework for modeling and analyzing several types of biochemical processes in Systems Biology. The extension that we present in this talk may be useful for obtaining a compact model for the dynamics of certain discrete deterministic systems. Our model relies on the definition of a priority relation between conflicting transitions, which is encoded by orienting the edges of a transition conflict graph. We provide a characterization in terms of a local consistency condition of those deterministic systems whose dynamic behavior can be encoded using our approach. Finally, we address the problem of providing an appropriate priority relation governing the dynamic behavior of the studied system by analyzing experimental data. Since performing wet-lab experiments is typically expensive and time-consuming, our aim is to design the experiments in such a way that as few of them suffice to gain the required information.

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 and other concurrency models 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, specifically when multiple scales and multiple levels come into play. We are looking for approaches helping to bridge the gap between different formalisms, with Petri nets being one them, as they 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).

Topics of interest include, but are not limited to:

  • qualitative approaches (e.g., qualitative Petri nets), if kinetics are unknown or deliberately abstracted away;
  • stochastic approaches (e.g., stochastic Petri nets) to account for intrinsic noise of molecular fluctuation, and/or sources of extrinsic noise;
  • continuous approaches (e.g., continuous Petri nets, and thus Ordinary Differential Equations) as averaged deterministic abstractions;
  • hybrid approaches (e.g., hybrid Petri nets), or how to handle different abstraction and time scales in biological processes;
  • dedicated support of space, multi-scale and/or multi-level issues;
  • case studies of metabolic, signalling, regulatory, and combined networks, or other biological applications;
  • dedicated analysis and simulation techniques;
  • related tool development, 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.

Objectives

This workshop intends to gather students and researchers, who have interests in the application of Petri nets or other concurrency modelling and analysis techniques for biological processes. Its main goal will be to demonstrate that concurrency modelling and analysis can be effective techniques 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 the applications of concurrency techniques to 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 will be published.

Proceedings

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 2015, and under the default copyright regulations:

The copyright for the individual items (subsuming any type of computer-represented files containing articles, software demos, videos, etc.) within a proceedings volume is owned by default by their respective authors. [http://ceur-ws.org]

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

Monika Heiner

Brandenburg Technical University (BTU), Computer Science Institute, Germany
Monika.Heiner@b-tu.de, Monika.Heiner@brunel.ac.uk

Annegret Wagler

University Blaise Pascal (Clermont-Ferrand II), Faculty of Sciences and Technology, France
wagler@isima.fr

Program Committee

Deadlines

  • April, 26 2015: Submission of papers.
  • May, 22 2015: Notification of acceptance/rejection.
  • June, 15 2015: Final version of papers.

Registration

Registration is handled by the hosting conference website PETRI NETS 2015

History of the workshop

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