The monthly newsletter from the National e-Science Centre
NeSC News
Issue 54 October 2007 www.nesc.ac.uk
6th AHM attracts international audience
Photograph by Peter Tuffy, University of Edinburgh
The 6th annual e-Science All
Hands Meeting was held in
Nottingham last month, from
September 10- 13, and was an
international success.
There were 31 exhibitors, and
over 500 delegates at this
year’s event, including people
from Australia, Germany,
Japan, Korea, the Netherlands,
New Zealand, Sweden and the
USA.
Next year’s AHM is expected to
take place in Edinburgh.
See pages 2 and 4 for full
reports from Iain Coleman.
UK National Grid Service Upgrades and Expands
THE UK National Grid Service (NGS)
launched its second phase at the All
Hands Meeting in September. This
will see an increase in data storage
capacity from the current 46TB to
192TB at the four core sites (the
universities of Leeds, Manchester,
Oxford and the Rutherford Appleton
Laboratory).
“This upgrade reflects the increases
in scale of data storage and
computation which are becoming
ever more commonplace in
today’s high tech world. The NGS
continues to provide access to
these large scale resources for all
UK researchers,” said Neil Geddes,
Director of the NGS.
A full replacement of the existing
four compute and database clusters
was undertaken by Clustervision to
increase capacity at the core sites.
The current four sites now have a
total of 580 dual-core AMD OpteronTM
CPUs distributed over quad and dual
socket systems with a ClearSpeed
AdvanceTM X620 Accelerator board.
As well as upgrading the core
services, the NGS also welcomed
two new affiliate members
– the University of Southampton
and Imperial College London.
The Microsoft Institute for High
Performance Computing at the
University of Southampton will
provide access to the Microsoft
Compute Cluster Service through a
Globus gateway, the first instance of
a Windows cluster being incorporated
into a production level Grid.
Prof. Simon Cox, Director of the
Institute said “This is an exciting
opportunity to offer, for the first time,
Microsoft Windows Compute Cluster
Server on the National Grid Service,
where it will interoperate with other
resources”. The CCS Globus
Gateway provides access to a cluster
under the Windows x64 platform
using the normal Globus client
tools and Grid security mechanism,
making it possible to share the
Windows based computational
resources with a wider user base in
the e-Science community.
Imperial College London is the first
GridPP site to join the NGS. Dr David
Colling, e-Science Team Leader
of the High Energy Physics Group
at Imperial College London,said:
“Imperial has been active in the UK
Grid community since 2000 and it
seems clear that the future is through
greater co-operation between UK
and European Grid projects as this
is how we will offer our resources,
efficiently, to the largest group of
users. For this reason Imperial felt
that it was important to become part
of the NGS”.
The first resource to be accessed
through the NGS is a 408 processor
Opteron based Beowulf cluster which
runs RedHat Enterprise Edition
Linux. However future resources
to be accessed include a 260 dual
processor Intel/Linux cluster which
will support high performance and
high throughput computing and a 200
core Woodcrest cluster. Dr David
Colling emphasised that “Imperial
was committed to bringing a growing
collection of resources to the NGS”.
Issue 54, October 2007
The vision of e-Science creating
a pervasive, empowering
infrastructure has always
looked forward to a moment of
metamorphosis, when e-Science
breaks out of the chrysalis of
computing research to emerge as
a set of technologies underpinning
vital activity in art, science and
commerce. This year’s UK
e-Science All Hands Meeting, held in
Nottingham from 10-13 September,
may mark that moment. Malcolm
Atkinson, in his keynote speech,
pointed to the great diversity of
projects now using e-Science that
were represented at the meeting as
exemplifying the momentum that
has built up in the use of distributed
computing to provide novel
solutions in research and industry.
His conclusion was that e-Science
now has to develop and change to
meet new challenges: it has moved
out into uncharted territory, and its
practitioners have to be adventurous
navigators.
A new strategy is needed, but how
should it be developed? That was
the question Timothy Foresman
raised in his keynote presentation.
He outlined two alternative paths:
evolution, or intelligent design.
Evolution by natural selection is
a potent force, and its economic
analogue in the competitive market
has provided an abundance
of diverse technology. But the
Invisible Hand is not to human
scale, and Foresman doubts that
evolved systems will be adequate
to tackle the urgent problems of
climate change, mass extinction
and resource depletion. Instead,
he argued in favour of deliberate
design, organising and integrating
our common digital resources in an
open and accessible way so that
we are empowered to take on these
global challenges.
