Wednesday     Thursday     Friday

Wednesday, 12th September

With the only exception of the invited talk of Ilka M. Axmann, all sessions will be placed in the room D3 at Faculty of Informatics, Masaryk University (building D).

8:45 – 9:15 Registration
9:15 – 9:30 Welcome Session
9:30 – 10:30 Invited talk: Andrew Phillips 
Programming Languages for Molecular and Genetic Devices  (abstract)
Chair: Jérôme Feret
10:30 – 11:00 coffee break
11:00 – 12:30 Session I – Modelling and Engineering
Chair: Carolyn Talcott

Keenan Breik, Cameron Chalk, David Doty, David Haley and David Soloveichik. Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks
Samuel M.D. Oliveira, Mohamed N.M. Bahrudeen, Sofia Startceva, Vinodh Kandavalli and Andre S. Ribeiro. Modeling and Engineering Promoters with Pre-Defined RNA Production Dynamics in Escherichia Coli
Luca Laurenti, Alessandro Abate, Luca Cardelli, Marta Kwiatkowska and Boyan Yordanov. Experimental Biological Protocols with Formal Semantics


12:30 – 14:00 lunch
14:00 – 15:10 Session II.A (Flash Poster Presentations)
Chair: Milan Češka

in the order as listed in accepted flash posters
5 minutes per each presentation
15:10 – 15:40 Session II.B (Oral Presentation)
Chair: Milan Češka

Christoph Flamm, Jakob Lykke Andersen, Daniel Merkle and Peter Florian Stadler. Discovering Reaction Patterns in Chemical Reaction Networks


15:40 – 16:00 coffee break
16:00 – 17:10 transfer to Mendel Museum (by trolleys 25,26 or by trams 1,6 or by foot)
17:10 – 18:15 Invited talk: Ilka Axmann 
What Time Is It?  (abstract)  (slides)
room: Mendel Refectory in Mendel Museum
Chair: François Fages
18:15 – 18:30 Moravian wine session (Jan Obdržálek)
18:30 – 22:30 Welcome Reception in The Garden of The Augustinian abbey (winelist)

Thursday, 13th September

All sessions will be placed in the room D3 at Faculty of Informatics, Masaryk University (building D).

9:00 – 10:00 Invited talk: Mustafa Khammash 
Biomolecular Control Systems  (abstract)
Chair: David Šafránek
10:00 – 10:30 coffee break
10:30 – 12:30 Session III – Learning From Data
Chair: Boyan Yordanov

Carolyn Talcott, Akos Vertes, Mark-Oliver Stehr, Brian Davis, et al. Inferring Mechanism of Action of an Unknown Compound from Time Series Omics Data
Misbah Razzaq, Roland Kaminiski, Javier Romero, Torsten Schaub, Jeremie Bourdon and Carito Guziolowski. Computing Diverse Boolean Networks from Phosphoproteomic Time Series Data
Taisa Kushner, Sriram Sankaranarayanan and Souradeep Dutta. Robust Data-Driven Control of Artificial Pancreas Systems using Neural Networks
Emine Güven, Michael J Wester, Bridget S Wilson, Jeremy S Edwards and Ádám M Halász. Characterization of the Experimentally Observed Clustering of VEGF Receptors


12:30 – 14:00 lunch
14:00 – 15:00 Invited talk: Andrew Turberfield 
Modelling Biomimetic Structures and Machinery Using DNA  (abstract)
Chair: Milan Češka
15:00 – 15:30 coffee break
15:30 – 17:10 Session IV – Stochastic Analysis of Biochemical Systems
Chair: Tatjana Petrov

Luca Bortolussi and Luca Palmieri. Deep Abstractions of Chemical Reaction Networks
Pavol Bokes, Michal Hojcka and Abhyudai Singh. Buffering Gene Expression Noise by MicroRNA Based Feedforward Regulation
(Tool) Justin Feigelman, Daniel Weindl, Fabian J Theis, Carsten Marr and Jan Hasenauer. LNA++: Linear Noise Approximation with First and Second Order Sensitivities
(Tool) Andrzej Mizera, Jun Pang, Hongyang Qu and Qixia Yuan. ASSA-PBN 3.0: Analysing Context-sensitive Probabilistic Boolean Networks


17:10 – 17:30 business meeting (public part)
19:30 – 22:30 Conference Dinner and Best Paper Award at SunSet Restaurant

Friday, 14th September

All sessions will be placed in the room D3 at Faculty of Informatics, Masaryk University (building D).

9:00 – 10:00 Invited talk: Chris J. Myers 
A Standard-Enabled Workflow for Synthetic Biology  (abstract)  (slides)
Chair: Luca Bortolussi
10:00 – 10:30 coffee break
10:30 – 12:20 Session V – Analysis of Biochemical Systems
Chair: Loïc Paulevé

Timothy Self, David Gilbert and Monika Heiner. Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models
Cameron Chalk, Niels Kornerup, Wyatt Reeves and David Soloveichik. Composable Rate-Independent Computation in Continuous Chemical Reaction Networks
Jonathan Laurent, Hector F Medina-Abarca, Pierre Boutillier, Jean Yang and Walter Fontana. A Trace Query Language for Rule-based Models
(Tool) Pierre Boutillier, Ferdinanda Camporesi, Jean Coquet, Jerome Feret, Nathalie Theret, Kim Quyen Ly and Pierre Vignet. KaSa: a Static Analyzer for Kappa


12:20 – 13:30 lunch
13:30 – 15:20 Session VI – Synthesis and Inference
Chair: Christoph Flamm

Jeremy Revell and Paolo Zuliani. Stochastic Rate Parameter Inference using the Cross-Entropy Method
Ashutosh Gupta, Ankit Shukla and Somya Mani. Synthesis for Vesicle Traffic Systems
Hillel Kugler, Sara-Jane Dunn and Boyan Yordanov. Formal Analysis of Network Motifs
(Tool) François Fages and Sylvain Soliman. On Robustness Computation and Optimization in BIOCHAM-4


15:20 – 15:45 coffee break
15:45 – 16:45 Session VII (Oral Presentations) – System Identification
Chair: David Šafránek

Igor Schreiber, Vuk Radojkovic, František Muzika, Radovan Jurašek, Lenka Schreiberová and Jan Červený. Reaction Network Theory as a Tool for Finding Network Motifs for Oscillatory Dynamics and Kinetic Parameter Estimation in Complex Biochemical Mechanisms
Jan H. van Schuppen, Jana Němcová and Kaihua Xi. System Identification of a Continuous-Time Polynomial System by a Subalgebraic Procedure


16:45 Conference Closing