myGrid Personalised e-Science on the Grid - NeSC Opening 250402

							       myGrid:
Personalised e-Science
             e-Biology
     on the Grid

   Professor Carole Goble
  http://www.mygrid.org.uk
Contact mygrid@cs.man.ac.uk
       myGrid:
Personalised e-Science
     on the Grid

           Personalised
  extensible environments for
          data-intensive
in silico experiments in biology
      e-Science & Biology
• Biology is a multi-faceted & increasingly
  multi-disciplinary science.
• Bioinformatics is an “e-Science”.
  – Discovery is done in silico on results obtained
    from experiments using a number of analysis
    & data resources.
• Molecular biology & genomics are our
  particular focus.
         Circadian Rhythms
• Has anyone studied the effect of
  neurotransmitters on the circadian rhythms in
  Drosophila?
• How do the functions of the clusters of
  proteins from my experiment interrelate?
  What are the proteins with a particular
  function?
• Is a structure known for this protein and what
  other proteins have a similar structure?
• Can I build a homology 3D model?
• What is known about the homologous protein?
Information Weaving
         • Large amounts of data
           & many applications.
         • Highly heterogeneous.
           – Different types,
             algorithms, forms,
             implementations,
             communities, service
             providers
         • Highly complex and
           inter-related.
         • Highly volatile.
         • Obstacles Everywhere
Descriptive knowledge
               Circadian Rhythms
1.   Has anyone else studied the effect of
     neurotransmitters on the circadian           1
     rhythms in Drosophila?
2.   How do the functions of the clusters
     of proteins from my experiment               2
     interrelate? And what are the proteins
     with a particular function?
3.   Is a structure known for this protein
     and what other proteins have a similar       3
     structure?
4.   Can I build a homology 3D model?
5.   What is known about the homologous
     protein?                                 4       5
             E-Science Q & A
Who else has asked this question & can
   I use/adapt their approach?               1
  – Workflow.
What were the results at each stage?
                                             2
  – Dynamic Data Repositories.
When was P12345 last updated?
Which BLAST did I use?
  – Provenance.                              3
Has PDB changed since I last ran this?
  – Notification.
                                         4       5
Personalisation.
       myGrid Objectives
• Straightforward discovery, interoperation,
  fusion, sharing of data, knowledge and
  workflows.
• Explicit management of workflows.
  – information & processes & best practice.
• Improving quality of experiments & data.
  – provenance & propagating change.
• Scientific discovery is personal & global.
  – personalisation & collaborative working.
• Security, ownership -> valuable assets.
      Who is myGrid for?
–   Users, developers, maintainers.
–   Biologists.
–   Bioinformaticians, resource providers.
–   Tool builders, system administrators.
                                      myGrid users
                         biologists            IS specialists

                                              tool       systems
                infrequent
                         problem              builders administrators
                         specific bioinformaticians service
                                                      provider
                                  bioinformatics
                                  tool builders
          myGrid Outcomes
1. e-Scientists
  –   Environment built on toolkits for service access,
      personalisation & community.
  –   Gene function expression analysis (fly & yeast).
  –   Annotation workbench for the PRINTS pattern
      database.
2. Developers
  –   Protocols and service descriptions.
  –   myGrid-in-a-Box developers kit of core services.

  –   Reference implementation services & applications.
  –   Bio services – already delivered.
              myGrid Stack
                    Applications

Client        Admin Portal User Agent Collaboration
 Framework
Semantic
           Info. Extraction Data   Workflow Ontology
Services
Metadata
           Personalisation   Provenance     Directory
Services
Coordination Services
 Governance     Workflow           Data     Directory

                 Networked Services
      myGrid Pre-Prototype
                   Portal



                                       Metadata:
 Personal           Workflow
Repository                             Ontology
                   Enactment
                                       Metadata:
                                        Service
Workflow                               Directory
Repository   Bioinformatic Services
              Bioinformatic Services
Locating a       Repository Workflow Ontology
                   Client
                             Portal
                             Client   Client

 workflow     Personal                      Meta Data:
             Repository                      Ontology

