systems biology today and tomorrow the wtec visit to the netherlands
Download
Skip this Video
Download Presentation
Systems Biology: Today and Tomorrow; the WTEC visit to The Netherlands

Loading in 2 Seconds...

play fullscreen
1 / 58

Systems Biology: - PowerPoint PPT Presentation


  • 356 Views
  • Uploaded on

Systems Biology: Today and Tomorrow; the WTEC visit to The Netherlands. The Institute for Molecular Cell Biology, BioCentre Amsterdam, Free University Amsterdam. The WTEC visit to The Netherlands: the program.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Systems Biology: ' - mike_john


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
systems biology today and tomorrow the wtec visit to the netherlands

Systems Biology: Today and Tomorrow; the WTEC visit to The Netherlands

The Institute for Molecular Cell Biology, BioCentre Amsterdam, Free University Amsterdam

the wtec visit to the netherlands the program
The WTEC visit to The Netherlands:the program
  • 11:45 Welcome address (Hans Westerhoff): 12:15 Marvin Cassman: Aims of the WTEC study
  • 12:30 lunch13:15 Welcoming remarks by Pier Vellinga (Dean Faculty of Earth and Life Sciences)
  • 13:45-17:00 Examples of Dutch Systems Biology 16:40 Teaching Systems Biology
  • 16:50 Drinks 17:05 General discussion (chair: Roel van Driel): Systems Biology and its future
  • 17:45 Departure for the restaurant (De Molen; Amstelveen)
system biology where it matters
System Biology: Where it matters
  • International developments
  • European developments/potential
  • Dutch Systems Biology
what is has been happening internationally
What is/has been happening internationally?
  • Institutes (ISB-Seattle) [BCA/IMC here]
  • Conference (ICSB)
  • Electronic cells
  • Alliances
biocentre amsterdam and its institute for molecular cell biology
BioCentre Amsterdam and its Institute for Molecular Cell Biology
  • BCA: From Entering the living cell to Molecular Systems Biology
  • IMC:
electronic cells
Electronic cells
  • E-cell
  • Virtual cell
  • Silicon cell
bottom up international alliances
Bottom up international alliances
  • IEcA (International E. coli Alliance)
  • YSBN (Yeast Systems Biology Network)
  • EGF Signalling network
slide10

Round Table discussion 2:

Developing a White Paper

www.ieca2004.ca

ieca status quo
IEcA status quo
  • Manifest being written
  • Genome Canada supports workshop funding organizations plus scientists to put together an international prokaryotic SB program
  • To prepare concrete action plan
  • Genome Canada looks for European partners (e.g. German SysMo)
  • US partner needed ……….
ysbn status quo
YSBN status quo
  • White paper has been written
  • Committees have been formed
  • Funding unclear
gf signalling alliance
GF signalling alliance
  • In preparation only
  • Kholodenko, Goryanin (GSK)
system biology where it matters16
System Biology: Where it matters
  • International developments
  • European developments/potential
  • Dutch Systems Biology
what is happening in europe
What is happening in Europe?
  • National programs
    • Germany (BMBF):
      • German Hepatocyte: Systeme des Lebens (20-50 ME); has begun
      • SysMo (Systems Biology of Microorganisms (10 ME); call in 2005
    • Finland: System Biology and Bioinformatics (10.5 ME); has begun
    • The Netherlands: SBNL; set of organism focused programs (L. lactis, S. cerevisiae, E. coli, Silicon cell, Signal transduction, Xomics, Cell Biophysics, …..); some funded (IOP) most still in limbo
    • UK: BBSRC Integrative Biology 10 years program:

