CMSB 2016

14th International Conference on Computational Methods in Systems Biology

21st - 23rd September 2016, Computer Laboratory, University of Cambridge (UK)

Program

Timetable

Time Tue, 20 Sep Wed, 21 Sep Thu, 22 Sep Fri, 23 Sep
09:00-09:30 Registration and welcome Invited talk: Luca Cardelli Invited talk: Radu Grosu
09:30-10:00 Invited talk: Jane Hillston
10:00-10:30 Coffee break Coffee break
10:30-11:00 Coffee break Session 2.1: Case studies Session 3.1: Abstraction/Reduction/Approximation
11:00-11:30 Session 1.1: Estimation/Inference/Synthesis
11:30-12:00 Session 2.2: Poster flashes
12:00-12:30 Lunch
12:30-13:00 Lunch Lunch + Poster session
13:00-13:30
13:30-14:00 Session 3.2: Tools
14:00-14:30 Invited talk: Joelle Despeyroux Session 2.3: Reaction networks (1)
14:30-15:00 Workshop Session 3.3: Optimisation and control (2)
15:00-15:30 Coffee break Coffee break Closing
15:30-16:00 Session 1.2: Optimisation and control (1) Session 2.4: Reaction networks (2)
16:00-16:30 Session 1.3: High-performance methods
16:30-17:00
17:00-17:30 Award ceremony
17:30-18:00 Business meeting
18:00-18:30
18:30-19:00


19:00-21:30

Social event and dinner

Social Event: Dinner at Emmanuel College

Dinner on Thursday night will be at Emmanuel College, in central Cambridge. Emmanuel is one of the larger Cambridge colleges, and famed for the quality of its food.

Additional tickets can be purchased for guests - see the registration page.

There will be a drinks reception from 19:00, with dinner served at 19:30.


Detailed program

Tuesday, 20th September

Wednesday, 21st September

  • 09:00 - 09:30. Registration and welcome

  • 09:30 - 10:30. Invited talk: Jane Hillston. Chair: Pietro Lio'

    Embedding Machine Learning in Formal Stochastic Models of Biological Processes

  • 10:30 - 11:00. Coffee break

  • 11:00 - 12:30. Session 1.1: Estimation, inference and synthesis methods. Chair: Verena Wolf

  • 12:30 - 14:00. Lunch

  • 14:00 - 15:00. Invited talk: Joelle Despeyroux. Chair: Carolyn Talcott

    (Mathematical) Logic for Systems Biology

  • 15:00 - 15:30. Coffee break

  • 15:30 - 16:00. Session 1.2: Optimisation and control (1). Chair: Ezio Bartocci

    • Chieh Lo and Radu Marculescu. Autonomous and Adaptive Control of Populations of Bacteria through Environment Regulation

  • 16:00 - 17:00. Session 1.3: High-performance and parallel methods. Chair: Ezio Bartocci

    • Andrzej Mizera, Jun Pang and Qixia Yuan. Fast Simulation of Probabilistic Boolean Networks

    • Martin Demko, Nikola Benes, Lubos Brim, Samuel Pastva and David Šafránek. High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study

Thursday, 22nd September

  • 09:00 - 10:00. Invited talk: Luca Cardelli. Chair: François Fages

    Morphisms of reaction networks

  • 10:00 - 10:30. Coffee break

  • 10:30 - 11:30. Session 2.1: Case studies. Chair: Olivier Roux

  • 11:30 - 12:30. Session 2.2: Poster flashes. Chair: Nicola Paoletti

    • Priya Anand, Monika Borkowska-Panek, Karin Fink and Wolfgang Wenzel. Modelling Peptide Adsorption on Inorganic Surfaces

    • Loïc Paulevé. Pint, a static analyzer for dynamics of Automata Networks

    • Nadia S. M. Goncalves, Samuel M. D. Oliveira, Jose M. Fonseca and Andre S. Ribeiro. Temperature Dependence of Leakiness of Transcription Repression Mechanisms of Escherichia coli

    • Andrzej Mizera, Jun Pang and Qixia Yuan. GPU-accelerated Steady-State Analysis of Probabilistic Boolean Networks

    • James Smith, Kai Loell and Albert Koulman. Revealing biomarker mixtures in lipid pools from large-scale lipidomics

    • James Smith and Ahmed Ibrahim. Game theoretic consideration of transgenic bacteria in the human gut microbiota converting omega-6 to omega-3 fats

    • Benjamin Hall, Nir Piterman and Jasmin Fisher. Linear Temporal Logic for Biologists in BMA

    • Mariana Esther Sanchez, Elena Alvarez-Buylla and Marcia Hiriart. The CD4+ T cell regulatory network mediates inflammatory responses during acute hyperinsulinemia

    • David Shorthouse, Angela Riedel, Jacqueline Shields and Benjamin Hall. Deregulation of Osmotic Regulation Machinery Explains and Predicts Cellular Transformation in Cancer and Disease

  • 12:30 - 14:00. Lunch + Poster session

  • 15:00 - 15:30. Coffee break

  • 15:30 - 17:00. Session 2.4: Reaction Networks (2). Chair: David Gilbert

    • Luca Laurenti, Luca Cardelli and Marta Kwiatkowska. A Stochastic Hybrid Approximation for Chemical Kinetics Based on the Linear Noise Approximation

    • Michael Backenköhler, Luca Bortolussi and Verena Wolf. Generalized Method of Moments for Stochastic Reaction Networks in Equilibrium

    • Chunyan Mu, Peter Dittrich, David Parker and Jonathan E. Rowe. Formal Quantitative Analysis of Reaction Networks Using Chemical Organisation Theory

  • 17:00 - 17:30. Award ceremony

  • 17:30 - 18:30. Business meeting

Friday, 23rd September

  • 09:00 - 10:00. Invited talk: Radu Grosu. Chair: Joelle Despeyroux

    From Artificial to Biological Neural Networks

  • 10:00 - 10:30. Coffee break

  • 10:30 - 12:00. Session 3.1: Abstraction, reduction and approximation methods. Chair: David Šafránek

    • Jasha Sommer-Simpson, John Reinitz, Leonid Fridlyand, Louis Philipson and Ovidiu Radulescu. Hybrid reductions of computational models of voltage-gated ion channels coupled to cellular biochemistry

    • Loïc Paulevé. Goal-Oriented Reduction of Automata Networks

    • Jerome Feret and Quyen Kim Ly. Local traces: an over-approximation of the behaviour of the proteins in rule-based models

  • 12:00 - 13:30. Lunch

  • 13:30 - 14:30. Session 3.2: Tools. Chair: Giulio Caravagna

    • Alejandro F. Villaverde, Kolja Becker and Julio R. Banga. PREMER: parallel reverse engineering of biological networks with information theory

    • Matej Troják, David Šafránek, Jakub Hrabec, Jakub Šalagovič, Františka Romanovská and Jan Červený. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria

    • Andrzej Mizera, Jun Pang and Qixia Yuan. ASSA-PBN 2.0: A Software Tool for Probabilistic Boolean Networks

  • 14:30 - 15:00. Session 3.3: Optimisation and control (2). Chair: Pietro Lio'

  • 15:00 - 15:30. Closing