The monthly newsletter from the National e-Science Centre
NeSC News
Issue 52 July 2007 www.nesc.ac.uk
Tracing the Paths of the Mind
by Iain Coleman
Mental illness can be terrifying.
Changes in behaviour and
personality are often profoundly
distressing for sufferers and their
loved ones, particularly when the
illness seems mysterious and
inexplicable. We no longer ascribe
the symptoms to possession by
spirits, but there is still a lingering
sense that there is something
peculiarly different about mental
illness as compared to physical
ailments such as cancer or
diabetes.
That’s something the University of
Edinburgh’s neuroimaging team
has set out to change, with the
help of Eddie, a new cluster at
the Edinburgh Compute and Data
Facility (EDCF), which is enabling
them to analyse brain scans at
unprecedented speed and volume.
This, they hope, will allow them to
tie down how the presence and
onset of mental illnesses are related
to the structure of patients’ brains.
MRI scans are able to trace the
structure of the brain’s white matter
by detecting how water diffuses
through it. The white matter is
made up of fibres, and fluids will
preferentially move in a direction
that is aligned with those fibres.
If the structure breaks down in a
particular area the flow becomes
less directional, and more isotropic.
Thus, MRI measurements of
fractional anisotropy can indicate
where the brain is damaged, and
scans of the whole brain can allow
damaged and healthy brains to be
compared.
The question is, does this damage
cause the illness, or is it caused by
it? In other words, can we predict
mental illnesses like schizophrenia
and bipolar disorder from brain
scans of healthy people, or do
we have to wait until symptoms
An example of tractography showing a coronal view of the posterior limb of the internal
capsule (image courtesy of Jonathan Clayden)
appear before identifying those in
need of medical help? To address
this problem, the Edinburgh
researchers have assembled
samples of hundreds of people
who are considered to be at risk of
developing these illnesses because
they have several relatives who
are already affected by them. By
performing brain scans at regular
intervals, and comparing these
scans with one another as time
goes on, they hope to be able to
find differences in the brains of
those subjects who do go on to
become ill, that are detectable in
the scans taken before the illness
developed.
This is where the power of the new
computing cluster is essential. No
two brains are exactly the same
size or shape, so before scans from
different brains can be compared
the images have to be warped to fit
a standard template. The best way
of constructing a template, to give
the most accurate analysis, involves
selecting - from the total sample of
scans - the individual scan that is
closest to the average shape. This
process requires comparing each
scan to every other scan in the
sample, so as the sample size goes
up the processing time increases
exponentially.
A recent test run, involving just
60 brain scans, took just 4 hours
on the new cluster: the same task
would have taken a single machine
75 days. To process the full set
of over 100 scans would take
the best part of half a year on a
desktop computer, but the cluster
should manage this job in less
than a day. Analyses which were
once completely impracticable are
suddenly made feasible.
The second type of analysis which
this new computing facility makes
possible is tractography – tracing
the linkages between different parts
of the brain. The same methods of
measuring diffusion directions in
the white matter are used for this
as for the whole-brain scans, but Issue 52, July 2007
in this case sophisticated statistical
modelling is applied to identify
individual tracts of connecting
material. This gives a whole new
dimension of information about
the inner workings of the brain,
and gives new insights into the
relationship between function and
structure, allowing researchers
to ask new questions about how
damage relates to functional
abilities. It is, however, very
computing-intensive. The Edinburgh
team are developing methods of
comparing tracts between different
patients, and are looking to
compare results from tractography
and whole-brain studies in the hope
of new insights into the physical
manifestation of mental illness.
Without the new cluster, this would
have been a pipe dream: now, it is
within their grasp.
There is tremendous potential for
other data-intensive analysis on
this scale, from studying strokes
to researching the effects of
aging, and computing clusters
like Eddie may offer new hope to
those touched by these debilitating
afflictions.
The ECDF project team involves
staff from the University of
Edinburgh Information Services,
the National e-Science Centre
and EPCC. More information
about the Edinburgh Compute
and Data Facility, the University
of Edinburgh’s centre for enabling
computation- and data-intensive
research, can be found at
http://www.ecdf.ed.ac.uk
For more information about the
Division of Psychiatry at the
University of Edinburgh go to http://
www.pst.ed.ac.uk/index.html
NGS User Forum
The latest NGS
(National Grid
Service) User Forum
was held on the
19-20th of June at
the newly opened
Oxford e-Research
Centre (OeRC) at
the University of
Oxford.
