Download myGrid: Personalised e-Biology on the Grid Professor Carole Goble

myGrid:
Personalised e-Biology
on the Grid
Professor Carole Goble
http://www.mygrid.org.uk
Contact [email protected]
myGrid:
Personalised e-Science
on the Grid
Personalised
extensible environments for
data-intensive
in silico experiments in biology
e-Science & Biology
• Discovery is
increasingly done in
integration
silico on results
mining
analysis
obtained from
experiments using
hypothesis
computational
prediction
analysis & data
integration
repositories.
mining
analysis
• A new era of
collection based
experiment
and simulation
results
based science.
e-Science & Biology
• Discovery is
increasingly done in
integration
silico on results
mining
analysis
obtained from
experiments using
curation
hypothesis
computational
prediction
analysis & data
integration
repositories.
mining
analysis
• A new era of
collection based
experiment
and simulation
results
based science.
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.
2.
3.
4.
5.
Has anyone else studied the effect of
neurotransmitters on the circadian
rhythms in Drosophila?
How do the functions of the clusters
of proteins from my experiment
interrelate? And 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?
1
2
3
4
5
E-Science Q & A
Who else has asked this question & can
I use/adapt their approach?
– Workflow.
What were the results at each stage?
– Dynamic Data Repositories.
When was P12345 last updated?
Which BLAST did I use?
– Provenance.
Has PDB changed since I last ran this?
– Notification.
Personalisation.
1
2
3
4
5
E-Science Q & A
Who else has asked this question & can
I use/adapt their approach?
– Workflow.
What were the results at each stage?
– Dynamic Data Repositories.
When was P12345 last updated?
Which BLAST did I use?
– Provenance.
Has PDB changed since I last ran this?
– Notification.
Personalisation.
1
2
3
4
5
E-Science Q & A
Who else has asked this question & can
I use/adapt their approach?
– Workflow.
What were the results at each stage?
– Dynamic Data Repositories.
When was P12345 last updated?
Which BLAST did I use?
– Provenance.
Has PDB changed since I last ran this?
– Notification.
Personalisation.
1
2
3
4
5
E-Science Q & A
Who else has asked this question & can
I use/adapt their approach?
– Workflow.
What were the results at each stage?
– Dynamic Data Repositories.
When was P12345 last updated?
Which BLAST did I use?
– Provenance.
Has PDB changed since I last ran this?
– Notification.
Personalisation.
1
2
3
4
5
E-Science Q & A
Who else has asked this question & can
I use/adapt their approach?
– Workflow.
What were the results at each stage?
– Dynamic Data Repositories.
When was P12345 last updated?
Which BLAST did I use?
– Provenance.
Has PDB changed since I last ran this?
– Notification.
Personalisation.
1
2
3
4
5
E-Science Q & A
Who else has asked this question & can
I use/adapt their approach?
– Workflow.
What were the results at each stage?
– Dynamic Data Repositories.
When was P12345 last updated?
Which BLAST did I use?
– Provenance.
Has PDB changed since I last ran this?
– Notification.
Personalisation.
1
2
3
4
5
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.
myGrid Middleware
removing the obstacles
myGrid Middleware
Who is myGrid for?
myGrid users
biologists
IS specialists
tool
builders
systems
administrators
infrequent
problem
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 Pre-Prototype
Portal
Personal
Repository
Workflow
Repository
Workflow
Enactment
Metadata:
Ontology
Metadata:
Service
Directory
Bioinformatic
BioinformaticServices
Services
Locating a
workflow
Repository Workflow Ontology
Portal
Client
Client
Client
Personal
Repository
Meta Data:
Ontology
Workflow
Repository
Meta Data:
Service Type
Directory
How do the functions of the
clusters of proteins from
my experiment interrelate?
Locating a
workflow
Repository Workflow Ontology
Portal
Client
Client
Client
Personal
Repository
Meta Data:
Ontology
Workflow
Repository
Meta Data:
Service Type
Directory
Locating a
workflow
Repository Workflow Ontology
Portal
Client
Client
Client
Personal
Repository
Meta Data:
Ontology
Workflow
Repository
Meta Data:
Service Type
Directory
Locating a
workflow
Repository Workflow Ontology
Portal
Client
Client
Client
Personal
Repository
Meta Data:
Ontology
Workflow
Repository
Meta Data:
Service Type
Directory
Locating a
workflow
Repository Workflow Ontology
Portal
Client
Client
Client
Personal
Repository
Meta Data:
Ontology
Workflow
Repository
Meta Data:
Service Type
Directory
Locating a
workflow
Repository Workflow Ontology
Portal
Client
Client
Client
Personal
Repository
Meta Data:
Ontology
Workflow
Repository
Meta Data:
Service Type
Directory
Running a
workflow 4
Personal
Repository
Provenance
Data
Repos.
Client
3
Workflow
Client
1
Service Selection
Client
2?
Workflow
Enactment
2
Bioinformatic Services
2?
Service
Directory
Running a
workflow 4
Personal
Repository
Provenance
Data
Repos.
Client
3
Workflow
Client
1
Service Selection
Client
2?
Workflow
Enactment
2
Bioinformatic Services
2?
Service
Directory
Running a
workflow 4
Personal
Repository
Provenance
Data
Repos.
Client
3
Workflow
Client
1
Service Selection
Client
2?
Workflow
Enactment
2
Bioinformatic Services
2?
Service
Directory
Running a
4
workflow
Personal
Repository
Provenance
Data
Repos.
Client
3
Workflow
Client
1
Service Selection
Client
2?
Workflow
Enactment
2
Bioinformatic Services
2?
Service
Directory
Running a
4
workflow
Personal
Repository
Provenance
Data
Repos.
Client
3
Workflow
Client
1
Service Selection
Client
2?
Workflow
Enactment
2
Bioinformatic Services
2?
Service
Directory
Running a
4
workflow
Personal
Repository
Provenance
Data
Repos.
Client
3
Workflow
Client
1
Service Selection
Client
2?
Workflow
Enactment
2
Bioinformatic Services
2?
Service
Directory
Two videos
• Experimental pre-prototype for
requirements capture.
• How do the functions of a
cluster of proteins
interrelate?
• The other one, with
provenance and temporary
parking in repository.
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
Networked Services
Directory
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
(Jini, Corba)
Grid Computing
An early adopter
for OGSA
Agents
ACL, methodology
Web
Technologies
SOAP, WSDL, UDDI, WSFL
DAML+OIL, OWL, RDF(S)
The myGrid Team
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Carole Goble
Norman Paton
Brian Warboys
Stephen Pettifer
Luc Moreau
Dave De Roure
Chris Greenhalgh
Tom Rodden
John Brooke
Paul Watson
Alan Robinson
Rob Gaizauskas
Robert Stevens
Ian Horrocks
Neil Wipat
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Matthew Addis
Nick Sharman
Rich Cawley
Simon Harper
Karon Mee
Simon Miles
Vijay Dailani
Xiaojian Liu
Tom Oinn
Martin Senger
Milena Radenkovic
Kevin Glover
Angus Roberts
Chris Wroe
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Mark Greenwood
Phil Lord
Neil Davis
Darren Marvin
Justin Ferris
Peter Li
Nedim Alpdemir
Luca Toldo
Robin McEntire
Anne Westcott
Tony Storey
Bernard Horan
Paul Smart
Robert Haynes
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 [email protected]