EGI Services for Structural Biology - S Brewer EGI

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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.

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  • Structural Biology (Wikipedia)Structural biology is a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules, especially proteins and nucleic acids, how they acquire the structures they have, and how alterations in their structures affect their function. This subject is of great interest to biologists because macromolecules carry out most of the functions of cells, and because it is only by coiling into specific three-dimensional shapes that they are able to perform these functions. This architecture, the "tertiary structure" of molecules, depends in a complicated way on the molecules' basic composition, or "primary structures.“ Hemoglobin, the oxygen transporting protein found in red blood cells Biomolecules are too small to see in detail even with the most advanced light microscopes. The methods that structural biologists use to determine their structures generally involve measurements on vast numbers of identical molecules at the same time. These methods include:Macromolecular crystallography, NMR, EPR, Cryo-electron microscopy (cryo-EM), Multianglelight scattering, Small angle scattering, Ultra fast laser spectroscopy, and Dual Polarisation Interferometry and circular dichroism. Most often researchers use them to study the "native states" of macromolecules. But variations on these methods are also used to watch nascent or denatured molecules assume or reassume their native states. See protein folding.A third approach that structural biologists take to understanding structure is bioinformatics to look for patterns among the diverse sequences that give rise to particular shapes. Researchers often can deduce aspects of the structure of integral membrane proteins based on the membrane topology predicted by hydrophobicity analysis. See protein structure prediction. In the past few years it has become possible for highly accurate physical molecular models to complement the in silico study of biological structures.STUBI – Oxfordhttp://www.strubi.ox.ac.uk/strubi/index.jspThe Division of Structural Biology (STRUBI) is part of the Nuffield Department of Clinical Medicine (NDM) at the University of Oxford. STRUBI is also part of the Wellcome Trust Centre for Human Genetics. The Division includes the Oxford Protein Production Facility (OPPF) and the Oxford Particle Imaging Centre (OPIC).STRUBI is situated in the Old Road Campus in the Headington area of Oxford. The Division applies the techniques of structural biology, particularly macromolecular crystallography and electron microscopy, to the study of biomedically important processes. The research interests of the Division include the structural study of viral proteins and intercellular recognition. The work of the laboratory is supported by many sources, but principally the MRC, Cancer Research UK, the BBSRC, the Royal Society, the EU FP6 & FP7 and the Wellcome Trust.INSTRUCT:Integrated structural biology unlocking the secrets of lifeInstruct is the dynamic hub of structural biology; integrating the infrastructure of expertise, technology platforms and education to further the frontiers of science. We provide structural and cell biologists from industry and academia with the opportunity to further their research.WeNMRWeNMR  is both a three years project funded under the European Commission’s 7th Framework Programme (e-Infrastructure RI-261571) and a Virtual Research Community supported by EGI, the largest one within the life science area. WeNMR aims at bringing together complementary research teams in the structural biology and life science area into a virtual research community at a worldwide level and provide them with a platform integrating and streamlining the computational approaches necessary for NMR and SAXS data analysis and structural modelling.
  • Data taken from EGI Operations portal today.Enmr is a large VO within Life Sciences and has recently emerged as the largest. So, EGI is already significantly supporting Structural Biology.
  • Project Objectives:A sustainable production infrastructureResource providers in Europe and worldwide With new technologies as they matureSupport structured international researchSustain current domain specific services Attract new user communities (e.g. ESFRI)
  • Under the new model this is a representation of how a community will be responsible for running their own VRE. This would comprise many services and resources specific to them but also may encompass core and shared EGI services. EGI would help construct the VRE, typically in conjunction with partners and partner projects.This slide essentially maps to your slide on core and shared services that we have discussed previously.
  • EGI Services for Structural Biology - S Brewer EGI

    1. 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 1 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    2. 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, 2012EGI-InSPIRE RI-261323 www.egi.eu
    3. 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, 2012EGI-InSPIRE RI-261323 www.egi.eu
    4. 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. 4 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    5. 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 5 CECAM, Oxford - May 22, 2011EGI-InSPIRE RI-261323 www.egi.eu
    6. 6. Contents 1. The background: integrated software for integrated structural biology 2. The landscape for integrated e-infrastructure 3. Defining the roadmap for collaboration 6 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    7. 7. C21: Digital Research Extracting Knowledge from the Data Deluge 7 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    8. 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)” 8 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    9. 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 9 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    10. 10. EGI • European – Over 35 countries • Grid – Secure sharing • Infrastructure – Computers – Data – Instruments – …. and beyond!! 10 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    11. 11. EGI Resource Infrastructure Providers – RPs (April 2012) 11 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    12. 12. EGI Resource Centres (April 2012) 12 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    13. 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 … 13 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    14. 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 14 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    15. 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) 15 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    16. 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) 16 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    17. 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 17 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    18. 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) 18 CECAM, Oxford - May 22, 2011EGI-InSPIRE RI-261323 www.egi.eu
    19. 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 19 CECAM, Oxford - May 22, 2011EGI-InSPIRE RI-261323 www.egi.eu
    20. 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 20 CECAM, Oxford - May 22, 2011EGI-InSPIRE RI-261323 www.egi.eu
    21. 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) 21 CECAM, Oxford - May 22, 2011EGI-InSPIRE RI-261323 www.egi.eu
    22. 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 22 CECAM, Oxford - May 22, 2011EGI-InSPIRE RI-261323 www.egi.eu
    23. 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 23 CECAM, Oxford - May 22, 2011EGI-InSPIRE RI-261323 www.egi.eu
    24. 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) 24 CECAM, Oxford - May 22, 2011EGI-InSPIRE RI-261323 www.egi.eu
    25. 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! 25 CECAM, Oxford - May 22, 2011EGI-InSPIRE RI-261323 www.egi.eu
    26. 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 26 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    27. 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, 2012EGI-InSPIRE RI-261323 www.egi.eu
    28. 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? 28 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    29. 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) 29 CECAM, Oxford - May 22, 2011EGI-InSPIRE RI-261323 www.egi.eu
    30. 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 30 CECAM, Oxford - May 22, 2011EGI-InSPIRE RI-261323 www.egi.eu
    31. 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 31 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu
    32. 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 32 CECAM, Oxford - May 22, 2011EGI-InSPIRE RI-261323 www.egi.eu
    33. 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 33 CECAM, Oxford - May 22, 2012EGI-InSPIRE RI-261323 www.egi.eu

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