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 RibchesterInvestigating 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