A concrete case for more rational
planning was made by John Wood.
His keynote speech concentrated on
efforts to create an e-infrastructure
NeSC News
by Iain Coleman
Photograph by Peter Tuffy, University of Edinburgh
From inspiration to reality
e-Science Envoy Malcolm Atkinson addresses All Hands 2007
in the UK and in Europe. While there
have been substantial successes,
particularly in the UK, the lack of
Europe-wide strategic planning
is allowing the global competition
to catch up. His case is that we
cannot afford the inefficiencies of an
evolutionary approach, in which any
of up to twenty seven member states
develop their own facilities. With
greater cooperation and effective
top-down planning we could reap the
economies of scale and establish
a critical mass of researchers at a
few centres of excellence. Faster
decision-making is essential, and
linking basic research to exploitation
is becoming increasingly important.
That link was the basis of two
sessions at the All Hands Meeting:
a set of presentations organised
by the Grid Computing Now!
knowledge transfer network, and
a keynote speech by Thomas
Hartkens of IXICO. Hartkens and his
colleagues used grid technologies
to develop a dynamic atlas of the
human body, based on large data
sets from MRI scans. They have
now turned this medical system
into a drug development tool for the
pharmaceutical industry: by directly
observing the effects of medication
during a trial period, such as the
changes in bones effected by an
arthritis treatment, they can accelerate
the development process and cut the
costs of creating new drugs. With each
new treatment costing roughly a billion
dollars to bring to market, the potential
savings are huge.
The biggest challenge they faced
was in turning an effective software
application into a complete end-toend solution. The pharmaceutical
companies don’t want to buy software:
they want to pay for a service. This
meant IXICO providing an audit trail,
a quality management system and
software validation, and meeting
the stringent requirements of public
regulators. This demonstrated the
considerable differences between
a research implementation and a
production system: quality of service,
not innovative technology, is the real
selling point.
Other models of commercial
exploitation were outlined by the
www.nesc.ac.uk
Issue 54, October 2007
speakers at the Grid Computing Now!
event. Jim Austin founded Cybula
to sell high-performance pattern
recognition software as a spin-out
from research at the University of
York, but he was determined to
maintain close links between the
company and the academic research
department. This proved invaluable,
not just in encouraging continued
innovation, but also in giving the
company access to early adopters
and expensive new technology.
Yike Guo developed InforSense out
of a workflow engine developed at
Imperial College London. From its
roots in enabling scientists to build
analytical services, it is now in use by
some of the world’s largest financial
and pharmaceutical companies. For
Guo, the main challenge was to strike
the right balance between meeting
the immediate needs of the market
and doing the work that will result in
more innovation a few years down
the line. Lastly, Dave Berry gave an
overview of what industry does and
doesn’t care about, with a warning
to academics not to underestimate
the achievements of the commercial
sector.
In contrast to the demand for
planning from Wood and Foresman,
these sessions were all about
evolution. Start-ups and spin-outs
abound, and only the marketplace
determines which ones thrive
and prosper. But by sharing good
practice, and candidly discussing the
pitfalls as well as the opportunities,
the speakers effectively gave
evolution a helping hand. The
watchmaker may be blind, but
with guidance he can more quickly
produce a working model, avoiding
at least some of the mis-steps and
failures along the way.
Whatever course e-Science takes in
coming years, there is little doubt that
we are in the middle of a dramatic
change not just in what people do,
but in how they think. Readers of
this very article will be the subjects
of historians and sociologists in the
future, as they try to understand not
just what they were doing, but how
and why. Archive up your emails, and
don’t forget to back up your blog.
NeSC News
GCN! Webinar - The Business Case and
Methods for the Green Data Centre
2.30pm, October 25, 2007
Gartner reports that “The energy from manufacturing, distribution and use of
information and communications technology emits approximately 2% of total
global carbon dioxide, equal to the emissions from the airline industry.” The cost of running data centre equipment now typically exceeds the cost
of buying the hardware in the first place. Clearly, businesses will benefit
by adopting measures that reduce the amount of power used by their IT
facilities.
This webinar will feature two speakers who will help to illuminate the path
towards reduced energy consumption. Zahl Limbuwala is chair of the BCS
Data Centre Specialist Group, who have developed a detailed model for data
centre energy efficiency. Zahl will present some of the shifts in behavior that
lie ahead for data centre owners and operators.
