Entrance hall of the ICMS Workshop

Information, probability and inference in systems biology (IPISB 2013)

Jul 15, 2013 - Jul 17, 2013

ICMS, 15 South College Street

Organisers

Name Institution
Bowsher, Clive University of Bristol
Colijn, Caroline Imperial College London
Swain, Peter University of Edinburgh

Workshop Report now available - download PDf file

The aim of this workshop is to bring experts in probability, information theory, and stochastic systems alongside experimental systems biologists to develop understanding of the principles underlying cellular signalling and decision-making, and to develop quantitative techniques to investigate those principles experimentally. Key topics to be addressed include:


1) New information theoretic approaches to sensing and signal transduction by cells with an emphasis on dynamic problems, including the quantification and statistical estimation of information in molecular biology.

2) Study of stochastic biochemical networks: new developments in Monte Carlo simulation methods, approximate analytical techniques, and the need for a more developed theory of stochastic chemical reaction networks.

3) Inferential methods for statistical modelling of time series data from single cells, including simulation-based methods, likelihood free inference, diffusion approximations, particle filtering techniques and reversible jump MCMC.

4) Cellular decision-making, both intracellular and intercellular: how to apply mathematics of decision theory to the biological context.

5) Design of signal transduction networks for use in synthetic biology, particularly when the cellular outcome is controlled in response to a changing environment.


Invited speakers:

Clive Bowsher, University of Bristol

Caroline Colijn, Imperial College, London

Robert Endres, Imperial College, London

Ramon Grima, University of Edinburgh

Des Higham, Strathclyde University

Martin Howard, John Innes Centre

Nick Jones,  Imperial College, London

Mustafa Khammash, ETH-Zurich

Tetsuya Kobayashi, University of Tokyo

Heinz Koeppl, ETH-Zurich

Markus Kollmann, Universitat Duesseldorf

Andre Levchenko, Johns Hopkins University

Ilya Nemenman, Emory Unviersity

Ted Perkins, Ottawa Hospital Research Institute

Hong Qian, University of Washington

David Rand, University of Warwick

Michael Stumpf, Imperial College, London

Savas Tay (talk given by Michael Junkin), ETH-Zurich

Peter Rein Ten Wolde AMOLF, Amsterdam

Gasper Tkacik, IST Austria 

Lev Tsimring, University of California, San Diego

Vladislav Vyshemirsky, University of Strathclyde

Hans Westerhoff, University of Manchester

Darren Wilkinson, Newcastle University

Ruth Williams, University of California, San Diego

Carsten Wiuf, University of Copenhagen


SPEAKERS: Invited Speakers will receive a personalised e-mailed invitation with a link to their own registration form. 
Invited Speakers will be contacted separately by email regarding accommodation - ICMS will book accommodation for Invited Speakers and will email full details of the booking.

 

Arrangements

The meeting will be held at ICMS, 15 South College Street, Edinburgh, EH8 9AA. Follow this link for information on the location of 15 South College Street.

  • A poster session will take place on Monday 15 July. If you would like to present a poster please enter a title and abstract on the application form. 
  • Invited speakers are encouraged to bring talks on a memory/usb stick (or, alternatively, may use their own laptop).

Accommodation


Speakers' accommodation will be arranged by ICMS, for those who wish. Other accepted participants are asked to make their own accommodation arrangements. A list of Edinburgh accommodation of various sorts and prices is available here.  ICMS recommends you use Edinburgh First accommodation as other workshop participants, including the speakers, will be staying at Pollock Halls. Due to the British Open in golf being played at Muirfield golf course near Edinburgh this week, the Pollock Halls campus will be hosting event staff and for this reason all parking is suspended for visitors (apart from disabled parking). 

Edinburgh is a top tourist destination and the month of July is during the peak tourist season. We recommend that you book your accommodation as early as possible. 

Registration Fee and Financial Matters


The registration fee for this workshop is 50 GBP.  Further details regarding payment will follow at a later date.
Some financial assistance is available to assist with travel and accommodation costs of non-speakers. Priority will be given to early career researchers and PhD students. We anticipate being able to contribute up to 50 GBP per night (for up to four nights) for accommodation and up to 75 GBP for travel for a number of these participants. If you require financial support, please provide details of amounts required in the relevant section of the application form. Reimbursement will take place after the workshop.

Meals and Refreshments


Refreshments will be provided during the breaks in the programme.  There will be a buffet lunch each day. There will be a workshop dinner on Tuesday 16 July. Drinks will be served during the poster session on Monday 15 July.

Programme

Final version of the programme, published 4 July.

 

Monday 15 July 2013

08.45 - 09.30

Registration in the Chapterhouse, Level 1

09.30 - 09.40

Clive Bowsher (Scientific Organsing Committee) and Helene Frossling (ICMS)
Welcome, and a few housekeeping rules

09.40 - 10.20

Hans Westerhoff (University of Manchester)
The arrow of time: how pointed can it be in a molecular world?

