latest update: June 25, 2016, at 08:57 AM
session chair: Anna Gambin
session chair: Monika Heiner
regular papers: 30'
short poster presentation: 10'
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.
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).
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.
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.
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.
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 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]
Division of Mathematics, Informatics and Mechanics, Computational Biology Group, Poland
Registration is handled by the hosting conference website PETRI NETS 2016