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data structures and software dependability

computer science department

brandenburg university of technology cottbus - senftenberg

7th International Workshop on Biological Processes & Petri Nets (BioPPN 2016)

latest update: June 25, 2016, at 08:57 AM


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Programme


9.00 -14.00 Registration

14.00 - 15.00 Invited Talk BioPPN - joined session

session chair: Anna Gambin

15.00 - 15.15 coffee break

15.15 - 16.45 Session Talks BioPPN

session chair: Monika Heiner

regular papers: 30'
short poster presentation: 10'

  • Simon Hardy, Mathieu Pagé Fortin (regular paper):
    Analysis of the Signal Transduction Dynamics Regulating mTOR with Mathematical Modeling, Petri Nets and Dynamic Graphs [ slides ]
  • Christian Rohr (regular paper):
    Discrete-time leap method for stochastic simulation [ slides ]
  • Dorota Formanowicz, Marcin Radom, Piotr Formanowicz (short poster presentation):
    The influence of IL-18 on the process of atherosclerosis modeled and analyzed by stochastic Petri nets [ slides ]
  • Dorota Formanowicz, Agnieszka Rybarczyk, Piotr Formanowicz (short poster presentation):
    Selected aspects of essential hypertension and cardiovascular disease – modeled and analyzed using timed Petri nets [ slides ]
  • Weronika Wronowska, Grzegorz Bokota, Michał Kadlof, Jacek Sroka, Maciej Cytowski, Andrzej Kierzek, Dariusz Plewczyński (short poster presentation):
    iCell: Multiscale modelling of breast tumour growth;

16.45 - 17.15 coffee break/Poster Session

17.15 - 18.15 Invited Talk PNSE - joined session

  • Gabriele Taentzer
    Philipps University Marburg

    Model-Driven Development of Platform-Independent Mobile Applications

Invited Talk

Andrzej M Kierzek
Visiting Professor of Systems Biology
Faculty of Health and Medical Sciences, University of Surrey, UK
Head of Systems Modeling, Simcyp a Certara company, Sheffield, UK

Quasi-Steady State Petri Nets

We can sequence any DNA of interest, including full genome of an individual, but we are not making full use of this information yet. The ability to predict phenotype emerging from interactions between genotype and environmental conditions will revolutionise medicine and biotechnology. I am convinced that Molecular Biology knowledge will be used to reverse engineer molecular machinery of the cell as a computer model and use mechanistic simulation to predict cellular behaviour for particular sets of genetic and environmental perturbations.

The major limitation of mechanistic simulation of molecular cell biology is the determination of quantitative parameters at whole-cell scale. This challenge has been addressed in the special case of metabolic networks at steady state. Constraint Based Methods enable qualitative prediction of metabolic capabilities of Genome Scale Metabolic Networks (GSMN) without knowledge of rate constants and molecular concentrations. I will present application of this approach for the analysis of transcriptome data on individual breast cancer tumours in the context of Recon2 human GSMN revealing low prognosis cluster with active serotonin production.

Moreover, Systems Biology has lead to legacy of stochastic kinetic and ODE models of small, quantitatively parameterised sub-networks. This motivates iterative integration of GSMNs, large-scale rule-based models of regulatory networks and legacy of small-scale dynamic models towards whole-cell mechanistic simulations. I will introduce Quasi Steady State Petri Net (QSSPN) – a hybrid simulation algorithm allowing multi-formalism simulation integrating
i) qualitative rule based
ii) stochastic kinetic
iii) deterministic kinetic, and
iv) flux balance models.

I will present dynamic simulation of molecular interaction network describing gene regulation, signalling and whole-cell metabolism in human hepatocyte. I will also introduce a new version of the SurreyFBA software supporting multi-scale, multi-formalism simulations with QSSPN as well as wide range of constraint-based methods.

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 modelling formalisms and/or 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.

There will be a joined poster session of all workshops. The workshop presentations (talks) are single track.

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 2016, 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 a follow-up publication in Transactions on Petri Nets and other models of Concurrency (ToPNoC) or Fundamenta Informaticea.

Organizers -- Programme Committee

Anna Gambin

Warsaw University, Division of Mathematics, Informatics and Mechanics, Computational Biology Group, Poland
aniag@mimuw.edu.pl

Monika Heiner

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


Program Committee

Deadlines

  • April, 20 2016: Submission of papers.
  • May, 20 2016: Notification of acceptance/rejection.
  • June, 10 2016: Final version of papers.

Registration

Registration is handled by the hosting conference website PETRI NETS 2016

History of the workshop

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