Program

Wednesday     Thursday     Friday

Wednesday, 18th September

All sessions will take place in room 3B, building H3, University of Trieste

 

8:15- 8:50	Registration
8:50 – 9:00	Conference Opening
9:00 – 10:00	Invited talk: Trevor Graham   Title: Measuring cancer evolutionary dynamics from genomic data Chair: Guido Sanguinetti
10:00 – 10:50	Regular Session 1 – Boolean Networks Chair:  Paolo Ballarini Hugues Mandon, Cui Su, Jun Pang, and Loïc Paulevé.  Sequential Reprogramming of Boolean Networks Made Practical Jérémie Pardo, Sergiu Ivanov, and Franck Delaplace.  Sequential Reprogramming of Biological Network Fate
10:50 – 11:20	Coffee Break
11:20 – 12:05	Tool Session 1 – Model Structure and Behaviour Chair:  Laura Nenzi Judah Goldfeder and Hillel Kugler.  BRE:IN – A Backend for Reasoning about Interaction Networks with Temporal Logic Russ Harmer and Eugenia Oshurko.  KAMIStudio: an environment for biocuration of cellular signalling knowledge Maria Pia Saccomani.  A new version of DAISY to test structural identifiability of biological models
12:05 – 12:55	Highlight Talks Chair:  Luca Bortolussi Carolyn Talcott, Akos Vertes, Albert-Baskar Arul, Peter Avar, Andrew Korte, Lida Parvin, Ziad Saab, Deborah Bunin, Merrill Knapp, Denise Nishita, Andrew Poggio, Mark-Oliver Stehr, Brian Davis, Christine Morton and Maria Zavodszky.  Transcriptional response of SK-N-AS cells to methamidophos Ankit Gupta, Mustafa Khammash and Guido Sanguinetti.  Bayesian parameter estimation for stochastic reaction networks from steady-state observations Kaan Öcal, Ramon Grima and Guido Sanguinetti.  Parameter estimation for biochemical reaction networks using Wasserstein distances Lenka Pribylova and Barbora Losova.  Symmetry breaking for GATA-1/PU.1 model Julien Martinelli, Jérémy Grignard, Sylvain Soliman and François Fages.  On Inferring Reactions from Data Time Series by a Statistical Learning Greedy Heuristics
12:50 – 14:20	Lunch
14:20-15:20	Invited talk: Gaspar Tkacik  Title: On the arc between optimality theories and dataChair: Francois Fages
15:20 – 16:10	Regular Session 2 – Simulation Chair: Jerome Feret Michael Backenköhler, Luca Bortolussi and Verena Wolf. Control Variates for Stochastic Simulation of Chemical Reaction Networks Guilherme Innocentini, Fernando Antoneli, Arran Hodgkinson and Ovidiu Radulescu. Effective computational methods for hybrid stochastic gene networks
16:10 – 16:40	Tool Session 2 – Modelling and Simulation Software Chair:  Jerome Feret Min Roh, Christopher Lorton, Joshua Proctor and Philip Welkhoff.  Compartmental Modeling Software: a fast, discrete stochastic framework for biochemical and epidemiological simulation George Assaf, Monika Heiner and Fei Liu.  Biochemical reaction networks with fuzzy kinetic parameters in Snoopy
16:40 – 17:05	Coffee Break
17:05 – 17:45	Highlight Talks Chair:  Loic Pauleve Milan Ceska and Jan Kretinsky. Semi-Quantitative Abstraction and Analysis of Chemical Reaction Networks Giovanni Iacono, Ramon Massoni-Badosa and Holger Heyn.  Single-Cell Transcriptomics Unveils Gene Regulatory Network Plasticity Ines Abdeljaoued-Tej, Alia Benkahla, Ghassen Haddad and Annick Valibouze.  Separators for polynomial dynamic systems with linear complexity Charlotte J. Beelen, Sabrina Asteriti, Lorenzo Cangiano, Karl-Wilhelm Koch and Daniele Dell’Orco.  A comprehensive model for deterministic and stochastic simulations of phototransduction in rods
17:45 – 19:00	Transfer to the Conference Reception
19:00 – 22:00	Conference Reception

Thursday, 19th September

All sessions will take place in room 3B, building H3, University of Trieste

9:00 – 10:00	Invited talk: Adelinde Uhrmacher  Title: Systematic, reproducible simulation studies – the elephant in the room Chair: Luca Bortolussi
10:00 – 10:50	Regular Session 3 – Design of CRN Chair: Milan Ceska Elisabeth Degrand, Mathieu Hemery, and François Fages. On Chemical Reaction Network Design by a Nested Evolution Algorithm Melania Nowicka and Heike Siebert. Designing Distributed Cell Classifier Circuits using a Genetic Algorithm
10:50 – 11:20	Coffee Break
11:20 – 12:50	Flash poster presentation Chair: Andrea Vandin 4 minutes per each presentation
12:50 – 14:20	Lunch
14:20 – 15:20	Invited talk: Kobi Benenson  Title: Apps for cells: from toys to therapies Chair: Carolyn Talcott
15:30 – 16:20	Poster Session
16:20 – 16:50	Coffee Break
16:50 – 18:05	Regular Session 4 – Modelling Chair: Adelinde Uhrmacher Paul Piho, Jane Hillston, Filip Margetiny, Ezio Bartocci, and Richard Ribchester. Investigating a Hodgkin-Huxley type model for Drosophila larval neuromuscular junctions via particle swarm fitting Pavol Bokes and Abhyudai Singhr. Cell volume distributions in exponentially growing populations Calin Guet, Thomas Henzinger, Claudia Igler, Tatjana Petrov, and Ali Sezgin. Long Lived Transients in Gene Regulatory Networks
19:30 – 22:30	Social Dinner

Friday, 20th September

All sessions will take place in room 3B, building H3, University of Trieste.

9:00 – 10:00	Invited talk: Manuel Zimmer  Title:  From structure to function: mechanisms underlying neuronal population dynamics in C. elegans Chair: David Šafranek
10:00 – 10:50	Regular Session 5 –Learning and Behaviours Chair: Guido Sanguinetti Josephine Lamp, Simone Silvetti, Laura Nenzi and Lu Feng. A Logic-Based Learning Approach to Explore Diabetes Patient Behaviors Mahmoud Bentriou, Paolo Ballarini and Paul-Henry Cournède. Reachability design through Approximate Bayesian Computation
10:50 – 11:20	Coffee Break
11:20 – 12:35	Regular Session 6 –Abstraction and Enumeration of CRN Chair:  Tatjana Petrov Carlo Spaccasassi, Boyan Yordanov, Andrew Phillips and Neil Dalchau. Fast enumeration of non-isomorphic chemical reaction networks Isabel Cristina Perez-Verona, Mirco Tribastone and Andrea Vandin. A large-scale assessment of exact model reduction in the BioModels repository Emilie Allart, Joachim Niehren and Cristian Versari. Computing Difference Abstractions of Metabolic Networks
12:35 – 13:05	Tool Session 3 – Simulation and Reproducibility Chair:  Tatjana Petrov Pierre Boutillier. The Kappa simulator made interactive Jacek Chodak and Monika Heiner.  Spike – reproducible simulation experiments with configuration file branching
13:05 – 13.20	Conference Closing