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
A Hybrid HMM Approach for the Dynamics of DNA Methylation
HSB
Controlling noisy expression through auto regulation of burst frequency and protein stability
HSB
Data-informed parameter synthesis for population Markov chains
HSB
Extracting landscape features from single particle trajectories
HSB
Fixed-point Computation of Equilibria in Biochemical Regulatory Networks
HSB
From Sensitive to Formal Barbaric Systems Biology
HSB
Fuzzy Matching in Symbolic Systems Biology
HSB
Geometric fluid approximation for general continuous-time Markov chains
HSB
Invited talk: Closed-loop neurohybrid interfaces: from in vitro to in vivo studies and beyond
HSB
Invited talk: Modelling and personalisation techniques for behavioural prediction and emotion recognition
HSB
Invited talk: Reaction networks, stability of steady states, motifs for oscillatory dynamics, and parameter estimation in complex biochemical mechanisms
HSB
Oded Maler: An odyssey from Computer Science to Biological Sciences
HSB
Poster flash: Comprehensive Modelling Platform
HSB
Poster flash: Formalizing metabolic-regulatory networks by hybrid automata
HSB
Rejection-Based Simulation of Stochastic Spreading Processes on Complex Networks
HSB
Temporal Logic Based Synthesis of Experimentally Constrained Interaction Networks
HSB
Timed Patterns: from Definition to Matching and Monitoring, a survey in memoriam Oded Maler
HSB
Using a hybrid approach to model central carbon metabolism across the cell cycle
HSB
rPrism -- A software for reactive weighted state transition models
HSB

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
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Sat 6 Apr

Displayed time zone: Amsterdam, Berlin, Bern, Rome, Stockholm, Vienna change

09:00 - 10:30
IHSB at S9
Chair(s): Milan Ceska Brno University of Technology
09:00
10m
Day opening
Opening
HSB

09:10
60m
Talk
Invited talk: Modelling and personalisation techniques for behavioural prediction and emotion recognition
HSB
Marta Kwiatkowska University of Oxford
10:10
10m
Short-paper
Poster flash: Comprehensive Modelling Platform
HSB
Matej Troják Masaryk University, David Safranek Masaryk University, Jan Červený Global Change Research Institute CAS, Marek Havlík Masaryk University, Lukrécia Mertová Masaryk University, Matej Hajnal Masaryk University, Jakub Hrabec Masaryk University, Jakub Šalagovič Masaryk University
10:20
10m
Short-paper
Poster flash: Formalizing metabolic-regulatory networks by hybrid automata
HSB
Lin Liu Freie Universität Berlin, Alexander Bockmayr Freie Universität Berlin
11:00 - 12:30
ModellingHSB at S9
Chair(s): Tatjana Petrov Universität Konstanz
11:00
30m
Talk
A Hybrid HMM Approach for the Dynamics of DNA Methylation
HSB
Charalampos Kyriakopoulos Saarland University, Pascal Giehr Saarland University, Alexander Lück Saarland University, Jörn Walter Saarland University, Verena Wolf Saarland University
11:30
30m
Talk
Controlling noisy expression through auto regulation of burst frequency and protein stability
HSB
Pavol Bokes Comenius University, Abhyudai Singh University of Delaware
12:00
30m
Talk
Using a hybrid approach to model central carbon metabolism across the cell cycle
HSB
Cecile Moulin Laboratoire de Recherche en Informatique, Université Paris-Saclay & UMR CNRS 8623, Laurent Tournier MaIAGE, INRA, Université Paris-Saclay., Sabine Peres Laboratoire de Recherche en Informatique, Université Paris-Saclay & UMR CNRS 8623.
14:00 - 15:30
Oded Maler memorial (1)HSB at S9
Chair(s): Nicola Paoletti Royal Holloway, University of London, UK
14:00
60m
Talk
Oded Maler: An odyssey from Computer Science to Biological Sciences
HSB
Thao Dang CNRS/VERIMAG
16:00 - 18:00
Oded Maler memorial (2)HSB at S9
Chair(s): Nicola Paoletti Royal Holloway, University of London, UK
16:00
60m
Talk
From Sensitive to Formal Barbaric Systems Biology
HSB
Alexandre Donze University of California, Berkeley
17:00
60m
Talk
Timed Patterns: from Definition to Matching and Monitoring, a survey in memoriam Oded Maler
HSB
Eugene Asarin IRIF, University Paris Diderot and CNRS, France

Sun 7 Apr

Displayed time zone: Amsterdam, Berlin, Bern, Rome, Stockholm, Vienna change

09:00 - 10:30
VHSB at S9
Chair(s): Nicola Paoletti Royal Holloway, University of London, UK
09:00
60m
Talk
Invited talk: Closed-loop neurohybrid interfaces: from in vitro to in vivo studies and beyond
HSB
Michela Chiappalone Italian Institute of Technology
10:00
30m
Talk
Temporal Logic Based Synthesis of Experimentally Constrained Interaction Networks
HSB
Judah Goldfeder Yeshiva University, Hillel Kugler Microsoft
11:00 - 12:30
AnalysisHSB at S9
Chair(s): Jerome Feret INRIA Paris
11:00
30m
Talk
Fixed-point Computation of Equilibria in Biochemical Regulatory Networks
HSB
Isabel Cristina Perez-Verona IMT Institute for Advanced Studies Lucca, Italy, Mirco Tribastone IMT Institute for Advanced Studies Lucca, Italy, Max Tschaikowski IMT Institute for Advanced Studies Lucca, Italy
11:30
30m
Talk
Rejection-Based Simulation of Stochastic Spreading Processes on Complex Networks
HSB
Gerrit Großmann Saarland University, Verena Wolf Saarland University
12:00
30m
Talk
rPrism -- A software for reactive weighted state transition models
HSB
Daniel Figueiredo University of Aveiro, Eugénio A. M. Rocha University of Aveiro, Madalena Chaves INRIA, Manuel A. Martins University of Aveiro
14:00 - 15:30
VIIHSB at S9
Chair(s): David Safranek Masaryk University
14:00
60m
Talk
Invited talk: Reaction networks, stability of steady states, motifs for oscillatory dynamics, and parameter estimation in complex biochemical mechanisms
HSB
Igor Schreiber University of Chemistry and Technology of Prague
15:00
30m
Talk
Geometric fluid approximation for general continuous-time Markov chains
HSB
Michalis Michaelides University of Edinburgh, Jane Hillston University of Edinburgh, Guido Sanguinetti University of Edinburgh
16:00 - 18:00
Synthesis and InferenceHSB at S9
Chair(s): Michela Chiappalone Italian Institute of Technology
16:00
30m
Talk
Extracting landscape features from single particle trajectories
HSB
Ádám Halász West Virginia University, Ouri Maler West Virginia University, Jeremy S Edwards University of New Mexico
16:30
30m
Talk
Fuzzy Matching in Symbolic Systems Biology
HSB
Adrian Riesco Universidad Complutense de Madrid, Beatriz Santos-Buitrago Seoul National University, Merrill Knapp SRI International, Gustavo Santos-Garcia Universidad de Salamanca, Carolyn Talcott SRI International
17:00
30m
Talk
Data-informed parameter synthesis for population Markov chains
HSB
Matej Hajnal Masaryk University, Tatjana Petrov Universität Konstanz, David Safranek Masaryk University, Morgane Nouvian University of Konstanz
17:30
10m
Day closing
Closing
HSB