Integrated e-infrastructure for integrated software for integrated structural biology: defining the roadmap for collaboration. EGI slides presented by D Wallom at CECAM meeting, Oxford.

1. EGI-InSPIRE
Integrated e-infrastructure for integrated
software for integrated structural biology:
defining the roadmap for collaboration
Steve Brewer steve.brewer@egi.eu
Presented by:
David Wallom david.wallom@oerc.ox.ac.uk
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

2. Outline
1. The background: integrated software for
integrated structural biology
2. The landscape for integrated e-infrastructure
3. Defining the roadmap for collaboration
2
CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

3. Outline
1. The background: integrated software for
integrated structural biology
2. The landscape for integrated e-infrastructure
3. Defining the roadmap for collaboration
3
CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

4. Background
• Structural Biology: the view from outside
– A range of in silico techniques to study biological
structures – including NMR:
• Nuclear magnetic resonance spectroscopy of proteins
– A major division of Biology
• therefore results need to be shared and re-used?
– At Oxford, The Division of Structural Biology -
(STRUBI), has a number of centres and projects
– At EU level – INSTRUCT an ESFRI project
– Also, WeNMR has been steadily building its own
international infrastructure & collaborating with EGI.
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

5. EGI and Structural Biology
– WeNMR VRC – representing the
Structural Biology community to
date (significant body of users)
– Participation in User Community
Board (UCB) (1st VRC)
• Synergy with other communities
• Requirements gathering
• Contact Alexandre Bonvin for further
info.
– www.wenmr.eu/
– enmr.eu >400 users
– Largest VO in Life Sci.
operations-portal.egi.eu/vo/usersMetrics
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CECAM, Oxford - May 22, 2011
EGI-InSPIRE RI-261323 www.egi.eu

6. Contents
1. The background: integrated software for
integrated structural biology
2. The landscape for integrated e-infrastructure
3. Defining the roadmap for collaboration
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

7. C21: Digital Research
Extracting Knowledge
from the Data Deluge
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

8. Digital Agenda for Europe
• Borderless Services
• Interoperability
• Supporting Innovation
remove barriers to
the free movement
of knowledge
“Europe should also build its innovative
Digital Agenda for Europe advantage in key areas through reinforced
e-Infrastructures (i.e. GEANT & EGI)”
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

9. What is EGI?
• European Grid Infrastructure (EGI)
– Federation of National Grid Infrastructures
– Represented by EGI.eu (Dutch foundation)
• National Grid Infrastructures (NGIs)
– Sole national point of contact for „Grids„
– Integrates individual resource centres
• Current Status:
– 35+ NGIs & 350+ resource centres
– 300,000 CPUs & 200PB+ storage
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

10. EGI
• European
– Over 35 countries
• Grid
– Secure sharing
• Infrastructure
– Computers
– Data
– Instruments
– …. and beyond!!
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

11. EGI Resource Infrastructure Providers – RPs
(April 2012)
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

12. EGI Resource Centres
(April 2012)
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

13. VO Statistics (April 2012)
Metrics Value Supported Research Communities
Archeology Fusion
Registered national and 226 (3.20% )
Astronomy Geophysics
international VOs
Astrophysics High Energy Physics
Registered users 20883 (14.30% ) Civil Protection Life Sciences
Active VOs 25/23/8 Comp. Chemistry Multimedia
(High/Medium/Low) Earth Sciences Material Sciences
Finance …
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

14. EGI.eu
• Coordination for European Grid resources
– Established February 8th 2010
– Central policy & services needed to run a grid
– Sustainable small coordinating organisation
• Based in Amsterdam
– Coordinating core (~20 people) in Amsterdam
– Technical services from partners (~20 people)
EGI and EGI.eu: Supported by the EGI-InSPIRE project
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

15. EGI-InSPIRE: project objectives
• A sustainable production infrastructure
– Resource providers in Europe and worldwide
– With new technologies as they mature
• Support structured international research
– Sustain current domain specific services
– Attract new user communities (e.g. ESFRI)
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

16. EGI-InSPIRE Project
Integrated Sustainable Pan-European Infrastructure for
Researchers in Europe
A 4 year project with €25M EC
contribution
– Project cost €72M
– Total Effort ~€330M
– Effort: 9261PMs
Project Partners (50)
EGI.eu, 38 NGIs, 2 EIROs
Asia Pacific (9 partners)
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

17. Technology Innovation
• Will come from outside EGI
– Moving research technologies into production
• Partnership with technology projects
– EMI (European Middleware Initiative)
– IGE (Initiative for Globus in Europe)
– EDGI (European Desktop Grid Initiative)
– StratusLab
– VenusC
– SAGA
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

