BRIDGES
Status Report
Dr Richard Sinnott
Technical Director National e-Science Centre
|||
Deputy Director Technical Bioinformatics
Research Centre
University of Glasgow
ros@dcs.gla.ac.uk
NeSC Review
27th May 2005
Bridges Project
C F G V ir t u a l
P u b lic a lly C u r a te d D a t a
E nsem bl
O r g a n is a t io n
O M IM
G la s g o w
S W I S S -P R O T
P riv a te
E d in b u r g h
MGI
VO Authorisation
P r iv a te
d ata
O x fo rd
Information
Integrator
st
Magna
Vista
Service
bl a
Synteny
Service
London
HUGO
…
RGD
L e ic e s te r
D ATA
HUB
OGSA-DAI
P riv a te
data
d ata
P r iv a te
d ata
N e th e rla n d s
P r iv a te
data
P riv a te
d ata
+
+
+
Achievements
Web site and project portal established
http://www.nesc.ac.uk/hub/projects/bridges
Local life science data repository developed
Linked to data that can be federated and populated with
data that cannot be federated (e.g. no programmatic
access)
Includes shared data sets of CFG scientists
X
QTL DB, microarray data
Driving forward bioinformatics focus of NGS
Data sets supported, applications required
Helping others via training at NGS induction and
training events
Release of code to wider community
Includes feedback/comments on how to re-use it
X
Numerous follow-ups/enquiries already
Achievements …ctd
GT3 based BLAST Grid service providing access to
and usage of high-throughput compute resources
X
X
includes access to and usage of NGS, ScotGrid, Condor pools…
implements own meta-scheduler with fine grained PERMIS-based
authorisation back-end
– demonstration later
SyntenyVista tool extended to allow Grid enabled
visual navigation of genomic data sets
MagnaVista tool developed to allow discovery and
analysis of genomic data sets
GeneVista tool (portlet) offering subset of
MagnaVista functionality (based upon user
demands)
X
Includes PERMIS based authorisation back-end
Achievements …ctd
Results are being widely known
Dissemination important
X
X
X
Conferences
Seminars
Commercial interest
Influencing standards development
GGF AuthZ
Feedback to relevant groups
Involved in GGF Life Science Grid Research
Group, STF
Publications:
Dissemination
UK e-Science All Hands Meeting 2003 (poster)
Invited paper to Life Science Grid Conference, Kanazawa, Japan 2004
UK e-Science All Hands Meeting 2004 (paper, 2 posters)
Intelligent Systems for Molecular Biology (ISMB)/European Conference on Computational
Biology (ECCB), Glasgow, Aug 2004 (poster)
Paper at European Grid Conference, Amsterdam, February 2005
Paper at Life Science Grid Conference, Singapore, May 2005
Paper and poster at UK e-Science All Hands Meeting, September 2005
Presentations/Seminars:
Seminar at University of Stirling, March 2004
Life Science Grid Research Group, Global Grid Forum, Hawaii, June 2004
HPCInform meeting, Strathclyde University, Glasgow, September 2004
Life Science Grid Research Group Global Grid Forum, Brussels, September 2004
Systems Biology workshop, Edinburgh, March 2005
PharmaGrid workshop, Edinburgh, March 2005
Demos:
Life Science Grid Research Group, Global Grid Forum, Hawaii, June 2004
Intelligent Systems for Molecular Biology (ISMB)/European Conference on Computational
Biology (ECCB), Glasgow, Aug 2004
UK e-Science All Hands Meeting, Nottingham, September 2004
HPCInform meeting, StrathClyde University, Glasgow, September 2004
Supercomputing 2004, Pittsburgh, US [actually 25 demonstrations!!! :o(]
Condor week, Condor Activities at NeSC Glasgow, October 2004
Invited talk at the Shimadzu Research Laboratory, Manchester, October 2004
JISC Core Middleware, Loughborough, May 2005
Team Changes
Jos Koetsier replaced Magnus Ferrier as
Grid Engineer in Edinburgh
Magnus left for a higher paid position in
industry
Derek Houghton (DB Designer/developer)
left for a higher paid 5-year position in
Edinburgh
Working with Richard “Mouse Atlas” Baldock
again
Derek’s remaining funds used to extend Micha
Bayer’s contract at Glasgow
X
Micha originally only 18 month contract
Exploitation
Via projects…
Scottish Bioinformatics Research Network (SBRN)
X
Four year proposal (£2.5M) just started
– Funded by Scottish Enterprise, Scottish Higher Education Funding
Council, Scottish Executive Environment and Rural Affairs
Department