> 6 national centres 5ME? each; bids (for first round) are now in

    • …..
  • Transnational programs:
    • SysMO: Germany intends to have this as a transnational program (Germany, Austria, Netherlands, France?)
    • ERANET:
      • Brussels catalyzed transnational activity; inspired by SysMO?
      • Paris meeting August 26 (joint with EUSYSBIO meeting)
  • European programs:
transnational initiatives sysmo
Transnational initiatives; SysMo
  • German BMBF
  • Preparing for microbial System Biology program
  • Wants to go transnational
  • Austrian, Dutch ?partners
  • 2005: call for proposals
what is happening in europe19
What is happening in Europe?
  • National programs
    • Germany (BMBF):
      • German Hepatocyte: Systeme des Lebens (20-50 ME); has begun
      • SysMo (Systems Biology of Microorganisms (10 ME); call in 2005
    • Finland: System Biology and Bioinformatics (10.5 ME); has begun
    • The Netherlands: SBNL; set of organism focused programs (L. lactis, S. cerevisiae, E. coli, Silicon cell, Signal transduction, Xomics, Cell Biophysics, …..); some funded (IOP) most still in limbo
    • UK: BBSRC Integrative Biology 10 years program:

> 6 national centres 5ME? each; bids (for first round) are now in

    • …..
  • Transnational programs:
    • SysMO: Germany intends to have this as a transnational program (Germany, Austria, Netherlands, France?)
    • ERANET:
      • Brussels catalyzed transnational activity; inspired by SysMO?
      • Paris meeting August 26 (joint with EUSYSBIO meeting)
  • European programs:
what is happening in europe20
What is happening in Europe?
  • European programs:
    • EU: FP6 (Specific Support Action EUSYSBIO; Computational Systems Biology not in third call; Synthetic Biology in April 2004 call)
    • EUREKA:
      • (New Safe Medicines Faster)
      • Virtual Cell
    • EMBO: SB in EMBL??
    • ESF: Forward look, towards EUROCORE and more?
fp6 specific support action eusysbio
FP6: Specific Support Action EUSYSBIO
  • Get science policy makers together
  • Help organize ICSB2004 (Heidelberg, October 9-13 2004)
  • Organize SB course (FEBS): March 2005
  • Set up ERANET: transnational funding possibilities
  • Set up European SB organization/group
wp8 dutch wp deliverables
WP8 (Dutch WP) deliverables
  • D26: Platform of excellent Eur SB groups:
      • -at ICSB form network of excellence?
  • D27: Workshop devoted to standards
      • At ICSB2004: October 10, Heidelberg (joint with ESF?)
  • D28: Strategy paper discussing scientific basis science policy planning
      • To be written on request of WP6
  • D29: Scientific journal
      • A book on Defining Systems Biology for now
biosim noe mosekilde
BioSim ( NoE): Mosekilde
  • Models for pharmaceuticals
fp6 future
FP6: Future
  • Computational Systems Biology:
    • Call for IP on Computational Systems Biology with deadline November 2004 failed (STREPS and Coordination Action remain)
    • Promises for 4th call and FP7
    • Problem?: too dry …?…..
what is happening in europe26
What is happening in Europe?
  • European programs:
    • EU: FP6 (Specific Support Action EUSYSBIO; Computational Systems Biology not in third call; Synthetic Biology in April 2004 call)
    • EUREKA:
      • (New Safe Medicines Faster)
      • InSysBio
    • EMBO: SB in EMBL??
    • ESF: Forward look, towards EUROCORE and more?
insysbio eureka s virtual cell initiative
InSysBio:Eureka’s virtual cell initiative
  • European, industry driven research
  • Aim: Making computer models of living organisms for drug development etc. and
  • (now also:) for food production (biotech)
    • Bioinformatics
    • Tool development
    • Models for pharma and Models for food
esf forward look
ESF forward look
  • Study to see if System Biology could be ESF theme
  • This would then make ESF catalyze common research programmes between

National science foundations

what is needed
What is needed?
  • Wet SB, not just dry (FP6, EUREKA)
  • Try to get the national SFs to coordinate their SB programs
  • Construct mechanisms for transnational funding
  • Become partners for USA, Japan, Canada, China, Korea
  • Provide funding anchors for the alliances
system biology where it matters32
System Biology: Where it matters
  • International developments
  • European developments/potential
  • Dutch Systems Biology
dutch eu sb integrative systems biology
Dutch/EU SB:Integrative Systems Biology
  • Look at all the leaves
  • individually