Kate Craig-Wood, Managing Director of Memset Ltd., is already running
carbon-neutral data centres. Kate will describe what Memset have done to
achieve this status, focusing on the options that are practical here and now. She will also explain the business benefits of adopting a “green” approach to
energy consumption.
More information is available here: http://mediazone.brighttalk.com/event/
gridcomputingnow/6e0721b2c6-783-intro.
NGS and OMII-UK launch National
Services Registry
The National Grid Service (NGS) has chosen to use one of OMII-UK’s major
software components - Grimoires - for its web services registry.
One of the main problems in any distributed services environment is the
difficulty of introducing consumers to service providers. The provision of web
services is no different.
If anything, the problem is compounded by the bewildering array of web
services on offer and the radically different user requirements of each of
them.
Grimoires, funded by the OMII-UK Commissioned Software Programme,
was developed to solve this problem. It offers a single point of reference for
service providers and consumers, providing an extended UDDI registry for
service discovery. In essence, this allows those publishing services in the
registry to attach searchable, domain-specific metadata to service entries.
The NGS are the principle provider of Grid resources to the UK academic
sector and provide many invaluable services to the e-Science community.
Further information on OMII-UK can be found on the OMII-UK website at
http://www.omii.ac.uk and information about the National Service Registry can
be found at http://www.grid-support.ac.uk/content/view/290/196/.”
www.nesc.ac.uk
Issue 54, October 2007
The visual and the virtual
e-Science
Institute
by Iain Coleman
When did you last use “I see” to
mean “I understand”? It’s more than
just a metaphor. The visual system is
our primary means of comprehending
the world: up to 50 per cent of the
neurons in our brains are associated
with vision, and loss of sight causes
greater distress than any other form
of sensory impairment. That’s why
visualisation is such a powerful tool
for coming to grips with extensive
and complex data.
There was a range of impressive
examples on show at this year’s
UK e-Science All Hands Meeting.
Ander’s Ynnerman’s keynote
presentation showed some stunning
examples of medical visualisation.
These have been made possible by
e-Science, but they have been made
necessary by the explosion in data
from medical scanning technology.
CAT scans have gone from providing
around 100 image slices per patient
(about 50 MB) to 24,000 slices
(20GB), with even greater data
volumes on the way. Now, you can’t
pin 24,000 images up on the wall
and look at them - not unless the
images are very small, and the wall
is very large. Instead, Prof Ynnerman
and his colleagues have developed
techniques for rendering the data into
three-dimensional images that can
be much more readily assimilated by
the human visual system.
It’s not just a matter of bunging
the slices together into a volume.
Each data point indicates how
efficiently X-rays are absorbed at a
particular spatial location. Different
types of bodily tissue have different
absorption characteristics, and by
choosing how absorption is related to
colour and opacity in the visualisation
the image can be tuned to show skin,
muscle, bone or blood vessels. You
can peel back the scalp to show the
skull, then remove that to expose
the brain, all by tuning the colour
coding parameters. The brain can
even be made to glow under the
skull, showing up fractures where the
simulated light leaks through.
NeSC News
Photograph by Peter Tuffy, University of Edinburgh
John Blower (right) receives his award from Ken Brodlie
This isn’t just eye candy. These
techniques can disclose information
that would otherwise lie hidden,
perhaps saving the life of a patient.
The shape of a tumour, for example,
can be revealed to the surgeon who
will try to remove it: with one chance
to get it right, such operations are
a life or death matter. Even after
death, these visualisations can be
invaluable. It only takes minutes to
perform high-powered CAT scan of
a body bag prior to a conventional
autopsy, and the data can then
be used to inform the forensic
scientists working on the case. Not
only can this provide vital clues that
might otherwise be missed, like the
presence of alien objects such as
bullets, it also gives the police a
permanent image of the body that
they can go back to and re-examine
as the investigation progresses.
More medical visualisations were on
display at the booth demonstrations.
The East Midlands e-Science
Centre team showed a rotating 3d stereoscopic image of a heart,
startling in its size and immediacy
as well as its detail. There was
another heart visualisation from the
Integrative Biology project, in this
case a detailed simulation based
on experimental data. This project
aims to investigate the causes of
heart attacks, and a comprehensive
model that can be used remotely by
geographically dispersed researchers
is at the core of their investigations.