18. VOs, VRCs and partner projects
• Virtual Organisations: rules defining people & resources
• VRCs are self-organised (virtual) research communities
which give individuals within their community a clear
mandate to represent the interests of their research
field within the EGI ecosystem.
• Current EGI VRCs: (http://www.egi.eu/community/vrcs/)
– WeNMR - Structural biology
– LSGC – Life sciences
– HMRC – Hydro-meteorology
– WLCG – High energy physics NEW!
– CLARIN/DARIAH – Humanities (with a Letter of Intent)
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CECAM, Oxford - May 22, 2011
EGI-InSPIRE RI-261323 www.egi.eu

19. European Grid
Infrastructure
EGI.eu (not-for-profit org)
• Established February 8th 2010
• Central policy & services
• Sustainable, ~20 people
• Based in Amsterdam, NL
• Partners provide services
EGI Ecosystem
EGI-InSPIRE project
• 4 year project, 25M EC funds
• 50 project partners
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CECAM, Oxford - May 22, 2011
EGI-InSPIRE RI-261323 www.egi.eu

20. EGI: strategy for 2020
• Pillars of the strategy:
1. European-wide coordination and interaction with research
communities and national resource infrastructure providers
2. Coordination, maintenance, operation and delivery of an open
uniform European-wide federated production infrastructure
3. Developing and promoting technologies for federating new
resources
4. Supporting the integration and operation of scalable
interdisciplinary Virtual Research Environments personalised
to each research community
http://go.egi.eu/EGI2020
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CECAM, Oxford - May 22, 2011
EGI-InSPIRE RI-261323 www.egi.eu

21. VRCs – VREs & EGI
Virtual Research Communities
Created by a
project such as
CLARIN, ELIXIR, Virtual
EGI Collaboration platform
LifeWatch, ...
Research EGI
Environment Community
Platform
VM
VM
DB SW
VM EGI Infrastructure platform
VM
Research facilities VM
DB SW
(e.g. detectors, sensor
networks)
EGI resources
Dedicated or shared resources/platforms (clusters, storages,...)
(e.g. Clusters; EC2, PRACE, XSEDE)
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CECAM, Oxford - May 22, 2011
EGI-InSPIRE RI-261323 www.egi.eu

22. Anatomy of a VRE
E Service access
EGI support G gateways - portal, desktop and mobile)
(Science
I
Service integration
s (workflows)
EGI support
u
p
Services
p (Applications & data)
o
Off-the-shelf Domain specific Off-the-shelf
EGI supportand custom
r and generic data and custom
VM images repositories applications
t
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CECAM, Oxford - May 22, 2011
EGI-InSPIRE RI-261323 www.egi.eu

23. EGI support:
Service access
• Catalogue of existing solutions
– http://go.egi.eu/sciencegateways
• Gateway components repository
– SCI-BUS portlet repository
will be used (see MoU)
• Plan: “How-to” documentation
– Develop an EGI science gateway primer
(through a new EGI Virtual Team project
and portal-community@mailman.egi.eu)
• Portal & gateway workshops
– CF & TF
– Portal workshops by NGIs
– Community workshops on portals
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CECAM, Oxford - May 22, 2011
EGI-InSPIRE RI-261323 www.egi.eu

24. EGI support:
Cross cutting support
• Applications Database (EGI software catalogue)
– Stores information about any EGI software
– Tags:
• Organise software into clusters
– Subscription:
• Join an item/cluster as supporter
(developer, operator, expert)
– Notifications:
• To get informed about changes
– Web gadgets:
• Embed customised lists of software into your website
– Write API  Planned
• Itegrate the catalogue with the EGI platform (e.g. Info system)
• Integrate the catalogue with other catalogues
• Training Marketplace
– Advertise and search for events, materials, online courses
– Web gadgets:
• Embed customised lists of software into your website
• Events
– Community and Technical Forums (Call for TF2012 co-located events is open!)
– Topical workshops (hosted by NGIs)
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CECAM, Oxford - May 22, 2011
EGI-InSPIRE RI-261323 www.egi.eu

25. EGI support:
Service development and operation
• Established & evolving processes from various EGI(-InSPIRE)
stakeholders:
– EGI Operations
– EGI Technology
– NGIs, VRCs, EGI.eu
– Pojects (e.g. BioVel, Scalalife, ...)
• But the EGI platform is about to change:
– Services will run in Virtual Machines
• EGI Strategic Plan; EGI Platform Roadmap
– Developers & operators will need new support mechanisms:
• VM image repository
• VM information system
• VM monitor with helpdesk integration
• ...
EGI Federated Cloud Task force  EGI Infrastructure platform
Join as user community!
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CECAM, Oxford - May 22, 2011
EGI-InSPIRE RI-261323 www.egi.eu