2. The phenomena; top down

Diagnosis; pattern recognition

3. Get to the roots; bottom up;

Understanding of the special

System properties/principles

dutch systems biology the ambition
Dutch Systems Biology:The Ambition
  • Ambition:
    • Not just ‘SB’; aim is to now understand living organisms from molecule to cell, organ, and human organism
    • Put a healthy man …. on earth

Dutch Niche:

  • mechanistic (bottom up SB)
  • wet plus dry
  • industry plus academia

Bring about ‘common goal’ synergism between national programs (European countries are too small for SB)

  • Generate superfund from Europe
what is happening in nl
What is happening in NL?
  • National programs
      • NWO (Dutch NSF) preludes (6 M$ each):
        • Bioinformatics
        • Molecule to Cell
        • Computational Biology
      • National Genomics Centres (200 M$):
        • Centre Medical Systems Biology (Leiden, VU, TNO; not really SB)
        • Kluyver Centre (some SB)
        • Plant Systems (not SB)
        • Cancer (not SB)
      • IBIVU: Integrative BioInformatics VU (3 M$)
      • IOP-Genomics: Vertical Genomics (2 M$)
      • Ecogenomics-BSIK (10 M$)
what is going to happen in nl
What is going to happen in NL?
  • National programs
    • SBNL; set of focused program proposals:
      • L. lactis (Kuipers, Teusink, Siezen, Hugenholz. …)
      • S. cerevisiae (Bakker, Teixeira, Pronk, Heijnen)
      • Silicon cell Amsterdam (-Stellenbosch, Blacksburg; Snoep)
    • SBNL: Industrial platform
    • Partner in Transnational SysMO
    • Partner in EUREKA
    • Attempt at National Program integrating top down with bottom up
wtec study systems biology network behavior in biological systems
WTEC study: Systems Biology, Network Behavior in Biological Systems
  • State of the art information on network behavior, also internationally
  • Research opportunities
  • Identify potential interagency collaborations
  • Identify potential international collaborations
  • Publish results of study
the wtec visit to the netherlands the program38
The WTEC visit to The Netherlands:the program
  • 11:15 Coffee, tea, cookies in G076
  • 11:45 Welcome address (Hans Westerhoff): Dutch and European Systems Biology; where it might matter
  • 12:15 Marvin Cassman: The aims of the WTEC study
  • 12:30 lunch13:15 Welcoming remarks by Pier Vellinga (Dean Faculty of Earth and Life Sciences)
  • 13:20 Coffee + informal discussions
the wtec visit to the netherlands the program39
The WTEC visit to The Netherlands:the program
  • 11:15 Coffee, tea, cookies in G076
  • 11:45 Welcome address (Hans Westerhoff): Dutch and European Systems Biology; where it might matter
  • 12:15 Marvin Cassman: The aims of the WTEC study
  • 12:30 lunch13:15 Welcoming remarks by Pier Vellinga (Dean Faculty of Earth and Life Sciences)
  • 13:20 Coffee + informal discussions
the wtec visit to the netherlands the program40
The WTEC visit to The Netherlands:the program
  • 13:45-16:40 Examples of Dutch Systems Biology 13:45 Barbara Bakker; Vertical genomics 14:00 Jurgen Haanstra: Network based drug design 14:15 Frank Bruggeman: Silicon cell as a tool for understanding regulation
  • 14:30 Jan Lankelma: Treating cancer: fighting a system
  • 14:45 Jorrit Hornberg: New principles of signal transduction
  • 15:00:Tea
the wtec visit to the netherlands the program41
The WTEC visit to The Netherlands:the program
  • 15:30 Systems Biology in Delft: Wouter van Winden
  • 16:30 Lactococcus lactis faster; a Systems Biology endeavor; Bas Teusink
  • 16:40 Teaching Systems Biology, Hans V. Westerhoff
  • 16:50 Drinks 17:05 General discussion (chair: Roel van Driel): Systems Biology and its future
  • 17:45 Departure for the restaurant (De Molen; Amstelveen)18:00 Dinner.
  • 19:45 Departure for the airport
  • 20:00 Check in; KLM; Schiphol airport
  • 21:05 flight to the UK......
the wtec visit to the netherlands the program42
The WTEC visit to The Netherlands:the program
  • 15:30 Systems Biology in Delft: Wouter van Winden
  • 16:30 Lactococcus lactis faster; a Systems Biology endeavor; Bas Teusink
  • 16:40 Teaching Systems Biology, Hans V. Westerhoff
  • 16:50 Drinks 17:05 General discussion (chair: Roel van Driel): Systems Biology and its future
  • 17:45 Departure for the restaurant (De Molen; Amstelveen)18:00 Dinner.
  • 19:45 Departure for the airport
  • 20:00 Check in; KLM; Schiphol airport
  • 21:05 flight to the UK......
slide43