They aim to have a model that can
be computationally steered over the
grid, so that researchers can interact
with the simulation in real time,
greatly enhancing the efficiency and
speed of discovery.
With the right kind of visualisations,
you can steer more than models.
The RRS James Clark Ross is
a 100m-long Antarctic research
ship, designed for geophysical
and biological research in the icy
seas of the South Atlantic. John
Blower (Reading e-Science Centre)
and colleagues from the British
Antarctic Survey and the British
Oceanographic Data Centre won this
year’s Best Paper Award for their
work in showing how real-time data
visualisation can be used to set the
course of this massive ship, directing
it to areas of scientific interest as
the research voyage proceeds.
Multiple data streams, from ship
location to ocean salinity to air
www.nesc.ac.uk
Issue 54, October 2007
temperature are streamed to Google
Earth in near-real-time, enabling
the ship to track marine predators
more effectively than ever before.
Speeding up the research in this way
saves substantial ship time, and that
translates to a good deal of money.
In his acceptance speech, Blower
argued that geospatial visualisations
can be extremely powerful tools
in enabling scientists to make
connections and experience insights
that would otherwise have passed
them by. Virtual globes like Google
Earth have serious limitations when
it comes to quantitative scientific
analysis, but in the early phases
of scientific discovery the ability
to easily merge different data
sources on a single spatial display,
or combine data from different
geographical regions into one
visualisation, can be invaluable. It
can lead to new ideas, or allow the
scientist to sanity-check a hypothesis
before proceeding with a full-scale
research program.
There was no award for the most allencompassing use of visualisation,
but if there had been it would
surely have gone to the North
Sea Paleoarchaeology project at
Birmingham University. Starting with
detailed surveys of the North Sea
bed, originally carried out for the
benefit of the oil and gas industry,
the researchers combined multiple
analysis techniques to determine
where rivers, hills and peat bogs
would have been ten thousand years
ago when this region was dry land.
They have been able to determine
where people would most likely have
settled, and where on the sea bed
the best-preserved archaeological
remains are to be found. It’s more
than a theoretical exercise: oil
and gas companies routinely drive
shallow pipelines through these
regions, throwing away precious
artefacts as they do so. Government
action to require the recording and
preservation of these materials, as
is done in Denmark, might result in
a future explosion of real information
about how our ancestors lived in
NeSC News
e-Science
Institute
Vacancy: Research Assistant on the
Scottish Imaging Network: A Platform for
Scientific Excellence project
Based in two institutes within the University of Edinburgh, the National
e-Science Centre and the SFC Brain Imaging Research Centre, you
will join a research team pioneering scientific data exploitation. You will
work on a project to generate the infrastructure to enable collaborative
studies in brain imaging. The work will entail designing, prototyping
and evaluating aspects of a distributed computational environment that
will support the medical research. You will have a research degree in a
relevant subject and experience in computing science.
Project web site: http://www.sbirc.ed.ac.uk/sinapse/sinapse.asp
Deadline: 1 November 2007
JISC Activity in the Arts & Humanities
and Physical Sciences
The Joint Information Systems Committee, which supports the innovative
use of ICT in UK further and higher education and research, has published
two short briefing papers outlining the activities it funds that are relevant to
researchers in the arts and humanities and in the physical sciences. Each
paper includes an article by an academic followed by a listing of relevant
services and programmes and links to further information. The papers are
available at www.jisc.ac.uk/artshumanitiesresearch and www.jisc.ac.uk/
physicalsciencesresearch. Please contact j.redfearn@jisc.ac.uk for hard copies.
these drowned lands. Until then, we
can only conjecture. The Birmingham
team have followed a sophisticated
kind of conjecture, in the form of
agent based modelling. This involves
simulating the actions of fictional
individuals in an ancient community,
acting and interacting according to a
set of quantitative rules - a Stone Age
version of The Sims. They then went
a stage further, and incorporated the
simulation data into a game engine
from a first-person shooter. The result
is a vivid 3-d landscape in which the
user can stroll by rivers and over
hills, wander through buildings and
villages, and even go on a wild boar
hunt.