Over two days 63
participants from 20
institutions had the
opportunity to meet
NGS staff and to
discuss the latest
developments in the
NGS as well as to hear how the
NGS services are being used by
researchers from across the UK.
User presentations included Peter
Coveney from UCL describing how
he has used NGS resources to
investigate the molecular dynamics
of clay based nanoparticles
and Jonathan Mitchell from the
University of Leeds who explained
how NGS resources are helping
him model the physical properties of
biomolecules.
As well as applications of NGS
resources, Matthew Mascord
from the University of Oxford
spoke about the perceived and
actual barriers to the uptake
of e-infrastructure to research
communities. Matthew is the
manager of the JISC funded
e-Infrastructure Use Cases and
Service Usage Models (eIUS).
Presentation slides and photos from
the day are available on the NGS
website.
Grid Computing Now events
Grid Computing Now Project Manager Ian Osborne spoke at a Transport
Modelling and Grid Computing workshop in London on July 12. The event
brought together Transport modellers and grid computing experts, to look at
ways grid can be used in transport planning for the future.
GCN will also be involved in an event looking at grid applications in the
medical industry, in September. Together with the London Technology
Network, GCN will look at the storage and security issues raised by new
medical imaging technologies.
For more information on grid-related events, visit:
http://grid.globalwatchonline.com/epicentric_portal/site/GRID/menuitem.0e9
a2effd1b58e9b08a38510eb3e8a0c/
NeSC News
by Dr Gillian Sinclair
The following day over 30 people
attended a Technology Update
for NGS Users Event led by Mike
Mineter and Guy Warner from
the NeSC Training, Outreach and
Education team (TOE). The one
day course included an overview
of recent deployment software
services on the NGS, the resource
broker and the NGS portal.
The next User Forum will be held at
AHM 2007 as a “Birds of a Feather”
meeting on the 12th of September.
All current and possible future users
of NGS are invited to attend.
Other NGS News
The NGS website (www.ngs.ac.uk)
has recently been redesigned in
order to make it easier for both
experienced NGS users and those
new to the community to find
information about all aspects of the
NGS. If you have any feedback
regarding the new website please
contact the NGS Support Desk
(support@grid-support.ac.uk).
The NGS has also recently
appointed Gillian Sinclair as Liaison
Officer who will be responsible
for dissemination, publicity and
outreach to communities. Gillian
was previously Programme
Manager for NCeSS (National
Centre for e-Social Science).
Photo Above: Peter Coveney from
UCL at the NGS User Forum.
Photo by Katie Weeks NGS.
www.nesc.ac.uk
Issue 52, July 2007
Scholarship 2.0
When a piece of technology is
taken up by people outside the
original community of users, it can
be transformed as newcomers
find innovative uses for its existing
capabilities, and generate demand
for new features never envisaged
by the designers. A prime example
is the explosion in tools and
features for the World Wide Web,
when it moved from academia into
the commercial world. Something
similar is happening to e-Science
as it meets the arts and humanities.
Scholars and artists have started
working in earnest with the new
tools of collaborative and distributed
working that e-Science affords
– and in doing so, are throwing
up new challenges for technology
developers.
Some eye-witness accounts of this
creative collision were presented
last month, with the start of the
summer lecture series in the eScience Institute’s “e-Science in
the Arts and Humanities” theme.
The first session, “Methods
and Technologies for Enabling
Virtual Research Communities”
concentrated on ways of bringing
geographically scattered scholars
together to form vibrant and
productive groups. Tools like
AccessGrid can collapse the
distance between researchers, and
allow them to work together as if
they were all in the same building
- at least, that’s the theory. David
Shepherd (Sheffield) presented
results of research that showed
the gap between the promise of
AccessGrid and the reality. It can
be tricky to manage an AccessGrid
meeting such that all members have
an equal chance to participate,
though careful setup, attentive
management and use of the jabber
facility can improve the experience.
When it comes to more ambitious
attempts to use AccessGrid for
artistic performance, considerable
further development will be needed
before the technology catches up
with the ambitions of the artists.
An emerging alternative system,
the Agora multimedia collaboration
e-Science
Institute
by Iain Coleman
tool, promises to enable more
fruitful scholarly collaboration
in a desktop environment that
combines videoconferencing,
collaborative editing, and the ability
to share desktops and a communal
whiteboard. Adrian Fish (Lancaster)
outlined the current stage of Agora’s
development, and stressed its userfriendly approach.