Orchestration of cellular processes in a simple cell: making Systems Biology work for Lactococcus lactis

Bas Teusink

Kluyver Centre (Hugenholtz,  Heijnen)

RUG (Kuipers, Kok, Jansen, Poolman)

VU (Westerhoff, Bakker, Snoep)

CMBI (Siezen,Teusink)

WCFS (Kleerebezem, Molenaar, de Vos)

UvA (Brul, Hellingwerf, Breit)

TNO-Food (Van der Werf, Smilde)

slide44

Evolution acts on the biological constraints:

T = 37 °C

T = 30 °C

Objective: use Systems Biology to understand the limits of growth of Lactococcus lactis

Limits of growth (at a given condition): -biological and physico-chemical constraints

slide45

Reference state: the pH-auxostat

- Possible to operate stably at maximal growth rate

- Study pH stress

slide46

WP1

Experimental design and

method development

Experimental protocols

Hypothesis and prediction

Applications

WP4

Data management

WP5

Translation and comparison to other biological systems

WP3

Model building

WP2

Experimental data acquisition

Experimental data

Overview of work packages

slide47

Overview of consortium members

1. Kluyver Centre (Hugenholtz,  Heijnen):

metabolome, proteome, modelling, metabolic engineering, fermentations

2. RUG (Kuipers, Kok, Jansen, Poolman):

transcriptome, protein, membrane proteome, protein interactions, bioinformatics, statistics, model building

3. VU (Westerhoff, Bakker, Snoep):

kinetic modelling, integrative bioinformatics, metabolome, activity-proteome, transport, hierarchical control analysis

4. CMBI (Siezen, Teusink):

bioinformatics, comparative genomics, genome mining, metabolic reconstruction

slide48

Overview of consortiummembers

5. WCFS (Kleerebezem, Molenaar, de Vos):

regulation, mining, bioinformatics, metabolic engineering, metabolomics

6. UvA (Brul, Hellingwerf, Breit):

DNA-array technology, signal transduction, experimental design

7. TNO-Food (Van der Werf, Smilde):

metabolome, data analysis, experimental design

the wtec visit to the netherlands the program49
The WTEC visit to The Netherlands:the program
  • 15:30 Systems Biology in Delft: Wouter van Winden
  • 16:30 Lactococcus lactis faster; a Systems Biology endeavor; Bas Teusink
  • 16:40 Teaching Systems Biology, Hans V. Westerhoff
  • 16:50 Drinks 17:05 General discussion (chair: Roel van Driel): Systems Biology and its future
  • 17:45 Departure for the restaurant (De Molen; Amstelveen)18:00 Dinner.
  • 19:45 Departure for the airport
  • 20:00 Check in; KLM; Schiphol airport
  • 21:05 flight to the UK......
teaching systems biology
Teaching Systems Biology
  • Masters
  • Ph D students
topmaster biomolecular integration systems biology
TopMasterBiomolecular Integration/Systems Biology

The real cell

The silicon cell

Experiments

Calculations

Ultrafast space- and time-resolved spectroscopy, single molecule biophysics and biochemistry, chemistry of complex molecules, molecular genetics in living cells, intracellular networks, hierarchical control analysis, Integrative bioinformatics, principles of Systems Biology, entering the living cell, Silicon Cell, Integrative genomics, confocal microscopy, tumor cell biology, medical Systems Biology, signal transduction, nanotechnology, computational biology, ecological control analysis

