2nd FEBS Advanced Lecture
Course on
Systems
Biology:
From Molecules
to Life
Gosau,
Austria, EU, March 10-16, 2007
Scientific
Program and powerpointfiles (as pdfs obtainable by clicking the links)
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Table of Contents
Saturday
March 10: Opening (co-organized
with AstraZeneca)
Sunday March 11: Symposium on Principles
Monday
March 12: Symposium on Yeast (with YSBN)
Tuesday
March 13: Symposium Mammalian (with
NucSys)
Wednesday
March 14: Symposium Towards Life
Thursday
March 15: Symposium Tools & Methods (with BioSim)
Index:
participants and topics
Saturday March 10: Opening (co-organized with AstraZeneca)
Saturday March 10: 18h00-24h00
Official Course
Opening 6:15
pm - 6:25 pm
Hans Westerhoff and Karl Kuchler
Opening session Chair: Hans V.
Westerhoff 6:25 pm - 10:30 pm
AstraZeneca Opening Lecture
OL-01 Leroy Hood 6:30
pm – 7:30 pm
Systems Biology and Systems
Medicine
Musical intermezzo
Frits
Kamp and Jelena
Petronievic 8:15
pm – 8:45 pm
Reinhart Heinrich Memorial Lecture
OL-02 Hans
Meinhardt 8:45pm-9:45pm
Opening
discussion and drinks 9:45
– 10:30 pm
rinciples
of Systems Biology Lectures 8:30
am - 12:30 pm
Chair: Edda Klipp
Chairs introduction 8:30 am -8:35 am
P-L01 Jan-Hendrik S. Hofmeyr [Main lecture hall] (plenary)
8:35 am - 9:20 am
The Regulatory
Design of Cellular Processes: Principles of Supply and Demand (didactic lecture)
P-L02 Adriano
Henney [Main lecture hall] (plenary) 9:20 am - 9:40 am
How does systems biology
work in and for industry? (methodology)
P-L03 Johan Paulsson [Main lecture hall] (plenary) 9:40 am - 10:00 am
Towards a
coherent stochastic theory for cellular kinetics (methodology)
Tutorials corresponding to lectures (3
in parallel) 10:20 am – 11:05 am
Jan-Hendrik S.
Hofmeyr [Main lecture hall]
Adriano Henney [Yellow room]
Johan Paulsson [Gosau room]
P-L02 Adriano
Henney [Main lecture hall] (plenary) 11:20
am - 11:40 am
How does systems
biology work in and for industry? (results)
Towards a
coherent stochastic theory for cellular kinetics (results)
Chair’s
Resumé and students posing issues;
General discussion 12:00 noon–12:30 am
[Main
lecture hall]
Sunday’s 
lack
Board Teaching / Computer practicals (parallel) 4:30 pm –
6:05 pm
Hierarchical
regulation analysis of cellular adaptive responses (black
board teaching)
Introduction to
dynamic modeling of biochemical networks (black
board teaching)
BB-03 Hans Meinhardt [Main
lecture hall-C] 4:30 pm – 5:15 pm
Model of biological pattern
formation (black board teaching)
BB-04 Guy Shinar [Gosau room] 4:30
pm – 5:15 pm
A
Mechanism for Robust Biochemical Concentrations – 1 (black board teaching)
CP-01 [Yellow room] 4:30 pm – 5:15 pm
CoPaSi
(computer practical )
Physiological modeling
(black board teaching)
BB-06 Uwe Sauer [Main lecture
hall-B] 5:20
pm – 6:05 pm
Metabolomics
and Flux analysis (black board teaching)
Differential Equation Models:
Parameter Estimation and Optimum Experimental Design (Black Board Teaching)
Tools for Systems Biologists:
using JWS Online for integration and storage of data and models (Computer Practicals)
CP-03 Igor Goryanin and Anatoly Sorokin [Gosau
room] 5:20 pm – 6:05 pm
Edinburgh Pathway Editor
(Computer Practicals)
Sunday: 
rinciples of Systems Biology Short Talks and discussion (plenary) 6:20
pm – 7:05 pm
P-S01 Naomi Siew [Main lecture hall] (plenary) 6:20 pm
-6:35 pm
Shedding Light on the ORFan Puzzle (short talk)
Adaptive response of a gene
network to environmental changes by fitness-induced attractor selection (short talk)
Speaker’s Panel addressing issues raised in the
morning 7:05 pm
– 7:25 pm
Poster Session 1 [Poster hall]
9:00
- 11:00 pm
Viewing posters 9:00
- 9:45 pm
Free poster wandering 9:45
– 10:30 pm
Round table poster discussion (presenters and
teachers only) 10:30 –
11:00 pm
Monday March 12: Symposium on Yeast (with YSBN)
east Lectures 8:30
am - 12:30 pm
Chair:
Lilia Albergina
Co-chair:
Jens Nielsen
Chairs introduction (plenary) 8:30
am - 8:35 am
Y-L01 Barbara Bakker [Main lecture hall] (plenary) 8:35 am - 9:20 am
Vertical
Genomics (didactic lecture)
Metabolic
networks and fluxes (methodology)
Y-L02 Steve Oliver [Main lecture hall] (plenary) 9:40 am – 10.00 am
How to deal with the complexity of a ‘simple’
eukaryotic cell (methodology)
Tutorials corresponding to lectures (3 in
parallel) 10:20 am–11:05 am
Barbara Bakker [Main lecture hall]
Steve Oliver [Yellow room]
Jens Nielsen [Gosau room]
Metabolic networks
and fluxes (results)
Y -L02 Steve Oliver [Main lecture hall] (plenary) 11:40
am –12:00noon
How to deal with the complexity of a ‘simple’ eukaryotic cell (results)
Chair’s Resumé and students posing issues. General discussion 12:00 noon – 12:30 am
[Main lecture hall]
Monday’s 
lack
board teaching / Computer practicals
Hierarchical
regulation analysis of cellular adaptive responses (black
board teaching)
Introduction to
dynamic modeling of biochemical networks (black
board teaching)
BB-03 Hans Meinhardt [Main
lecture hall-C] 4:30 pm – 5:15 pm
Model of biological pattern
formation (black board teaching)
BB-04 Guy Shinar [Gosau room] 4:30
pm – 5:15 pm
A
Mechanism for Robust Biochemical Concentrations – 2 (black board
teaching)
CP-01 [Yellow
room] 4:30 pm – 5:15 pm
CoPaSi
(computer practical )
Physiological modeling
(black board teaching)
BB-06 Uwe Sauer [Main
lecture hall-B] 5:20
pm – 6:05 pm
Metabolomics
and Flux analysis (black board teaching)
Differential Equation Models:
Parameter Estimation and Optimum Experimental Design (Black Board Teaching)
Tools for Systems Biologists:
using JWS Online for integration and storage of data and models (Computer Practicals)
CP-03 Igor Goryanin and Anatoly Sorokin [Gosau room] 5:20 pm – 6:05 pm
Edinburgh Pathway Editor
(Computer Practicals)
Monday:
east Short Talks and discussion
(plenary) 06:20 pm -
07:05 pm
Cell size at S
phase initiation: an emergent property of the G1/S network (short talk)
A Highly Connected
Network of Multiple Regulatory Layers Shapes Gene Expression in Fission Yeast (short talk)
Systems analysis of the
yeast Snf1 pathway (short talk)
Speaker’s Panel addressing issues raised in the
morning 7:05 pm
– 7:25 pm
[Main lecture hall]
Poster Session 2 [Poster hall] 9:00
- 11:00 pm
Viewing
posters 9:00
- 9:45 pm
Free
poster wandering 9:45
– 10:30 pm
Round
table poster discussion (presenters and teachers only) 10:30 – 11:00 pm
Tuesday March 13: Symposium Mammalian (with NucSys)
ammals Lectures 8:30
am - 12:30 pm
Chair:
Hans van Leeuwen
Chairs
introduction 8:30
am -8:35 am
M-L01 Ursula Klingmüller & Jens
Timmer [Main lecture hall] 8:35 am - 9:20 am
Data based modeling and model
based experimentation (didactic lecture)
M-L02 [Main lecture
hall] (plenary) 9:20 – 9:40 am
Reverse engineering of the
yeast cell cycle control system (methodology)
L-S04Takashi
Nakakuki [Main lecture hall]
(plenary) 9:40 – 10:00 am
Integrative analyses of
the ErB receptor signaling transcriptional network (methodology)
Tutorials corresponding to lectures (3 in parallel) 10:20 – 11:05
am
Ursula Klingmüller
& Jens Timmer [Main lecture hall]]
[Yellow room]
Takashi Nakakuki [Gosau room]
Y-L04 [Main lecture hall] (plenary) 11:20 – 11:40 am
Reverse engineering of the
yeast cell cycle control system (results)
L-S04Takashi
Nakakuki [Main lecture hall] (plenary) 11:40 – 12:00 noon
Integrative analyses of the
ErB receptor signaling transcriptional network (results)
Chair’s Resumé and students posing
issues. General discussion 12:00 noon – 12:30 pm
Towards 
ife Lectures 8:30
am - 12:30 pm
Chair: Marta Cascante
Chairs introduction 8:30
am - 8:35 am
Nonlinear
dynamics (didactic lecture)
Nose diving into Systems
Biology: Bacterial sensory
networks
(methodology)
T-L02 Jaroslav Stark [Main lecture hall] (plenary)
9:40 am -10:00 am
Modeling
methods: hormones and cells (methodology)
