HSB 2015 will be a two-day workshop, co-located with CONCUR 2015, the 26th Conference on Concurrency Theory), QEST 2015 (12th International Conference on Quantitative Evaluation of SysTems), FORMATS 2015 (13th International Conference on Formal Modeling and Analysis of Timed Systems), and among other events as part of the Madrid Meet 2015 meeting.
- Luca Cardelli, Microsoft Research
Morphisms of reaction networks
- Mustafa Khammash, ETH
Zurich
Cybergenetics: Synthetic Circuits and Systems for the Precise Control of Living Cells
Systems biology aims at providing a system-level understanding of biological systems by unveiling their structure, dynamics, and control methods. Living systems are intrinsically multi-scale in space and in time; they also exhibit a mixture of deterministic and stochastic behaviours. It is therefore very difficult to model them homogeneously, for example by means of systems of differential equations or by purely discrete models. Furthermore, such models are often not easily amenable to formal analysis and even their simulations are frequently impractical. Indeed, an important open problem is finding appropriate computational models that scale-up well for both simulation and formal analysis of biological processes.
Hybrid modelling techniques, combining discrete and continuous components and dynamics, are gaining more and more attention in systems biology. They have been applied to successfully capture the behaviour of several biological complex systems, including genetic regulatory networks, metabolic reactions, signalling pathways as well as higher level models of tissues and organs. As the challenges of scale and intrinsic heterogeneity and inhomogeneity are coming to the forefront of systems biology, the value of the hybrid dynamical modelling paradigm, integrating mathematical models that address distinct spatio-temporal scales and subsystems, becomes evident.
In this spirit, the scope of the HSB workshop is the general area of dynamical models in Biology with an emphasis on hybrid approaches — by no means restricted to a narrow class of mathematical models — and taking advantage of techniques developed separately in different areas.
Topics of interest include, but are not limited to:
- Models of metabolic, signalling, and genetic regulatory networks in living cells
- Models of tissues, organs; physiological models
- Biological applications of analysis techniques such as reachability computation, model checking, abstract interpretation, bifurcation theory, stability and sensitivity analysis
- Parametric and non-parametric system identification techniques (learning models from experimental data)
- Efficient techniques for combined (stochastic/deterministic, spatial/non-spatial) simulations for biological models
- Modelling languages for biological systems, with related analysis and simulation tools
- Models coping with incomplete and uncertain information
- Stochastic hybrid models in biology
- Hierarchical systems for multi-scale, multi-domain analysis
- Abstraction, approximation, discretisation, and model reduction techniques
- Game-theoretical frameworks in biology (e.g., population dynamics)
- Modelling and synthesis for synthetic biology
Submission of full and short papers and posters has been closed. See the list of accepted papers, list of accepted posters, and the workshop programme.
The registration can be done via the Madrid Meet 2015.
| Posters/Demos Submission: | - | August 15, 2015 (closed) | ||
| Paper Submission: | - | June 19, 2015 (closed) | ||
| Author Notification: | - | July 17, 2015 | ||
| Early Registration: | - | July 24, 2015 | ||
| Final Submission: | - | September 11, 2015 |
- Andreea Beica, Calin Guet and Tatjana Petrov: Efficient reduction of Kappa models by static
inspection of the rule-set
- R. Ramanathan, Yan Zhang, Jun Zhou, Weng-Fai Wong and P. S. Thiagarajan: Parallelized Statistical Model Checking for Analysis of Biological Pathways
- Laura Nenzi, Ezio Bartocci, Luca Bortolussi, Dimitrios Milios and Guido Sanguinetti: Studying Emergent Behaviours in Morphogenesis using Signal Spatio-Temporal Logic
- Christoph Bock, Luca Bortolussi, Thilo Krüger and Linar Mikeev: Model-based whole genome analysis of DNA methylation fidelity
- Delphine Draelants, Przemyslaw Klosiewicz, Jan Broeckhove and Wim Vanroose: Solving General Auxin Transport Models with a Numerical Continuation Toolbox in Python: PyNCT
- Marta Kwiatkowska, Alexandru Mereacre, Nicola Paoletti and Andrea Patane: Synthesising robust and optimal parameters for cardiac pacemakers using symbolic and evolutionary computation techniques
- Benjamin M. Gyori, Bing Liu, Soumya Paul, R Ramanathan and P S Thiagarajan: Approximate Probabilistic Verification of Hybrid Systems
- Lubos Brim, Martin Demko, Samuel Pastva and David Šafránek: High-Performance Discrete Bifurcation Analysis for Piecewise-Affine Dynamical Systems