Transnational student projects

Career development support

International peer group

Connected Ph D studentships

Nature 427, 568

A Master’s of the CRbCS

Centre for Research on bioComplex Systems

Enquiries:

Prof. Dr. H.V. Westerhoff

Telephone +31 20 444 7228

E-mail: hans.westerhoff@falw.vu.nl

top bmi sb aims continued
TOP-BMI/SB : Aims continued:
  • obtain expertise in advanced conceptual and modeling methodologies for bioinformation and computing technologies, such as medical Systems Biology, signal transduction, computational biology, ecological control analysis, intracellular networks, hierarchical control analysis, Integrative bioinformatics, principles of Systems Biology, entering the living cell, Silicon Cell
  • obtain insight in the most important biological and biomedical issues, and in how they might be addressed scientifically
  • insight into what systems biology and integrative molecular biophysics may mean for society
  • unique and excellent profile for advanced interdisciplinary research between the physical sciences and the life sciences
top bmi sb curriculum structure 2 year 120 ects credit points
TOP-BMI/SB : Curriculum structure (2 year, 120 ECTS credit points)
  • Portal course 14 ECTS
  • 6 obligatory (5 ECTS) courses with each of the CRbCS professors 30 ECTS
  • 1 international experts’ lecture course 6 ECTS
  • orientation on future research project (including literature thesis) 12 ECTS
  • refereeing of research proposal 3 ECTS
  • 8 months research project in Amsterdam and foreign laboratory 40 ECTS
  • scientific article about research project 5 ECTS
  • following and discussing, reporting on scientific seminars 2 ECTS
  • scientific conference (co-organizing, participating, reporting) 3 ECTS
  • preparation for final comprehensive exam 5 ECTS
top bmi sb obligatory courses
TOP-BMI/SBObligatory courses:
  • Portal course: entry course of mathematics and physics for the biologist and biology for the physics/chemistry/mathematics bachelor
  • Biomolecular dynamics (Van Grondelle)
  • Single molecule biophysics and biochemistry (nanobiology) (Schmidt)
  • Chemistry of complex biomolecules (Van der Vies)
  • Looking at Integrating molecules (Lill)
  • Intracellular networks (Westerhoff)
  • Integrative bioinformatics (Heringa)
  • Current topics in biomolecular integration and systems biology (international lecturers, e.g. Heinrich)
top bmi sb
TOP-BMI/SB
  • Research projects:
  • One research exchange project in two laboratories (partly in Amsterdam and partly in one of the collaborating International Centers of Excellence), on Biomolecular Integration / Systems Biology
sb teaching to ph d students
SB teaching to Ph D students
  • Joint graduate school with Humboldt U (Berlin); Heinrich et al
  • Now extended with Goteborgh Yeast Center (Hohmann et al), EU funded
  • Many exchange projects already
  • Annual joint courses
sb teaching human capital problems
SB teaching/human capital problems
  • Very difficult field because of combination top experiments and top theory
  • Lack of appreciation peer groups (Biologists look down upon physicists and mathematicians and vv)
  • Lack of society appreciation (insufficient job opportunities)
  • Insufficient interest young students in science
the wtec visit to the netherlands the program58
The WTEC visit to The Netherlands:the program
  • 15:30 Systems Biology in Delft: Wouter van Winden
  • 16:30 Lactococcus lactis faster; a Systems Biology endeavor; Bas Teusink
  • 16:40 Teaching Systems Biology, Hans V. Westerhoff
  • 16:50 Drinks 17:05 General discussion (chair: Roel van Driel): Systems Biology and its future
  • 17:45 Departure for the restaurant (De Molen; Amstelveen)18:00 Dinner.
  • 19:45 Departure for the airport
  • 20:00 Check in; KLM; Schiphol airport
  • 21:05 flight to the UK......
ad