ETAPS 2019
Sat 6 - Thu 11 April 2019 Prague, Czech Republic

The workshop centres on dynamical models in biology, with an emphasis on both hybrid systems (in the classical sense, i.e., mixed continuous/discrete/stochastic systems) and hybrid approaches that combine modelling, analysis, algorithmic and experimental techniques from different areas.

Hybrid systems and approaches are essential to the understanding of complex living systems, which are characterized by stochasticity and heterogeneous (continuous and discrete) spatiotemporal scales. These methods are crucial also for the design and analysis of artificial biochemical systems (e.g., engineered bacteria or molecular machines) and of medical cyber-physical systems such as pacemakers and infusion pumps. The complexity of such models makes their formal analysis challenging, and even their simulations are frequently impractical, calling for appropriate model abstractions and scalable analysis methods.

HSB aims at bringing together researchers from different disciplines interested in applying these methods to the study of structure, dynamics, and control mechanisms of living systems.

Workshop webpage

http://hsb2019.fit.vutbr.cz/

Invited speakers

  • Marta Kwiatkowska, University of Oxford (UK)
  • Michela Chiappalone, Istituto Italiano di Tecnologia of Genova (IT)
  • Igor Schreiber, University of Chemistry and Technology Prague (CZ)

In memory of Oded Maler

HSB will have a special session dedicated to the memory of Oded Maler, very much missed member of HSB’s steering committee and one of the founders of the workshop. The session will celebrate his life and scientific contributions with invited talks by:

  • Thao Dang, CNRS/VERIMAG, France,
  • Eugene Asarin, IRIF, France,
  • Alexandre Donzé, Decyphir Inc. and University of California at Berkeley, USA

Accepted Papers

Title

Call for Papers

Topics of interest

HSB is a single-track workshop centring on dynamical models in biology, with an emphasis on both hybrid systems (in the classical sense, i.e., mixed continuous/discrete/stochastic systems) and hybrid approaches that combine modelling, analysis, algorithmic and experimental techniques from different areas.

HSB solicits original research articles, tool papers, posters, and presentations on the modelling and analysis of biological systems. Hybrid dynamical modelling but also other dynamical modelling approaches are equally part of the scope of the workshop. Interdisciplinary contributions, such as combining modelling, analysis, algorithmic and experimental techniques from different areas, are especially welcome.

Topics of interest include, but are not limited to:

  • Modelling and analysis of metabolic, signalling, and genetic regulatory networks in living cells.
  • Models of tissues, organs, physiological models.
  • Models and methods coping with incomplete, uncertain and heterogeneous information including learning for biological systems, parametric synthesis and inference.
  • Stochastic and hybrid models in biology.
  • Hierarchical systems for multi-scale, multi-domain analysis.
  • Abstraction, approximation, discretisation, and model reduction techniques.
  • Modelling, analysis and design for synthetic biology, cyber-biological systems and biomedical studies (e.g. therapies, teleoperation).
  • Game-theoretical frameworks and population models in biology (e.g. Mixed-Effects and Bayesian modelling).
  • Biological applications of quantitative and formal analysis techniques (e.g. reachability computation, model checking, abstract interpretation, bifurcation theory, stability and sensitivity analysis).
  • Efficient techniques for combined and heterogeneous (stochastic/deterministic, spatial/non-spatial) simulations for biological models.
  • Modelling languages and logics for biological systems, with related analysis and simulation tools.
  • Control architectures of biological systems including biology-in-the-loop systems and bio-robotics.

In general, the workshop is open to new theoretical results with potential applications to systems and synthetic biology, as well as novel applications and case studies of existing methods, tools, or frameworks.

HSB 2019 will have informal pre-proceedings available during the workshop. Post-proceedings will be published as a volume in the Springer LNCS/LNBI series, indexed by ISI Web of Science, Scopus, ACM Digital Library, DBLP, and Google Scholar.

A journal special issue is under consideration.

Call for Papers

We solicit high-quality submissions, to be refereed by the Program Committee. Submitted papers will describe original work that has not been previously published and is not under review for publication elsewhere. We accept the following two types of paper submissions:

  • regular papers (max 15 pages + max 2 pages of references)
  • tool papers (max 6 pages + max 2 pages of references)

Tool papers require the submission of an executable artifact that contains clear instructions for the reviewer on how to run the tool. Submissions can contain a well-marked appendix that is not counted to the page limit. The appendix will not be published in the proceeding and the reviewers are not required to read the appendix and thus the submission must be intelligible without it.

Each accepted paper will have a slot for oral presentation at the workshop.

Format and Submission

Papers should be written in English and have to be formatted in Springer LNCS style. Each submission will be reviewed by at least three reviewers. Papers need to be submitted electronically as PDF files via EasyChair online submission system (coming soon).

Call for Posters

HSB 2019 also solicits poster abstracts presenting original unpublished work. The abstracts must be written in English, formatted in Springer LNCS style and should not exceed 2 pages including references. Poster abstracts should be submitted via EasyChair online submission system. The program committee will select best abstracts for publication in the conference proceedings.

Each accepted poster will also have a slot for a 5-minute flash oral presentation at the workshop.

