1. the European Nutrigenomics Organisation Un Oslo Un Munich Un Florence Un Balearic Illes Un Cork Trinity Un. Ulster Rowett Un Newcastle Un Reading IFR DiFE Un Krakow Inserm Marseille TNO Un Wageningen Un Maastricht EBI NuGOGO Un Lund Rikilt Rivm

2. the European Nutrigenomics Organisation The NuGO Black Box project: A distributed bioinformatics infrastructure for nutrigenomics research Tony Travis University of Aberdeen Rowett Institute of Nutrition and Health

3. the European Nutrigenomics Organisation NuGO is a virtual organisation Why? Management of research projects spans institutional boundaries Avoids duplication of effort, and share resources to solve problems effectively How? Scientists working in different research labs collaborate and share their data Labs develop trust relationships, and share intellectual property rights

4. the European Nutrigenomics Organisation Why is data sharing important? It's evidence that a trust relationship exists Help to reconcile conflicts of interest –Take measures to restrict access to data –Avoid accidental 'prior-disclosure' –Prevent unauthorised or inappropriate use –Support potential patent applications –Permit correct attribution of scientific work Lack of trust - disincentive to data sharing

5. the European Nutrigenomics Organisation NuGO is virtually organised Strengths Apply the aggregate resources of many partners to problem e.g. PPS (Proof of Principle Study)‏ Free exchange of ideas within NuGO Weaknesses Trust relationships are quite fragile... Conflicts due to 'prior disclosure' of unpublished data Unfair attribution of work accomplished

6. the European Nutrigenomics Organisation Utopian view Property is theft…  Share data freely  Everyone benefits  Ideas develop  Science prospers

7. the European Nutrigenomics Organisation Not everyone agrees! Big pharma make a profit by exploiting academic science ISV's promote proprietary software Knowledge is power... Freedom is a threat

8. the European Nutrigenomics Organisation Reconciliation... IPR –Intellectual property rights are important Freedom –Intellectual freedom is important Attribution –Supports IPR –Defends freedom

9. the European Nutrigenomics Organisation Data management Single most difficult problem for science –No simple solution to 'schema' integration –Data centres are appropriate for business –Business methods are not appropriate for science...

10. the European Nutrigenomics Organisation Business computing methods Bottom line –Minimise the cost of ICT infrastructure –Centralise resources –Maximise profit Rigid and inflexible ICT policies –Reduce costs –Use industry 'standards' –Avoid expensive 'non-standard' solutions

11. the European Nutrigenomics Organisation Scientific computing methods Intellectual freedom –Maximise the benefit of ICT to scientists –Collaborative development of software –Freedom to innovate Flexible ICT policies –User administered PC's –Devolution of authority –Well supported and documented

12. the European Nutrigenomics Organisation Data centres are quite good The problem is business methods –Profit, not the 'customer' is the priority A well-managed data-centre is a good place to store your data! Users don't need to worry about backups and disaster recovery Science is sometimes underfunded, so economies of scale can be important

13. the European Nutrigenomics Organisation Let's compromise... Size matters –A large, remote data centre is too big –A typical laptop/desktop is too small The solution should be scaled appropriately –Our unit of collaboration is the lab –Let's say five of six people in a lab –Everyone has their own PC We need a 'lab-scale' solution

14. the European Nutrigenomics Organisation NBX strategy Server-grade PC –Designed to be running 24/7/365 –Resilient to hardware failure –Powerful enough for five or six people Use all available resources –The NBX is a web server 'appliance' –The lab PC's are clients that use the NBX –The NBX does most of the work –The client PC's display the results

15. the European Nutrigenomics Organisation IT policy at NuGO partners Limited access requested – Port 22 (SSH) and 80 (HTTP) open – Tunnel insecure protocols via SSH Client PC requirements modest – Java enabled web browser – Optional installation of Windows clients Remote admin of NBX's by NuGO

16. the European Nutrigenomics Organisation Why a ‘black-box’ approach? Don’t need to know how it works to use it Deploy a pre-configured Linux server easily –Install from ‘live’ DVD on existing hardware –Pre-installed on systems supplied by NuGO –Reduce need for IT support in every lab –Automatic backup and software updates Autonomous system – able to discover peer NBX systems – cooperate with peers to share workload

17. the European Nutrigenomics Organisation NuGO Black Box (NBX)‏ lab-scale server –Based on Bio-Linux –NERC/NEBC Web-appliance –Web browser –Web services NBX network –Bioinformatics infrastructure

18. the European Nutrigenomics Organisation

25. NuGO data sharing network

26. the European Nutrigenomics Organisation NBX roll-out to NuGO partners Limited access – Port 22 (SSH) and 80 (HTTP) open Client PC – Web browser – Optional clients NBX Admin –Local “manager” –Remote “nugo”

27. the European Nutrigenomics Organisation NuGO-Grid Network of NuGO-Linux servers – Interconnected to create Grid Compute Grid – Load-balance between servers Data Grid – Pool data and share resources P2P (Peer-to-peer) – Local control of resource sharing