By allowing us to enter intellectually
and imaginatively into the lives
of people long dead, these
visualisations help to achieve the
ultimate goal of archaeology. As
with medical science and forensics,
displaying data in a rich visual
format enables us to understand
the information that our scientific
instruments have delivered to us
in the most direct and detailed
way. As our computing resources
become more and more capable,
so we will rely more and more on
visualisation techniques to link our
most powerful sense with our most
advanced technology.
www.nesc.ac.uk
Issue 54, October 2007
e-Science
Institute
UK NGS Makes Life Easier for Users
The UK National Grid Service (NGS)
is pleased to announce the release
of a new, easy way to access its
computing resources and installed
applications.
The NGS Applications Repository
(https://portal.ngs.ac.uk) is a portal
application that can be used for:
Creating templates for applications
Sharing templates with others
Viewing and using public templates
Job submission and monitoring
Many people wish to use the
applications they are familiar with on
their local resources. Often a certain
level of grid computing knowledge
is needed to use those applications
on the grid. This deters users from
adopting grid technologies.
The Applications Repository has
been developed to help overcome
this problem. User communities
already familiar with specific
applications can use it to get started
on the grid.
what is on there. Certificates are only
needed to run a job.
Templates are stored in the
repository and contain details for
each application on; Overview of
template; Arguments to application;
Input and output files; Environment
variables to set up; Hosts to
run application on; and The Job
Submission Description Language
(JSDL) of the job
“We would like to open up the grid to
a whole new community of users,”
explains Dr Dave Meredith, the
lead developer. “Researchers who
want to use the software they are
familiar with can now use the portal
to describe, publish and submit their
job, without the need for middleware
commands or Grid knowledge.”
With the search function you can find
templates in your area of interest
such as bioinformatics. Loading and
modifying templates is simple. You
can save your modified templates
for personal use or share them with
others.
For further information about the
NGS Applications Repository, or for
requests for software application
installations, please contact the NGS
support centre at support@gridsupport.ac.uk
By using the Repository you have
access to the expertise of domainexperts and resource providers.
You can also share your expertise
with others in your community. No
certificate or account is required to
explore the repository and find out
New videos showcase
collaborative research
Photograph by Gillian Sinclair, NGS
Dr Andrew Richards, NGS Executive Director, announces the official start
of NGS2 hardware in production usage.
NeSC News
Researchers can get a feel for how
Virtual Research Environments
can make a positive difference to
their work and their collaborations,
by watching two new videodemos
on the JISC VRE1 programme.
Projects highlighted in the 11-minute
videos include those showing
how researchers in the materials
sciences have been able to share
results in real time with other remote
teams of specialists; how dancers
have been performing in remote
environments; and how groups
of historians have been ‘meeting’
remotely and collaborating across
more than a dozen institutions.
Both films emphasise the degree to
which VREs can and indeed should
be tailored to a particular team’s
requirements and, looking to the
future, suggest how VREs are likely
to become increasingly established
as a research tool in the future.
To look at the videos, please go
to: www.jisc.ac.uk/whatwedo/
programmes/programme_vre/
projects or contact a.gugan@jisc.
ac.uk for a CD copy.
www.nesc.ac.uk
Issue 54, October 2007
Call for Chapters
The Handbook of Research on
Computational Grid Technologies
for Life Sciences, Biomedicine and
Healthcare aims�������������������������
to collect state-of-the
art methodologies and developments
of Grid technologies applied in different
fields of life sciences, from basic
science to clinical and healthcare
applications.
The book will be organised by taking
into consideration the use of Grid
technologies to support research
and application ���������������
to each of the
information levels (molecule, cell,
tissue, individual, population) where
life science research takes place.
According to an agreed taxonomy,
bioinformatics is related to the molecule
and cell, medical informatics is related
to tissue/organ and individual, while
public health informatics is related to
population. The book will address the
use of the Grid in and for these three
broad areas.
Specific fields that have recently
experienced the use of the Grid,
such as computational genomics
and proteomics, biomedical imaging,
drug discovery, biomedicine, and
healthcare, will be also addressed.
The Grid has been also demonstrated
as a valuable tool for collaboration and
cooperation, for instance enabling the
remote use of medical instruments
in the so called virtual laboratory.
Thus, the use of the Grid to improve
collaboration among scientists and
to enhance the healthcare provision
to the final users is another important
topic that will be addressed by the
book.
Recommended topics include, but
are not limited to, the following:
Grid for Life Sciences and
Bioinformatics
Grid for Medical Informatics
Grid for Healthcare Informatics
GCN competition
winner visits
National e-Science
Centre
GOKOP Goteng, a doctoral
researcher at Cranfield University
and the winner of last year’s Grid
Computing Now! competition, has
completed a week’s placement at
the National e-Science Centre in
Edinburgh.