Tutorials corresponding to lectures (3 in parallel) 10:20 am – 11:05 am
Erik Mosekilde [Main lecture hall]
Judy Armitage [Gosau room]
Jaroslav Stark [Yellow room]
Nose diving into
Systems Biology: Bacterial
sensory networks (results)
T-L02 Jaroslav Stark [Main lecture hall] (plenary) 11:40am-12:00noon
Modeling methods:
hormones and cells (results)
Chair’s Resumé and students posing issues. General discussion 12:00 noon – 12:30 pm
Wednesday: 
lack
Board Teaching / Computer practical (in parallel) 4:30 pm – 6:05 pm
Hierarchical
regulation analysis of cellular adaptive responses (black
board teaching)
Introduction to
dynamic modeling of biochemical networks (black
board teaching)
BB-03 Hans Meinhardt [Main
lecture hall-C] 4:30 pm – 5:15 pm
Model of biological pattern
formation (black board teaching)
BB-04 Guy Shinar [Gosau room] 4:30
pm – 5:15 pm
Kinetic
proofreading (black board teaching)
CP-01 [Yellow room] 4:30 pm – 5:15 pm
CoPaSi
(computer practical )
Physiological modeling
(black board teaching)
BB-06 Uwe Sauer [Main
lecture hall-B] 5:20
pm – 6:05 pm
Metabolomics
and Flux analysis (black board teaching)
Differential Equation Models:
Parameter Estimation and Optimum Experimental Design (Black Board Teaching)
Tools for Systems Biologists:
using JWS Online for integration and storage of data and models (Computer Practicals)
CP-03 Igor Goryanin and Anatoly Sorokin [Gosau
room] 5:20 pm – 6:05 pm
Edinburgh Pathway Editor
(Computer Practicals)
Wednesday: 
ammals Short Talks and discussion (plenary) 06:20pm-07:05 pm
Identification
of new therapeutic strategies in immunology through the modeling of the Th1
lymphocyte response (short talk)
Speaker’s Panel addressing issues raised in the
morning 7:05pm–7:25
pm
[Main lecture hall]
Poster Session 3 [Poster hall] 9:00
- 11:00 pm
Viewing posters 9:00
- 9:45 pm
Free poster wandering 9:45
– 10:30 pm
Round table poster discussion (presenters and
teachers only) 10:30 – 11:00
pm
Thursday March 15: Symposium Tools & Methods (with BioSim)
ools
and Methods Lectures 8:30
am - 12:30 pm
Chair: Uwe Sauer
Co-chair:
Erik Mosekilde
Chairs
introduction 8:30 am-8:35 am
Systems biology of
growing bacteria: flows, concentrations,
fluctuations and control
systems (didactic lecture)
Towards macromolecular
organization: assembly, forces and organization of the cytoskeleton (methodology)
Robust systems
in control (methodology)
[total file for
methodology, tutorial and results combined]
Tutorials corresponding to lectures (3 in parallel) 10:20 am
– 11:05 am
Måns Ehrenberg [Main lecture hall]
Marileen
Dogterom [Gosau room]
Hans V.
Westerhoff [Yellow
room]
Towards
macromolecular organization: assembly, forces and organization of the
cytoskeleton
(results)
Robust systems
in control (results)
Chair’s Resumé and students posing issues. General discussion. 12:00 noon – 12:30 pm
Thursday:
Tools and Towards 
ife Short
Talks and discussion (plenary) 4:30
pm – 5:45 pm
Constraint-based
prediction of intracellular fluxes in Escherichia
coli (short
talk)
Regulation at the RNA level (short talk)
Towards an understanding of
the interrelations between metabolic and gene regulation (short talk)
Systems biology to
investigate biochemical pathways for metabolic functions in vivo (short talk)
L-P08 Jurgen R. Haanstra [Main lecture hall] (plenary) 5:30 pm-5:45 pm
Control and regulation analysis of phoshoglycerate kinase (PGK) RNA levels in Trypanosoma brucei (short talk)
General discussion 6:10
pm-6:45 pm
losing
lecture
Chair:
Karl Kuchler
CL-01 Tom Kirkwood [Main
lecture hall] 7:00 pm -
8:00 pm
Systems Biology at last:
ageing (keynote lecture)
Banquet and Farewell Party 8:00
pm – am
Presentation of “Gosau YOUNG SysBio
INVESTIGATOR AWARDS” 8:30 - 8:45 pm
Marta Cascante and Lilia Alberghina
Official Course
Closure: clicking here loads movie (takes a long long time!) 8:45 - 9:00 pm
Hans Westerhoff and Karl Kuchler