28. the European Nutrigenomics Organisation Current status of NuGO-Grid

29. Kerrighed Active EU FP6 project Funded until 2010 http://www.kerrighed.org Uses ideas from openMosix and OpenSSI

30. Prototype NBX clusters Maastricht –Four NuGO NBX's RINH –Four NuGO NBX's –Four RINH NBX's –Eight BioSS NBX's Collaboration with Mario Negri Institute Objectives –Aggregate CPU and memory of locally connected NBX's –Incremental upgrade of NBX's instead of NBX replacement –Adjust resource to scale of problem

31. the European Nutrigenomics Organisation XtreemOS Grid operating system INRIA, Paris –Kerrighed-based –SSI kernel patch –Grid capabilities in Linux kernel space –No middleware –Virtual organisations

32. the European Nutrigenomics Organisation XtreemOS proof of concept NuGO project at RINH and Mario Negri –Evaluate Kerrighed and XtreemOS for NBX –Using Bio-Linux 5.0 version of NuGO-Linux –Prototype seven node Kerrighed cluster EasyUbuntuClustering Wiki –http://wiki.ubuntu.com/EasyUbuntuClusteringhttp://wiki.ubuntu.com/EasyUbuntuClustering –Community-based collaborative development –Part of the 'biobuntu' blueprint

33. Harnessing the power of Disruptive Technologies A PEER-TO-PEER approach for data sharing in clinical trials and bioinformatics research

34. Peer-to-peer data sharing Luca Clivio, Mario Negri Institute Milan –p2pDB for clinical data –Case study 1: SINPE-DOMUS (in production) Italian Registry of Domiciliar Artificial Nutrition ~3000 patients enrolled in 60 centres Each patient visited about 10 times –Case study 2: (under test) Italian Gynaecologic Ovarian Cancer Tissue Bank Three tissue/cell line banks at the Oncology Dept.

35. SINPE-DOMUS (web model) Central Web server centre

36. SINPE-DOMUS (distributed DB) Centre MARIO NEGRI Institute

37. SINPE-DOMUS (p2pDB) Centre MARIO NEGRI Institute

38. Storage Peer High performance Cluster Peer Partner Index node A Index node C Index node B Index node D p2p Network coordination Partner Push-based p2pDB

39. Proposed Infrastructure Array express GEO Microarray Experiments DB (LIMS) Clinical Trials DB BioBank DB (tissue banks or cell lines) Microarray experiments Analysis workflow Tony Travis (RRI/BioSS) NUGO Black Boxes (European nutrigenomics) Output Duccio Cavalieri (Istituto Toscano Tumori) Giovanna Chiorino (Fondo Edo Tempia)

40. Unbalanced networks Inevitable in 'omics' research – The huge amount of data involved does not allow a fully replicated distributed database – Unpublished data can not be shared without explicit agreement between collaborators – Unverified data should not be shared at all p2p data sharing – Designed for unbalanced networks – map/reduce moves computation to data

41. the European Nutrigenomics Organisation The wrong cloud * Amazon Web Services (AWS) –Elastic Compute Cloud (EC2) –Simple Storage Service (S3) Cost effective if you seldom use a computer –The more you use a computing and storage infrastructure the less economic it becomes to rent it from someone else Nothing new: Computer bureaux and expensive BIG iron Private clouds are the way forward –Maximise use of resources within an organisation * Peter Lucas, Joseph Ballay, Ralph Lombreglia (MAYA Design, Inc., March 2009). www.maya.com/file_download/126/The%20Wrong%20Cloud.pdf

42. the European Nutrigenomics Organisation Development of NuGO-Grid NBX Data Grid –Data sharing –NuGO-Linux NBX Compute Grid –Kerrighed –XtreemOS

43. the European Nutrigenomics Organisation NuGO-Linux USB stick Installation –Workstation/server Rescue –Disaster recovery Personal NBX –'live' USB stick –demo/evaluation NuGO-Linux DVD 'iso' image at: http://nbx1.nugo.org/biobuntu Contact: NuGO communications manager: sian.astley@bbsrc.ac.uk

44. the European Nutrigenomics Organisation Summary Viable NBX Data Grid Basic NBX Compute Grid Bio-Linux 5.0 NBX's being deployed XtreemOS NBX proof of concept project Collaboration with NEBC and NTC Proposed p2bDB infrastructure NuGO-Linux USB stick http://www.nugo.org/nbx

45. the European Nutrigenomics Organisation Acknowledgements  NBX project  Ulrich Harttig (NIN and NBX repository)‏  Harrie Kools (NBX installation)‏  Philippe Rocca-Serra (base2)‏  Philip de Groot (GenePattern)‏  Chris Evelo, Martijn van Iersel, Thomas Kelder (Desktop)‏  Duccio Cavalieri (EuGene and NBX access policy)‏  Patrick Ahles, Charly John, Olivier Riche (NBX upgrade)‏  Lars Eissen, Caroline Reiff (NBX help-desk)‏  Marten Renkema (NuGO-Net NBX pages)  Kerrighed/XtreemOS proof of concept project  Luca Clivio, Alicia Mason (Kerrighed and XtreemOS)‏  Ruan Elliott (WPT coordinator and NBX tester)  p2pDB (IRFMN) project  Luca Clivio, Bioinformatics Dept.  Sergio Marchini, Oncology Dept.  Maddalena Fratelli, Biochemistry Dept.  Giovanna Chiorino, Fondo Edo Tempia, Biella  Duccio Cavalieri, Istituto Toscano Tumori, Università di Firenze‏