The placement, part of Goteng’s
prize for the competition, allowed him
to meet a broad range of researchers
who could advise him on aspects of
his doctorate.
Goteng’s project is titled:
Development of a Grid Service for
Multi-Disciplinary Optimisation. In
essence, this is looking at the use
of grid in complex development
situations. Goteng gives the example
of aircraft designers – “One of
the development teams might be
in the UK, working on the wing
design, while the engine designers
NeSC News
Grid for Collaboration and
Cooperation in Life Sciences and
Healthcare
Methodologies, middleware, and
tools for Grid-based Life Sciences
applications
More details are available at
http://www.icar.cnr.it/cannataro/
LifeSciencesGrid/
Individuals interested in submitting
chapters (8,000-10,000 words) on
the above-suggested topics, or
other related topics in their area of
interest, should submit via e-mail a
2-3 page manuscript proposal clearly
explaining the mission and concerns
of the proposed chapter by November
1, 2007.
The organisers are also keen to hear
of other topics that have not been
listed, particularly if the topic is related
to the research area in which you have
expertise.
resources such as data, algorithms,
etc, and submit a job.”
Gokop Goteng
are working in France, and the
fuselage is being created by a
team in Germany. If the team in
the UK changes the wing, that has
repercussions for the engine, the
fuselage and so on – and so I’m
looking at how grid can allow them
to put their CAD (Computer Aided
Design) model, or whatever they’re
using, on a shared grid to work
properly together,” he says.
He is currently at the stage of having
built a prototype using Globus and
Condor, with 12 computers in a
cluster, running Web MDS. “I want
to customise the Web MDS form so
that an expert in aircraft design – or
any area – can query optimisation
His time at NeSC allowed him to talk
to developers working in a range of
areas, all of whom had insights and
suggestions that he says have been
very helpful. “I gave a presentation
on what I’m doing, and the feedback
I’ve received has been really useful,
and it’s helped me to trim down my
research plans and understand more
about what I can do,” Goteng said.
Last year’s GCN! competition looked
for practical uses of grid for 21st
century problems. Goteng won with
his entry “Combating global terrorism
with the world wide grid”. His
suggestion combined many aspects
of grid, using processing power to
crunch real time data in terms of
CCTV footage and biometric data to
identify potential high-risk incidents.
Different information sources and
multi disciplinary teams, for example
police, custom offices and transport
industry, would be able to link
together and collaborate as one
central mechanism to help combat
terrorism.
www.nesc.ac.uk
Issue 54, October 2007
European R&D and Innovation for Human-Centric ICT
Winterthur/Zurich - 16 November, 2007
Information and Communication Technologies are becoming pervasive in different forms, influencing day-to-day life of
all citizens. ICT are oriented more towards the needs of the users, and the ease of usage in accessing the information
through different media.
Why to participate: To facilitate the setup of FP7 project consortia (ICT Call 3); To offer and find technologies for your
business development
Who should participate: Companies and researchers from all over Europe interested in the most recent research and
development results, share new project ideas and technologies in Human and Context Aware Systems (Cognitive
Systems, Human-Machine interaction, Robotic systems) and Knowledge Interfacing Applications (Technologyenhanced learning, Knowledge Management, Content Creation, Digital Libraries)
More information is available here: http://www.ictsummit.eu/ict/summit/switzerland/european-innovation-humancentric.html
Mardi Gras Conference 2008
The Center for Computation &
Technology at LSU, in cooperation
with ACM SIGAPP, is hosting the
15th Mardi Gras Conference from 31
January - 2 February 2008, in Baton
Rouge, Louisiana.
This year’s theme is: From
lightweight mash-ups to lambda
grids: Understanding the spectrum of
distributed computing requirements,
applications, tools, infrastructures,
interoperability, and the incremental
adoption of key capabilities.
The field of distributed computing
has been recognised for decades but
only in the last few years has there
been a vast expansion of distributed
computing approaches and tools
that are gaining serious, wide-spread
use. This wide-spread use goes far
beyond computational science and
engineering, to include business,
government, art, and popular culture.