- Eugenio Cinquemani: Reconstructing statistics of promoter switching from reporter protein population snapshot data
- Gustavo Santos-Garcia, Javier De Las Rivas and Carolyn Talcott: Analysis of Cellular Proliferation and Survival Signaling by Using Two Ligand/Receptor Systems Modeled by Pathway Logic
- Adam Streck and Heike Siebert: Comparative Statistical Analysis of Qualitative Parametrization Sets
- Louis Fippo Fitime, Christian Schuster, Peter Angel, Olivier Roux and Carito Guziolowski: Integrating time-series data on large-scale cell-based models
- Md. Ariful Islam, Richard Defrancisco, Chuchu Fan, Radu Grosu, Sayan Mitra and Scott Smolka: Model Checking Tap Withdrawal in C. Elegans
- Md. Ariful Islam, Richard Defrancisco, Chuchu Fan, Radu Grosu, Sayan Mitra and Scott Smolka: Model Checking Tap Withdrawal in C. Elegans
- Monika Varga, Ales Prokop and Bela Csukas: Unified dynamic modeling of conservation low and sign based, hybrid, multiscale biosystems
- Hiroshi Yoshida: A model towards multicell-turnover patterns using multivariable polynomials - Polynomial Life
- Matej Klement, David Šafránek, Jan Červený, Tadeáš Děd, Matej Troják, Lubos Brim and Stefan Mueller: E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria
- Delphine Draelants, Przemyslaw Klosiewicz, Jan Broeckhove and Wim Vanroose: Numerical Continuation Toolbox in Python: PyNCT
- Milan Ceska, Caroline Schneider, Alessandro Abate, David Šafránek, Louis Mahadevan and Marta Kwiatkowska: Stochastic Modelling of the Interface between Regulatory Enzymes and Transcriptional Initiation at Inducible Genes
- Miriam García Soto: Demo abstract of AVERIST: Algorithmic verifier of stability
- Ratan Lal: Bounded reachability analysis of parameterized linear hybrid systems
- Katherine Casey and Jamie Vicary: Graphical Logic for Biological Modelling
- Daniel Figueiredo and Manuel A. Martins: Two CS paradigms in biological boolean networks
- Linar Mikeev and Verena Wolf: SHAVE - Stochastic Hybrid Analysis of Markov Population Models
- Alessandro Abate, University of Oxford, Oxford, UK
- David Šafránek, Masaryk University, Brno, Czech Republic
- Alessandro Abate, University of Oxford, UK - (co-chair)
- Ezio Bartocci, Vienna University of Technology, Austria
- Gregory Batt, INRIA Rocquencourt, France
- Sergiy Bogomolov, IST Austria
- Luca Bortolussi, Univerity of Trieste, Italy
- Kevin Burrage, University of Oxford, UK
- Luca Cardelli, Microsoft Research, Cambridge, UK
- Pieter Collins, Maastricht University, The Netherlands
- Milan Češka, Masaryk University, Czech Republic
- Neil Dalchau, Microsoft Research, Cambridge, UK
- Thao Dang, VERIMAG/CNRS, Grenoble, France
- Hidde de Jong, INRIA Grenoble - Rhône-Alpes, France
- Alexandre Donzé, UC Berkley, USA
- François Fages, INRIA Rocquencourt, France
- Eric Fanchon, TIMC-IMAG Laboratory, Grenoble, France
- Giancarlo Ferrari-Trecate, University of Pavia, Italy
- Elisa Franco, University of California at Riverside / Caltech, USA
- Sicun Gao, MIT CSAIL, USA
- Radu Grosu, Vienna University of Technology, Austria
- Ádám Halász, West Virginia University, USA
- Joao Hespanha, University of California, USA
- Jane Hillston, University of Edinburgh, UK
- Agung Julius, Rensselaer Polytechnic Institute, USA
- Heinz Koeppl, TU Darmstadt, Germany
- Hillel Kugler, Microsoft Research, Cambridge, UK
- Marta Kwiatkowska, Oxford University, UK
- Pietro Lio', University of Cambridge, UK
- Oded Maler, VERIMAG/CNRS, Grenoble, France
- Andrzej Mizera, University of Luxembourg
- Stefan Müller, RICAM ÖAW, Austria
- Chris Myers, University of Utah, USA
- Nicola Paoletti, University of Oxford, UK
- Ion Petre, Åbo Akademi University, Finland
- Tatjana Petrov, IST Austria
- Carla Piazza, University of Udine, Italy
- Nir Piterman, University of Leicester, UK
- Alberto Policriti, University of Udine, Italy
- Guido Sanguinetti, University of Edinburgh, UK
- Abhyudai Singh, University of Delaware, USA
- Kateřina Staňková, Maastricht University, The Netherlands
- David Šafránek, Masaryk University, Czech Republic - (co-chair)
- P.S. Thiagarajan, National University of Singapore, Singapore
- Jana Tůmová, Royal Institute of Technology, Sweden
- S.A. Wahl, Delft University of Technology, The Netherlands
- Verena Wolf, Saarland University, Germany
- Boyan Yordanov, Microsoft Research, Cambridge, UK
- Paolo Zuliani, Newcastle University, UK
- Ezio Bartocci, Vienna University of Technology, Austria
- Luca Bortolussi, Univerity of Trieste, Italy
- Thao Dang, VERIMAG/CNRS, Grenoble, France
- Ádám Halász, West Virginia University, USA
- Oded Maler, VERIMAG/CNRS, Grenoble, France
- Carla Piazza, University of Udine, Italy
- HSB 2014, Vienna, Austria, July 23-24, 2014 at CAV 2014
- HSB 2013, Taormina, Italy, September 2, 2013 at ECAL 2013
- HSB 2012, Newcasle upon Tyne, UK, September 3, 2012 at CONCUR 2012
