Development of Usable Grid
Services for the Biomedical
Community
Prof Richard Sinnott
Technical Director National e-Science Centre
|||
Deputy Director (Technical) Bioinformatics Research Centre
University of Glasgow
26th January 2006
Usability Talk,
26th January 2006
Overview of BRIDGES
Biomedical Research Informatics Delivered by Grid
Enabled Services (BRIDGES)
NeSC (Edinburgh and Glasgow) and IBM
Started October 2003 – successfully concluded end of 2005!
Supporting project for CFG project
Generating data on hypertension
Rat, Mouse, Human genome databases
Variety of tools used
BLAST, visualisation, …
Variety of data sources and formats
Microarray data, genome DBs, project partner research data, …
Aim is integrated infrastructure supporting
Data federation
Security
Usability Talk,
26th January 2006
IT background of scientists
From
what’s a browser…?
to quite IT savvy individuals
None of them
knew much about the Grid
had the time or inclination to really want to learn about
how to use the Grid

Idea of asking them to get X.509 certificates a complete non-starter
They were largely sceptical
fairly tough customers who had research to do
wanted software to solve problems not add to them or
distract them from their daily work
Usability Talk,
26th January 2006
BRIDGES Project
CFG Virtual
Publically Curated Data
Ensembl
Organisation
OMIM
Glasgow
SWISS-PROT
Private
Edinburgh
MGI
VO Authorisation
Private
data
Oxford
Information
Integrator
Synteny
Service
Magna
Vista
Service
London
HUGO
…
RGD
Leicester
DATA
HUB
OGSA-DAI
Private
data
data
Private
data
Netherlands
Private
data
Private
data
+
Usability Talk,
26th January 2006
+
+
Bridges Portal
Usability Talk,
26th January 2006
MagnaVista
www.nesc.ac.uk
Usability Talk,
26th January 2006
MagnaVista
Usability Talk,
26th January 2006
Seriously clever solution…
Dealing with complex remote data sets where schemas
were often not given and they changed at arbitrary times
(normally during live demos!)
But… they hated it!
User interface was far too complicated
Pull down menus, tabs, options, …
Few of them (actually none!) ever used the profile capabilities

In short a general “don’t have time to read the manual attitude”
They used and were comfortable with Google
hence we decided to give them a Google-like solution
Usability Talk,
26th January 2006
GeneVista
Usability Talk,
26th January 2006
Better solution…
But still suffers from changing schemas
Requires constant monitoring
Remote schema changes manifest as cryptic SQL
exceptions to users
This used to fix client wrappers to remote databases
Off-putting for users
Discourages wider take-up
Usability Talk,
26th January 2006
Grid Blast Interface
• Allows ‘genome scale’ blasting
• Transparently uses NGS,
ScotGrid, other GU clusters,
Condor pools
• Many databases already
deployed across nodes
• No user certificates
• Fine grained security at
back-end
Usability Talk,
26th January 2006
Lessons learned
The customer is always right!
There has to be less middleware push and more
scientific pull
Understanding requirements crucial

Rapid prototyping, feedback best model… but need time to do this!
Public data resource openness
Often cannot query directly

Often not easy/possible to find schemas
Grid middleware still painful experience
But ok for us - should not be for scientists

Why should biologist go on training course to run BLAST on the NGS?
Take the certificates away from end users
Usability Talk,
26th January 2006
Conclusions
BRIDGES experiences helping to shape MANY
other projects in Glasgow
Clinical Trials
Genetics & Healthcare
Scottish Bioinformatics Research Network
Occupational Data
Numerous security oriented projects
Access to and usage of Grid via Shibboleth
...

Happy to discuss in more detail... probably off-line though
Usability Talk,
26th January 2006
Scientific Pull… (Work!)
Once we have (securely) connected all relevant data sets
simplified access to and usage of HPC resources, wrapped
your favourite bioinformatics applications as Grid services...
what questions would you like to ask?
– How does a cell work?
– Why do people who eat less tend to live longer?
– How many people across Scotland had a heart attack in the last 5 years took drug
X, and of those that did where genes A or B influenced by this drug?
– Who has performed an experiment similar to mine and where their results similar?
– …
We need to be thinking about these things now and making sure the
infrastructures we are developing will allow to answer these questions!!!
Usability Talk,
26th January 2006