While the fundamental requirements
of distributed computing are generally
understood, the ubiquitous availability
of networks and servers has enabled
the development of many different
tools to suit the needs of different
NeSC News
communities. Besides what have
become traditional grids, there
is growing use of lambda grids,
enterprise service buses, serviceoriented architectures, and Web
2.0. All of these approaches enable
the sharing of resources in “virtual
organisations” but with widely
differing support for discoverability,
reliability, security, management,
quality-of-service, etc.
In all cases, interoperability at
the infrastructure level and at the
application domain level is a critical
issue.
While network connectivity has
become ubiquitous, and has enabled
the creation of virtual organisations,
it is still an open issue how tightly
coupled these organisations can be.
Bandwidth and latency determine
how interactive and collaborative
distributed participants can work
together.
Hence, advanced networks such as
lambda networks (dedicated optical
networks) have the potential for
enhancing interactiveness on a largescale, and actually being an enabling
technology for application domains
that require tight coupling.
The goal of Mardi Gras 2008 is to
improve our understanding of the
drivers for all of these technologies,
how they relate to one another,
and how user communities can
transition from simpler approaches,
like Web 2.0 mash-ups, to more
full-service grids, when better
discovery, reliability, security, etc., are
needed -- while achieving sufficient
interoperability -- and how tightly
coupled virtual organisations can be.
To this end, we are seeking the best,
most insightful papers on all of these
technologies, and the application
domains that are driving their
requirements and development.
Authors are invited to submit original
and unpublished work (also not
submitted elsewhere for review).
Submission: Oct 10, 2007 (no
extensions)
Notification: Nov 7, 2007
Final Papers: Nov 28, 2007
More information is available here:
http://www.mardigrasconference.org/
www.nesc.ac.uk
Issue 54, October 2007
OGSA-DAI 3.0 released
A completely redesigned and
rewritten version of the database
access and integration software has
been released.
Imagine a census database,
containing myriad facts such as the
price of a loaf of bread or the number
of cancer deaths within various
regions of the UK. This database
could be used to answer questions
such as ‘How many cancer deaths
were there in the Scottish Highlands
in 2006?’. Now imagine a separate
database of UK regions, in which
the area bounded by each region
is represented as a polygon. This
database could provide a polygonal
representation of the Highlands and
the areas it contains.
These two databases could be
joined and the polygons for the
Highlands annotated with the
census information. A graphical
visualisation of cancer deaths across
the Highlands could then be readily
created. By swapping the census
database for other data sets, the
same solution could be used to
visualise the results of other queries.
How would you build a system to
implement such a scenario? The
problems to be surmounted include:
the use of multiple databases; the
heterogeneous nature of the data
in the databases; how to transform
and join this data; and how to deliver
what could be large data sets in an
efficient manner
Since 2002 the Open Grid Services
Architecture - Data Access and
Integration (OGSA-DAI) project has
been developing the OGSA-DAI
product for the e-Science community.
OGSA-DAI provides an extensible
framework intended to solve just
such problems as those above.
It is designed for the exposure of
structured data resources – whether
databases, files or other types of
data – onto a Grid. It allows these
NeSC News
resources to be accessed via Web
services.Most importantly, it provides
a workflow engine for the execution
of data-centric workflows involving
data access, update, transformation
and delivery operations.
The JISC-funded SEcurE access
to GEOspatial services (SEEGEO) project used OGSA-DAI to
construct a geo-linking service that
implements the visualisation scenario
described above. It uses OGSADAI’s support for application-specific
data resources to access the census
and region data and for applicationspecific functionality to execute the
joining.
The actual query-join-transformdeliver process is represented as an
OGSA-DAI workflow, populated with
the users’ query, and then executed.
OGSA-DAI’s workflow engine, outof-the-box functionality and support
for application-specific extensions
provided a framework allowing for
experimentation with different data
access, transform and integration
scenarios.
Driven by requirements from users
such as SEE-GEO, the OGSA-DAI
team has produced OGSA-DAI 3.0.
This is a complete redesign and
rewrite of the OGSA-DAI software
and includes a number of major
changes implemented in response
to requirements from existing users:
OGSA-DAI’s workflow units have
been simplified and unified to be both
more extensible and standardised,
and to allow workflows to be
composed more easily.
Multiple databases can be utilised
within the scope of a single workflow.
Different parts of a workflow can
operate upon different parts of a
datastream concurrently.
Resources and services have been
refactored to improve modularity and
reduce functional overloading.
APIs have been completely
refactored to allow developers
to utilise application-specific
functionality and databases within
OGSA-DAI more easily.
