Publications


2012


  • D Maccagnola, E Messina, Q Gao, D Gilbert:
    A Machine Learning Approach for Generating Temporal Logic Descriptions of Complex Model Behaviours;
    Winter Simulation Conference 2012, accepted for publication.

    This paper gives more details of the clustering clustering methodology introduced in [6] which combines principal component analysis (PCA), distance similarity and density factors through the application of DBScan, and also describes a pattern mining approach for generating high-level classificatory descriptions of the behaviour of the clusters in temporal logic.
  • M Heiner and D Gilbert:
    BioModel Engineering for Multiscale Systems Biology;
    Progress in Biophysics and Molecular Biology, 2012. [ doi ]

    We discuss some motivational challenges arising from the need to model and analyse complex biological systems at multiple scales (spatial and temporal), and present a biomodel engineering framework to address some of these issues within the context of multiscale Systems Biology. Our methodology is based on a structured family of Petri net classes which enables the investigation of a given system using various modelling abstractions: qualitative, stochastic, continuous and hybrid, optionally in a spatial context. We illustrate our approach with case studies demonstrating hierarchical flattening, treatment of space, and hierarchical organisation of space.
  • Q Gao, F Liu, D Maccagnola, D Gilbert, M Heiner, D Tree:
    Multiscale Modelling and Analysis of Planar Cell Polarity in Drosophila Wing;
    Journal IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol 99, 2012. [ doi ].

    This paper refines the model introduced in [4] by a couple of biologically more faithful principles (e.g. circular topology at the intracellular level, a variety of biasing mechanisms to induce polarity, different clone shapes) and extends the applied computational technology by constraint solving, automated clustering and PLTLc model checking of primary and secondary data.

2011


  • J Wegener, M Schwarick and M Heiner:
    A Plugin System for Charlie;
    In Proc. International Workshop on Concurrency, Specification, and Programming (CSP 2011), Bialystok University of Technology, pages 531–554, September 2011. [ pdf ]

    This paper presents a tool for analyzing place/transition Petri nets (or the net structure underlying stochastic, continuous or hybrid Petri nets) which comes with a transparent rule system and an easy to vary functionality thanks to the supported plugin mechanism.
  • Q Gao, F Liu, D Gilbert, M Heiner and D Tree:
    A Multiscale Approach to Modelling Planar Cell Polarity in Drosophila Wing using Hierarchically Coloured Petri Nets;
    In Proc. 9th International Conference on Computational Methods in Systems Biology (CMSB 2011), Paris, ACM digital library, pages 209–218, September 2011. [ link ]

    This paper introduces an approach to model at different spatial scales, using the new concept of hierarchically coloured Petri Nets (HCPN). As a proof of concept, it is used to model the PCP tissue phenomenon, which involves intra- and inter-cellular signalling mechanisms. Computational experiments using stochastic and continuous simulation complemented by PLTL model checking confirm that model behaviour correctly reflects biological knowledge.
  • M Schwarick , C Rohr and M Heiner:
    MARCIE - Model checking And Reachability analysis done effiCIEntly;
    In Proc. 8th International Conference on Quantitative Evaluation of SysTems (QEST 2011), Aachen, Germany, IEEE CS Press, pages 91–100, September 2011. [ pdf ]

    This paper presents a multi-threaded analysis tool for Generalized Stochastic Petri Nets comprising symbolic and simulative engines. Architecture and most important distinguishing features are discussed. Extensive computational experiments demonstrate its strength in comparison with PRISM, and suggest that especially for biological networks MARCIE is currently the most efficient model checking tool.
  • Q Gao, F Liu, D Tree and D Gilbert:
    Multicell Modelling Using Coloured Petri Nets Applied to Planar Cell Polarity;
    In Proc. of the International Workshop on Biological Processes & Petri Nets (BioPPN 2011), satellite event of Petri Nets 2011, CEUR-WS.org, CEUR Workshop Proceedings, volume 724, pages 135–150, June 2011. [ pdf ]

    This paper discusses basic principles of using coloured Petri nets to model a multi-cellular system with hierarchical structure while keeping the model mathematically tractable. It illustrates different levels of abstraction to model planar cell polarity.
  • M Heiner and D Gilbert:
    How Might Petri Nets Enhance Your Systems Biology Toolkit;
    In Proc. PETRI NETS 2011, LNCS 6709, Springer, pages 17–37. [ link ]

    This paper gives an overview on the Petri net approach as an umbrella formalism to support the process of BioModel Engineering, specifically by unifying the qualitative, stochastic and continuous paradigms. It summarizes tools and techniques which have been shown to be useful so far, and describes some of the current open challenges.

latest update: November 24, 2012, at 08:43 AM