26. Summary of EGI
• EGI.eu established in Amsterdam
– Supported through EGI-InSPIRE project
• EGI has transitioned from a federation of
regional to national resource providers
• EGI works with technology providers on
an open standards based architecture
• EGI will evolve to support the needs of its
current and new research communities
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

27. Outline
1. The background: integrated software for
integrated structural biology
2. The landscape for integrated e-infrastructure
3. Defining the roadmap for collaboration
27
CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

28. Roadmap for collaboration
• EGI wants to support Structural Biology
– work with INSTRUCT
– Continue working with WeNMR VRC
– Co-located meetings?
– Virtual Teams to achieve short-term goals
• Specific use cases and scenarios – descriptions?
• Formally involve specific NGIs – which?
• Virtualisation to achieve scalability of solutions?
• Identify which software applications are needed?
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

29. EGI activities: forums,
workshops, VTs and TFs
– Forums
• Every 6 months, around 500 people meet to share knowledge and plans
• Keynotes, presentations, workshops, training, demonstrations, posters
– Task Forces
• Federated Clouds
• MAPPER
• Identity
– Workshops (face-to-face and also „webinars‟)
• Integration of complex scientific workflow systems with EGI‟s services.
• Research Infrastructure interested in adopting EGI‟s operational tools to
support their own distributed production infrastructure
• Science Gateways Workshop
– Virtual Team (VT) projects – 3- 6 months (with NGIs)
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CECAM, Oxford - May 22, 2011
EGI-InSPIRE RI-261323 www.egi.eu

30. Technical Forum TF12 - Prague
– Theme of Technical Forum in September (17th – 21st):
• “Developing an open and sustainable EGI ecosystem to support open science in the
digital European Research Area.”
– 5 tracks:
1. Operational services
Operational services used by EGI to deliver a federated infrastructure composed of national resource providers
2. Physical Infrastructure services
Work of technology providers and platform integrators to provide generic infrastructure services that can be
integrated into virtual research environments upon which research communities depend
3. Virtualised Resources: challenges and opportunities
Work of technology providers, platform integrators and platform operators of the grand challenges that relate to
the integration of virtualized resource
4. Virtual Research Environments
Research communities are seeking to establish their own virtual research environments with their own
resources and operating their own customized services through the work of platform integrators and platform
operators
5. Coordination and Communication
Focus on reaching out to communities and partners across the ecosystem
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CECAM, Oxford - May 22, 2011
EGI-InSPIRE RI-261323 www.egi.eu

31. VT projects: examples
VT projects of interest to Structural Biology
1. The Federated Cloud Task Force is already providing a cloud infrastructure through
a few committed NGIs. This pilot resource is being made available to WeNMR and
other research communities participating in the Task.
2. The Message Passing Interface (MPI) group is providing support for application
developers to port and scale up parallel applications to the European Grid
Infrastructure.
3. A lively portal developer and provider community is being supported by EGI. The
group is able to setup and operate custom, application and/or community specific
portals for members of the Structural Biology community to interact with EGI.
4. A project to assess the possibilities for federated identity management in EGI and
the readiness of EGI member states for federated authentication and authorisation
mechanisms will deliver greater flexibility for integrated services.
5. EGI‟s operating resources and user support services continue to grow, with new
types of services and infrastructures, such as desktop grids, map-reduce
frameworks, GPU clusters continuously being developed and made available.
Suggestions for future VT projects may emerge from discussions at CECAM
Further information on VTs: https://wiki.egi.eu/wiki/Virtual_teams
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu

32. Conclusions
• EGI is more than a production infrastructure:
– A framework for sharing and innovation
– A forum for communication and collaboration
• Structural Biology research community has strong grid history
– Many years experience plus involved from the start of EGI
– Many grid-based applications, research and publications
– http://www.wenmr.eu
• Structural Biology community key part of future EGI Strategy
– EGI Strategy is aligned with EU 2020 strategy inc. Innovation Union
– EGI will support and partner various ESFRI projects and researchers
– EGI will develop requirements with technology developers & providers
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CECAM, Oxford - May 22, 2011
EGI-InSPIRE RI-261323 www.egi.eu

33. EGI-InSPIRE
Questions?
EGI user community support team:
ucst@egi.eu
See you at the EGI Technical Forum 2012,
Prague, Czech Republic between 17–21 September
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CECAM, Oxford - May 22, 2012
EGI-InSPIRE RI-261323 www.egi.eu