Previously published work

In addition to original contributions, HSB 2019 invites abstracts for oral and presentation of recent outstanding results already published or accepted for publication in a recognised journal or a high-quality conference during the last year. These non-original contributions will be presented at the workshop but will not be part of the proceedings.

Dates

Sat 6 Apr

hsb-2019-papers
09:00 - 10:30: HSB - I at S9
Chair(s): Milan CeskaBrno University of Technology
hsb-2019-papers09:00 - 09:10
Day opening
hsb-2019-papers09:10 - 10:10
Talk
Marta KwiatkowskaUniversity of Oxford
hsb-2019-papers10:10 - 10:20
Short-paper
Matej TrojákMasaryk University, David SafranekMasaryk University, Jan ČervenýGlobal Change Research Institute CAS, Marek HavlíkMasaryk University, Lukrécia MertováMasaryk University, Matej HajnalMasaryk University, Jakub HrabecMasaryk University, Jakub ŠalagovičMasaryk University
hsb-2019-papers10:20 - 10:30
Short-paper
Lin LiuFreie Universität Berlin, Alexander BockmayrFreie Universität Berlin
hsb-2019-papers
11:00 - 12:30: HSB - Modelling at S9
Chair(s): Tatjana PetrovUniversität Konstanz
hsb-2019-papers11:00 - 11:30
Talk
Charalampos KyriakopoulosSaarland University, Pascal GiehrSaarland University, Alexander LückSaarland University, Jörn WalterSaarland University, Verena WolfSaarland University
hsb-2019-papers11:30 - 12:00
Talk
Pavol BokesComenius University, Abhyudai SinghUniversity of Delaware
hsb-2019-papers12:00 - 12:30
Talk
Cecile MoulinLaboratoire de Recherche en Informatique, Université Paris-Saclay & UMR CNRS 8623, Laurent TournierMaIAGE, INRA, Université Paris-Saclay., Sabine PeresLaboratoire de Recherche en Informatique, Université Paris-Saclay & UMR CNRS 8623.
hsb-2019-papers
14:00 - 15:30: HSB - Oded Maler memorial (1) at S9
Chair(s): Nicola PaolettiRoyal Holloway, University of London, UK
hsb-2019-papers14:00 - 15:00
Talk
Thao DangCNRS/VERIMAG
hsb-2019-papers
16:00 - 18:00: HSB - Oded Maler memorial (2) at S9
Chair(s): Nicola PaolettiRoyal Holloway, University of London, UK
hsb-2019-papers16:00 - 17:00
Talk
Alexandre DonzeUniversity of California, Berkeley
hsb-2019-papers17:00 - 18:00
Talk
Eugene AsarinIRIF, University Paris Diderot and CNRS, France

Sun 7 Apr

hsb-2019-papers
09:00 - 10:30: HSB - V at S9
Chair(s): Nicola PaolettiRoyal Holloway, University of London, UK
hsb-2019-papers09:00 - 10:00
Talk
Michela ChiappaloneItalian Institute of Technology
hsb-2019-papers10:00 - 10:30
Talk
Judah GoldfederYeshiva University, Hillel KuglerMicrosoft
hsb-2019-papers
11:00 - 12:30: HSB - Analysis at S9
Chair(s): Jerome FeretINRIA Paris
hsb-2019-papers11:00 - 11:30
Talk
Isabel Cristina Perez-VeronaIMT Institute for Advanced Studies Lucca, Italy, Mirco TribastoneIMT Institute for Advanced Studies Lucca, Italy, Max TschaikowskiIMT Institute for Advanced Studies Lucca, Italy
hsb-2019-papers11:30 - 12:00
Talk
Gerrit GroßmannSaarland University, Verena WolfSaarland University
hsb-2019-papers12:00 - 12:30
Talk
Daniel FigueiredoUniversity of Aveiro, Eugénio A. M. RochaUniversity of Aveiro, Madalena ChavesINRIA, Manuel A. MartinsUniversity of Aveiro
hsb-2019-papers
14:00 - 15:30: HSB - VII at S9
Chair(s): David SafranekMasaryk University
hsb-2019-papers14:00 - 15:00
Talk
Igor SchreiberUniversity of Chemistry and Technology of Prague
hsb-2019-papers15:00 - 15:30
Talk
Michalis MichaelidesUniversity of Edinburgh, Jane HillstonUniversity of Edinburgh, Guido SanguinettiUniversity of Edinburgh
hsb-2019-papers
16:00 - 18:00: HSB - Synthesis and Inference at S9
Chair(s): Michela ChiappaloneItalian Institute of Technology
hsb-2019-papers16:00 - 16:30
Talk
Ádám HalászWest Virginia University, Ouri MalerWest Virginia University, Jeremy S EdwardsUniversity of New Mexico
hsb-2019-papers16:30 - 17:00
Talk
Adrian RiescoUniversidad Complutense de Madrid, Beatriz Santos-BuitragoSeoul National University, Merrill KnappSRI International, Gustavo Santos-GarciaUniversidad de Salamanca, Carolyn TalcottSRI International
hsb-2019-papers17:00 - 17:30
Talk
Matej HajnalMasaryk University, Tatjana PetrovUniversität Konstanz, David SafranekMasaryk University, Morgane NouvianUniversity of Konstanz
hsb-2019-papers17:30 - 17:40
Day closing