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

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

2. 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)

3. 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

4. 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

5. 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......

6. System Biology: Where it matters • International developments • European potential • Dutch Systems Biology

7. What has been happening internationally? • Leroy Hood: ISB (Seattle) • Al Gilman Alliance Cell Signalling • E-cell • Virtual cell • Silicon cell ,2003,2004 Model alliance yeast (2003)

8. www.siliconcell.net:Computer replica of parts of living cells (SA, NL, USA)

9. The 4th International Systems Biology Conference 2004 in Heidelberg Kitano et al.

10. What is happening internationally? • Leroy Hood: ISB (Seattle) • Al Gilman Alliance Cell Signalling • E-cell • Virtual cell • Silicon cell • ICSB2000,2001,2002,2003,2004 • Model alliances E. coli (2001) • Model alliance yeast (2003)

11. Bottom up international initiatives • IEcA (International E. coli Alliance) • YSBN (Yeast Systems Biology Network) • EGF Signalling network

12. Round Table discussion 2: Developing a White Paper www.ieca2004.ca

13. June 22:Round Table discussion: Developing a White Paper • 8:30 – 8:50: Mike Ellison: Introduction • 8:50 – 9:00: Randy Johnson; what is needed now • 9:00 – 10:00: Writing the white paper • 10h00 – 10h20: Coffee break • 10h20 – 1130: Writing white paper • 11h30 – 12h00: Further planning

14. 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)

15. YSBN • Copenhagen (2nd) working meeting 2004 May 15,16 • Yeast Systems Biology Network put together; • Committees proposed to deal with sub-issues

16. YSBN

17. YSBN

18. YSBN status quo • White paper has been written • Committees have been formed • Funding unclear

19. GF signalling alliance • In preparation only • Kholodenko, Goryanin (GSK)

20. 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:

21. Transnational initiatives; SysMo • German BMBF • Preparing for microbial System Biology program • Wants to go transnational • Austrian, Dutch ?partners • 2005: call for proposals

22. 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:

23. 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?

24. Partner No Partner No Name of Partner Name of Partner Country Country Responsibility Responsibility Involved in Involved in 1 1 Forschungszentrum Jülich GmbH Forschungszentrum Jülich GmbH GER GER WP2, WP6, WP9 WP2, WP6, WP9 See below See below 1a 1a Project Management Jülich of BMBF and BMWA, Division Biology (PTJ-BIO) Project Management Jülich of BMBF and BMWA, Division Biology (PTJ-BIO) GER GER Co-ordinationManagement(WP9), WP6 Co-ordinationManagement(WP9), WP6 WP4, WP2 WP4, WP2 1b 1b Project Management Jülich of BMBF and BMWA, Division of International Activities (PTJ-GIN) Project Management Jülich of BMBF and BMWA, Division of International Activities (PTJ-GIN) GER GER WP2 WP2 WP4, WP6, WP7 WP4, WP6, WP7 2 2 Fraunhofer-Institut für Systemtechnik und Innovationsforschung Fraunhofer-Institut für Sysemtechnik und Innovationsforschung GER GER WP1 WP1 WP4 WP4 3 3 DECHEMA e.V. DECHEMA e.V. GER GER WP3, WP7 WP3, WP7 3a 3a Association of German Biotechnology Companies (VBU) Association of German Biotechnology Companies (VBU) GER GER WP3 WP3 WP4, WP7 WP4, WP7 3b 3b Informationssekretariat Biotechnologie (ISB) Informationssekretariat Biotechnologie (ISB) GER GER WP7 WP7 WP4 WP4 4 4 Deutsches Krebsforschungszentrum (DKFZ) Deutsches Krebsforschungszentrum (DKFZ) GER GER WP4 WP4 WP8 WP8 5 5 University and BioCenter of Vienna (VBC), Department of Molecular Genetics University and BioCenter of Vienna (VBC), Department of Molecular Genetics AUT AUT WP5 WP5 WP4, WP8, WP7 WP4, WP8, WP7 6 6 Academy of Finland (ACFI) Academy of Finland (ACFI) FIN FIN WP2, WP4, WP6, WP7, WP2, WP4, WP6, WP7, 7 7 dialog<>gentechnik (DGT) dialog<>gentechnik (DGT) AUT AUT WP7 WP7 8 8 Free University Amsterdam (VUA) Free University Amsterdam (VUA) NL NL WP8 WP8 WP4, WP5 WP4, WP5 Associated Partner Associated Partner EuropaBio (EurBio) EuropaBio (EurBio) BEL BEL WP3, WP4 WP3, WP4

25. 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

26. WP8 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

27. Establish common procedures·Establish a strategy for sharing resources, including common databases, and link research activities: • Workshop at ICSB 2004 for agreement on standards: • Model systems • Data formats • Software tools • Requires preparative ‘white paper’

28. ‘Journal’.A publication medium • For now: a Book defining Systems Biology: • …… • Eur. Systems Biology Society??

29. 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?

30. FP6: present • Synthetic Biology in call deadline April 2004: • Make new biological systems; not really Systems Biology • A few Streps on topics related to systems Biology (e.g. Signal transduction; Hohmann) • (Probably) a related NOE: BioSim

31. BioSim ( NoE): Mosekilde • Models for pharmaceuticals

32. BioSim ( NoE): Models only

33. 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

34. 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?

35. 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

36. InSysBio: Eureka label approved June 20, 2004 • Press release • Project description • Projects

37. InSysBio aims • The INSYSBIO Cluster is centred on three Work Areas that converge on the same objective: to provide a framework that enables the prediction of the effects of drugs and food through Integrative Systems Biology Models.The Work Area A 'Integrative Data Management Tools' includes the integration and analysis of existing data in a middleware solution as well as the development of a global semantic level integrating all the cluster activities and data.

38. InSysBio ctd • The Work Area B 'Integrative Modelling Tools' includes, first of all, the development of data mining and molecular modelling tools that can generate hypotheses for the second step which is the modelling of the Biological Systems investigated.The Work Area C 'Integrative Applications' provides the application cases in Food & Drug R & D to devise computational models using the integrative data management and modelling tools developed in the aforementioned Work Areas.

39. 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

40. ESF Systems Biology:Where it matters

41. ESF: what is needed • Time window: 10 years from now • How can we make this a major Euro effort, supported by policy makers, industry, society and academia? • Outside message: invest in order to obtain: • better health, life and big savings

42. What is needed? • Wet SB, not just dry (FP6, EUREKA) • Find European niche (mechanisms of SB?) • Identify SB-related programs European National Science Foundations • Activate where these do not yet exist • Try to get the national SFs to coordinate their SB programs • Construct mechanisms for transnational funding • Become worthy partner for USA, Japan, Canada, China, Korea • Provide funding anchors for the alliances

43. ESF Systems Biology:The Ambition

44. ESF Systems Biology:The Ambition • European 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 European 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

45. European: 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

46. ESF Systems Biology:The Ambition • European 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 European 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