10.20 - 11.00

Theodore Perkins (Ottawa Hospital Research Institute)
What do molecules do when we're not looking? State sequence analysis for stochastic chemical systems

11.00 - 11.30

Coffee/tea served in the Chapterhouse

11.20 - 12.00

Des Higham (University of Strathclyde)
Multi-level Monte Carlo for Stochastic Simulation

12.00 - 12.40

Gasper Tkacik (IST Austria)
Information flow and optimization in small genetic circuits

12.40 - 13.20

Tetsuya Kobayashi (University of Tokyo)
Dynamics of Bayesian inference and its application to cellular decision-making

13.30 - 14.50

Lunch served in the Chapterhouse

14.50 - 15.30

Ruth Williams (University of California at San Diego)
Correlation effects of intracellular components due to limited processing resources

15.30 - 16.10

Markus Kollmann (University of Duesseldorf)
Scaling up the regulatory complexity of the living cell

16.10 - 16.50

Ramon Grima (University of Edinburgh)
Beyond the linear-noise approximation of stochastic biochemical networks

16.50 - 18.15

Poster session and wine reception in the Atrium (level 3) and the Cramond Room (level 2)

 

Tuesday 16 July 2013

09.00 - 09.40

Lev Tsimring (University of California at San Diego)
Synchronization of synthetic gene oscillators

09.40 - 10.20

Michael Junkin (Savas Tay) (ETH Zuerich)
Microfluidic analysis of transcription factor dynamics in single cells

10.20 - 10.50

Coffee and tea in the Chapterhouse

10.50 - 11.30

David Rand (University of Warwick)
Design principles and dynamics in clocks, cell cycles and signals

11.30 - 12.10

Mustafa Khammash (ETH Zuerich)
Cybergenetics: manipulating the dynamic behavior of living cells through feedback control

12.10 - 12.50

Martin Howard (John Innes Centre)
Implementation of analogue arithmetic division in food reserve utilisation

12.50 - 14.10

Lunch served in the Chapterhouse

14.10 - 14.50 

Clive Bowsher (University of Bristol)
The fidelity of dynamic signaling by noisy biomolecular networks

14.50 - 15.30

Pieter Rein Ten Wolde (AMOLF)
Protein clustering improves signaling reliability

15.30 - 16.30

Coffee and tea in the Chapterhouse

16.00 - 16.40

Information capacity of signal transduction networks: from bottlenecks to decision making

16.40 - 17.20

Robert Endres (Imperial College London)
Precision of sensing with memory in fluctuating environments

19.00

Workshop dinner at The Magnum Restaurant, 1 Albany Street

 

Wednesday 17 July 2013

09.00 - 09.40

Vladislav Vyshemirsky (University of Strathclyde)
Modelling growth dynamics of solid tumours

09.40 - 10.20

Caroline Colijn (Imperial College London)
Pertussis decisions: can we use metabolic models to understand two modes of growth?

10.20 - 10.50

Coffee and tea in the Chapterhouse

10.50 - 11.30

Carsten Wiuf (University of Copenhagen)
Model reduction in chemical reaction networks

11.30 - 12.10

Heinz Koeppl (ETH Zurich and IBM Research Zurich)
Statistical inference of cellular behavior from single-cell data

12.10 - 12.50

Ilya Nemenman (Emory University)
Inferring phenomenological models of cellular regulation from data

12.50 - 14.10

Lunch served in the Chapterhouse

14.10 - 14.50 

Darren Wilkinson (University of Newcastle)
Bayesian inference for Markov process models of stochastic biochemical network dynamics

14.50 - 15.30

Nick Jones (Imperial College London)
Mitochondrial Variability

15.30 - 16.00

Coffee and tea in the Chapterhouse

16.00 - 16.40

Michael Stumpf (Imperial College London)
Analog versus digital information processing in cellular systems

16.40 - 17.20

Hong Qian (University of Washington)
Stochastic dynamics and cellular biochemical systems: theories and computational challenges

19.00

Speakers' dinner at Wedgwood the Restaurant, 267 Canongate (Royal Mile)

 

 

Presentations:

Presentation Details
Bowsher, Clive
The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks
View Abstract Down
Colijn, Caroline
Pertussis decisions: can we use metabolic models to understand two modes of growth?
View Abstract Down
Endres, Robert
Precision of sensing with memory in fluctuating environments
View Abstract Down
Grima, Ramon
Beyond the linear-noise approximation of stochastic biochemical networks
View Abstract Down
Higham, Des
Multi-level Monte Carlo for Stochastic Simulation
View Abstract Down
Howard, Martin
Implementation of analogue arithmetic division in food reserve utilisation
View Abstract Down
Jones, Nick
Mitochondrial variability
View Abstract Down
Junkin, Michael
Microfluidic analysis of transcription factor dynamics in single cells
View Abstract Down
Khammash, Mustafa
Cybergenetics: manipulating the dynamic behavior of living cells through feedback control
View Abstract Down
Kobayashi, Tetsuya
Dynamics of bayesian inference and its application to cellular decision-making
View Abstract Down
Koeppl, Heinz
Statistical inference of cellular behavior from single-cell data
View Abstract Down
Kollmann, Markus
Scaling up the regulatory complexity of the living cell
View Abstract Down
Levchenko, Andre
Information capacity of signal transduction networks: from bottlenecks to decision making
View Abstract Down
Nemenman, Ilya
Inferring phenomenological models of cellular regulation from data
View Abstract Down
Perkins, Theodore
What do molecules do when we're not looking? State sequence analysis for stochastic chemical systems
View Abstract Down
Qian, Hong
Stochastic dynamics and cellular biochemical systems: Theories and computational challenges
View Abstract Down
Rand, David
Design principles and dynamics in clocks, cell cycles and signals.
View Abstract Down
Stumpf, Michael
Analog versus digital information processing in cellular systems
View Abstract Down
Ten Wolde, Pieter Rein
Protein clustering improves signaling reliability
View Abstract Down
Tkacik, Gasper
Information flow and optimization in small genetic circuits
View Abstract Down
Tsimring, Lev
Synchronization of synthetic gene oscillators
View Abstract Down
Vyshemirsky, Vladislav
Modelling growth dynamics of solid tumours
View Abstract Down
Westerhoff, Hans
The arrow of time: how pointed can it be in a molecular world?
View Abstract Down
Wilkinson, Darren
Bayesian inference for Markov process models of stochastic biochemical network dynamics
View Abstract Down
Williams, Ruth
Correlation effects of intracellular components due to limited processing resources
View Abstract Down
Wiuf, Carsten
Model reduction in chemical reaction networks
View Abstract Down

Participants

Name Institution
Aitken, Stuart University of Edinburgh
Angione, Claudio University of Cambridge
Azim, Qurat-ul-Ain Imperial College London
Bakker, Elco University of Edinburgh
Bosia, Carla Human Genetics Foundation Torino
Bowsher, Clive University of Bristol
Cappelletti, Daniele University of Copenhagen
Colijn, Caroline Imperial College London
Crane, Matthew University of Edinburgh
Endres, Robert Imperial College London
Faisal, Aldo Imperial College London
Feigelman, Justin Helmholtz Center Munich
Gillespie, Colin Newcastle University
Grima, Ramon University of Edinburgh
Higham, Catherine University of Glasgow
Higham, Des University of Strathclyde
Howard, Martin John Innes Centre
Jones, Harriet University of Edinburgh
Jones, Nick Imperial College London
Josephides, Christos University of Edinburgh
Junkin, Michael ETH Zuerich
Khammash, Mustafa ETH Zuerich
Kobayashi, Tetsuya University of Tokyo
Koeppl, Heinz ETH Zurich and IBM Research Zurich
Kollmann, Markus Universitaet Duesseldorf
Kumar, Sunil ETH Zurich
Levchenko, Andre Johns Hopkins University
Lubbock, Alexander University of Edinburgh
Makadia, Hirenkumar Thomas Jefferson University
Martins, Bruno University of Edinburgh
Mueller, Fabian ETH Zuerich
Nemenman, Ilya Emory University
Oyarzún, Diego Imperial College London
Pahle, Juergen The University of Manchester
Pairo-Castineira, Erola University of Edinburgh
Pan, Wei Imperial College London
Perkins, Theodore Ottawa Hospital Research Institute
Qian, Hong University of Washington
Rand, David University of Warwick
Ross Smith, Allister Ross Adam Smith College
Schnoerr, David University of Edinburgh
Sootla, Aivar Imperial College London
Sorokina, Oksana University of Edinburgh
Stewart, Donal University of Edinburgh
Strasser, Michael Helmholtz Center Munich
Stumpf, Michael
Swain, Peter University of Edinburgh
Szymańska, Paulina University od Warsaw
Ten Wolde, Pieter Rein FOM Institute AMOLF
Thomas, Philipp University of Edinburgh
Tkacik, Gasper IST Austria
Tsimring, Lev University of California, San Diego
Unger, Michael ETH Zurich
Vadigepalli, Rajanikanth Thomas Jefferson University
Villaverde, Alejandro Fernández CSIC
Voliotis, Margaritis University of Bristol
Vyshemirsky, Vladislav University of Glasgow
Weisse, Andrea University of Edinburgh
Westerhoff, Hans University of Manchester, University of Amsterdam and VU University Amsterdam
Whitby, Ariadne Imperial College London/MRC CSC
Wilkinson, Darren Newcastle University
Williams, Ruth University of California, San Diego
Wiuf, Carsten University of Copenhagen
Zimmer, Christoph Bioms, Heidelberg University