                                            Meta Data:
                          Workflow         Service Type
                          Repository         Directory



                          How do the functions of the
                          clusters of proteins from
                          my experiment interrelate?
Locating a       Repository Workflow Ontology
                   Client
                             Portal
                             Client   Client

 workflow     Personal                      Meta Data:
             Repository                      Ontology

                                            Meta Data:
                          Workflow         Service Type
                          Repository         Directory
Locating a       Repository Workflow Ontology
                   Client
                             Portal
                             Client   Client

 workflow     Personal                      Meta Data:
             Repository                      Ontology

                                            Meta Data:
                          Workflow         Service Type
                          Repository         Directory
Locating a       Repository Workflow Ontology
                   Client
                             Portal
                             Client   Client

 workflow     Personal                      Meta Data:
             Repository                      Ontology

                                            Meta Data:
                          Workflow         Service Type
                          Repository         Directory
Running a           Repos.     Workflow    Service Selection

workflow 4
                    Client      Client           Client
                                  1        2?
                                   Workflow
        Personal
                       3          Enactment
       Repository
                                                      2?
                                    2
      Provenance                                            Service
         Data                                              Directory
                             Bioinformatic Services
Running a           Repos.
                     Client
                                Workflow
                                 Client
                                            Service Selection
                                                  Client
workflow  4                        1        2?
                                    Workflow
        Personal
                        3          Enactment
       Repository
                                                       2?
                                     2
       Provenance                                            Service
          Data                                              Directory
                              Bioinformatic Services
myGrid generic technologies
1. Ontologies, Protocols & APIs.
2. Database access from the Grid.
      Reference implementation for UK DBTF.
3. Process enactment on the Grid.
4. Provenance services.
5. Metadata services.
  –   From Semantic Web: DAML+OIL, RDF(S).
6. Personalisation services.
7. Reference implementation of OGSA.
   Converging Technologies
Globus, Sun Grid
Engine, Condor, DS   Grid Computing
(Jini, Corba)

                                An early adopter
                                for OGSA

      Agents                              Web
ACL, methodology                       Technologies
                                SOAP, WSDL, UDDI, WSFL
                                DAML+OIL, OWL, RDF(S)
             The myGrid Team
•   Carole Goble       •   Matthew Addis       •   Mark Greenwood
•   Norman Paton       •   Nick Sharman        •   Phil Lord
•   Brian Warboys      •   Rich Cawley         •   Neil Davis
•   Stephen Pettifer   •   Simon Harper        •   Darren Marvin
•   Luc Moreau         •   Karon Mee           •   Justin Ferris
•   Dave De Roure      •   Simon Miles         •   Peter Li
•   Chris Greenhalgh   •   Vijay Dailani       •   Nedim Alpdemir
•   Tom Rodden         •   Xiaojian Liu        •   Luca Toldo
•   John Brooke        •   Tom Oinn            •   Robin McEntire
•   Paul Watson        •   Martin Senger       •   Anne Westcott
•   Alan Robinson      •   Milena Radenkovic   •   Tony Storey
•   Rob Gaizauskas     •   Kevin Glover        •   Bernard Horan
•   Robert Stevens     •   Angus Roberts       •   Paul Smart
•   Ian Horrocks       •   Chris Wroe          •   Robert Haynes
•   Neil Wipat
myGrid Partners



 m
          myGrid Summary
• myGrid aims to develop infrastructure
  middleware for an e-Biologist’s workbench.
• The setting is bioinformatics but the
  results are intended to be generally
 applicable to e-Science.
• A mix of standard, vanguard and bleeding
  edge technologies, advanced development
  and (some) research.
• Academic & commercial partnership.
• myGrid project is timely & reflects a
  community desire to “collaborate, or die”.
       myGrid:
Personalised e-Science
     on the Grid.

   Professor Carole Goble
  http://www.mygrid.org.uk
Contact mygrid@cs.man.ac.uk