This release provides a powerful
product for both data integrators and
developers of data applications to
build upon.
The OGSA-DAI project – which
involves both EPCC and NeSC – is
funded by EPSRC through OMII-UK.
IBM contests
IBM has announced two student
contests using IBM Mainframe and
System i technologies.
The Mainframe contest runs from
October 16 to December 31, and the
System i contest from October 22 to
December 31.
Details are available at http://
www-03.ibm.com/systems/uk/z/
mainframecontest/ and http://www304.ibm.com/jct09002c/university/
students/contests/systemi/eur/
eurinnovationchallenge.html.
Both technologies are widely used by
IBM’s clients, the company says, and
skills are in high demand.
Prizes include Sony PSPs, Lenovo
Thinkpads, Nintendo Wiis, iPod
nanos, training course vouchers,
and a trip to Nintendo in Redmond
Washington.
The contest is open to students at all
UK universities.
www.nesc.ac.uk
Issue 54, October 2007
Forthcoming Events Timetable
October
9-11
Final NextGRID Project Appraisal Meeting e-Science Institute http://www.nesc.ac.uk/esi/events/808/
11-12
An Introduction to Grid Data Services
using OGSA-DAI
e-Science Institute
http://www.nesc.ac.uk/esi/events/823/
19
Data and Storage on the National Grid
Service
e-Science Institute
http://www.nesc.ac.uk/esi/events/812/
22-24
PhyloInformatics Workshop
e-Science Institute
http://www.nesc.ac.uk/esi/events/710/
31-2 Nov
Distributed Programming Abstractions:
Workshop II
e-Science Institute
http://www.nesc.ac.uk/esi/events/825/
1-2
Chris Date seminar
e-Science Institute
1-2
Deploying Grid Data Services using
OGSA-DAI
e-Science Institute
http://www.nesc.ac.uk/esi/events/813/
2
The e-Science Institute Public Lecture
- “Building a better (fly) brain...”
e-Science Institute
http://www.nesc.ac.uk/esi/events/824/
5-7
OMII - Europe Face to Face Meeting
e-Science Institute
http://www.nesc.ac.uk/esi/events/819/
13-14
SRM2.2 Deployment Workshop
e-Science Institute
November
“Building a better (fly) brain...”
Dr Douglas Armstrong of the School of Informatics, University of Edinburgh and Deputy Director of the Edinburgh
Centre for Systems Biology will give the opening lecture on the eSI theme ‘Neuroinformatics and Grid Techniques to
Build a Virtual Fly Brain’ (http://www.nesc.ac.uk/esi/themes/theme_07/) which commenced in September.
Mental Health accounts for 11% of global disease burden, it is growing rapidly yet it is one of the most challenging
areas for drug discovery and development. Realistic models that capture the processes (and disorders) of the human
brain would provide new insights into the diagnosis and treatment of such disorders. However, to achieve this, we
need to begin by working from much simpler, more tractable models. The brain of the fruit-fly Drosophila contains in
the region of 100,000 neurons. Drosophila provide perhaps the simplest brain capable of what we would consider
complex behaviour – much of which offers insight into animal and human cognition. The genome was sequenced
in 2000 and efforts to improve the sequence and its functional annotation are highly integrated and span the entire
community. Of the estimated 12,000 Drosophila genes, more than 2,000 are conserved in human disease indications
and transgenic manipulation is rapid and advanced. This is a challenge that spans multiple levels of biology and
informatics from behaviour and molecules to data integration and high performance computing.
16:00 2 November 2007 at The e-Science Institute, Edinburgh.
There is no need to register to attend this lecture and it will also be webcast live. Further details, including the
webcast link, are available at: http://www.nesc.ac.uk/esi/events/824/
This is only a selection of events that are happening in the next few months. for the full listing go to the following
websites:
Events at the e-Science Institute: http://www.nesc.ac.uk/esi/esi.html
External events: http://www.nesc.ac.uk/events/ww_events.html
If you would like to hold an e-Science event at the e-Science Institute, please contact:
Conference Administrator,
National e-Science Centre, 15 South College Street, Edinburgh, EH8 9AA
Tel: 0131 650 9833 Fax: 0131 650 9819
Email: events@nesc.ac.uk
The NeSC Newsletter is produced by Gillian Law,
email glaw@nesc.ac.uk
The deadline for the November Newsletter is: 30th October 2007
NeSC News
10
www.nesc.ac.uk