» Involves Glasgow, Dundee, Edinburgh, Scottish Bioinformatics Forum
– Aim to provide bioinformatics infrastructure for Scottish health,
agriculture and industry
» Infrastructure support at Dundee, Edinburgh and Glasgow to support
first-rate research in bioinformatics at each academic institute
» Infrastructure support at three institutes, to support inter-institutional
sharing of compute and data resources through application of Grid
computing
» Outreach and training activities mediated by the Scottish Bioinformatics
Forum
Exploitation via projects…ctd
Virtual Organisations for Trials and Epidemiological Studies
3 year MRC funded project (£2.6M) expected to start imminently
Plans to develop Grid infrastructure to address key components of
clinical trial/observational study
X
X
X
Recruitment of potentially eligible participants
Data collection during the study
Study administration and coordination
– Involves Glasgow, Oxford, Leicester, Nottingham, Manchester, Imperial
Clinical Virtual Organisation Framework
Used to realise
CVO-1
(e.g. for data
collection)
CVO-2
(e.g. for
recruitment)
LeiNott
GLA
Transfer
Grid
GPs
OX
IMP
Clinical trial
data sets
Disease
registries
Hospital
databases
Exploitation via projects…ctd
Genetics and Healthcare Initiative
Five (2+3) year proposal (£4.4M) expected to start
imminently
X
X
Funded by Health Department and Department for Enterprise and Lifelong
Learning
Involves Glasgow, Dundee, Edinburgh, Aberdeen
– focus of genetics as applied to healthcare
– first two years emphasis on providing a platform for research into the
genetic basis of common complex diseases in Scotland
» Mental health, cardiovascular, …
» Plan to establish 15,000 family-based intensively-phenotyped cohort
recruited from the East and West of Scotland
– basis for neutralising heritable (genetic) risk factors in disease
surveillance, treatment optimisation, avoidance of adverse drug
events and prediction of response to therapy, health care planning
and drug discovery, …
Exploitation by others
Working with NGS on bioinformatics data sets and
applications
Fair to say that we are driving this work in the UK
Showing/training people how to use NGS and how to
develop applications using such facilities
BRIDGES case study lectures given at NGS training course
X
BRIDGES system used by Neil Geddes to demonstrate NGS
Code released for multiple scheduler job submission systems
Alternative models of job submission without explicit
user certificates
Based upon host certificates
Makes life simpler for users
X
Requires logging/accounting information is kept
BRIDGES being used to explore other security areas
such as Shibboleth, e.g. in projects such as DyVOSE
Commercial Exploitation?
Email from Colin Henderson (IBM UK) to head
of IBM clinical genomics US (Kareem M Saad)
17th May 2005
… It's actually very interesting to see what the guys at NeSC
have achieved here. This is a great reference for IBM. The group
are now looking to deploy some of their expertise and learning to
longitudinal clinical trials, a project called VOTES which we
supported. I just wanted to make you aware of this work and flag
it as an innovative project in Clinical Genomics and Grid.
…Perhaps there might be an angle from somewhere in IBM to
help us and the BRIDGES/VOTES team develop the relationship
further, hence develop the reference further?
Future plans
Continue to support CFG
New applications, refine existing applications
Modify delivery mechanisms (user issues with
WebStart)
X
JSR168 portlets in GridSphere, WebSphere
Refine OGSA-DAIT solution for data access
and usage
Integration of Grid based data access and
security solution
X
Extending spec’s from GGF
Future plans …ctd
Feed BRIDGES experiences/software into
other projects
SBRN, VOTES, GHI… and new ones
X
Including one BBSRC bid with Cornell, Riken Institute made
through contacts at SC2004! ;o)
Basis for future complete systems biology…?
Numerous projects/proposals submitted
looking at all parts of this picture!
Populations
Organisms
Physiology
Organs
Tissues
Cell signalling
Cell
Protein-protein interaction (pathways)
Protein functions
Protein Structures
Gene expressions
Nucleotide structures
Nucleotide sequences
Questions?