Ease of use, though, is only
half the battle. Practitioners in
the arts and humanities need
tools that support the distinctive
features of their work. Another
set of lectures, “Collaborative
Text Editing”, concentrated on
one of the core activities of the
humanities: the production of high
quality critical editions of texts. The
tools exist to edit and annotate
texts collaboratively – the trick is
to exploit these new possibilities
while maintaining the integrity of
more traditional scholarship. Gabriel
Bodard (King’s College London)
spoke about the advantages of
open source critical editions. These
can be much more than just texts:
they can incorporate sources,
supporting evidence and accounts
of the methodology used in creating
the edition. An edition of the Iliad,
for example, could include the
versions of the poem, fragments,
and secondary sources that fed into
this particular edition, as well as the
scholar’s arguments for particular
translations and interpretations.
This transparency and full
disclosure draws on the spirit of the
open source software movement,
a philosophy which corresponds
closely to traditional academic
practice.
As soon as texts are allowed to be
edited collaboratively, whether on
wikis or some other environment,
issues of quality control and
accountability become manifest.
Juan Garces (British Library)
discussed the various approaches
that can be taken, from anonymous
peer review to community editing on
the Wikipedia model. He proposed
that a hybrid approach might avoid
the slow response and elitism of
the former, without introducing the
insecurity and impermanence of the
latter. He stressed that any solution
has to allow the production of
properly attributed, canonical texts
that exist permanently and can be
reliably cited. The desire to improve
a work must not be allowed to
supersede the need to preserve the
intellectual history of a developing
field.
Annotation is another area where
it is important to maintain the
record of scholarly arguments as
they develop. This is a complex
information management task even
when confined to traditional texts:
the problems explode into whole
new dimensions once you start to
annotate audio and video sources
as well. Jean Carletta (Edinburgh)
explained how new technology
is enabling this to be done, in a
research project aimed at producing
full records of meetings. Not just
what was said, but how it was said,
to whom, and what everyone else
in the room was doing at the time.
This is a labour-intensive, multidisciplinary project, but it should
provide a rich resource for social
scientists - as well as helping
latecomers find out what went on
before they turned up.
Having developed these rich
information resources, the next
question is how best to share them
with the rest of the world. Describing
knowledge, for sharing and re-use,
is what ontologies are all about, and
the lecture session on “Ontologies
and Semantic Interoperability for
Humanities Data” sought to explore
some of the aspects of ontologies
that are particularly important to
the humanities. The problems of
multiple definitions of concepts and
shifts in meaning over time, familiar
to ontologists in the sciences, are
even greater in the humanities,
as Mark Greengrass (Sheffield)
demonstrated. Our contemporary
understanding of historical and
cultural movements and eras can
be very different from the ways
NeSC News
www.nesc.ac.uk
Issue 52, July 2007
they were understood by those
who participated in them, and
the categories we apply to order
our knowledge can shift radically.
There is a wealth of historical
material from the Eleven Years
Truce, for example – but none of
the people involved knew it was
going to last for eleven years. The
problems of creating ontologies
that are useful to and trusted by
practitioners in the humanities are
also substantial: with a tradition
of individual scholarship, and a
dearth of authoritative institutions,
widespread acceptance of such
grand intellectual designs can be
hard to achieve. Notwithstanding
these difficulties, Oscar Corcho
(Manchester) presented an example
of how ontologies and semantic web
technology can enable a shift from
information retrieval to question
answering. The development of
an ontology of Spanish authors
of the late nineteenth and early
twentieth centuries – the Silver Age
– is permitting scholars to develop
new strategies for obtaining and
combining information. While this
is still a work in progress, Corcho
anticipates that projects like this will
impel a paradigm shift in knowledge
acquisition.
What all these lectures made clear
is that the arts and humanities
can benefit tremendously from eScience technologies, but only if the
tools are suitable for their specific
purposes. Scholars and performers
have priorities and concerns that
are often different from those of
scientists and engineers. As this
Theme continues, those needs and
requirements should become still
more sharply defined, opening up
exciting new possibilities not only
for the Arts and Humanities, but for
e-Science itself.
Material from these lectures,
including webcasts and slides, can
be downloaded from http://wiki.esi.
ac.uk/E-Science_in_the_Arts_and_
Humanities
NeSC News
Register
Now!
Please join us at
the East Midlands
Conference Centre in
Nottingham from 10
th-13 th September
2007. We are sure
you will enjoy the
conference, the
exhibition and the
opportunity to meet
friends old and new.
This year sees
e-Science firmly
established as an
important discipline
with an expanding set
of practitioners. All
Research Councils
are engaged, and
JISC is committed
to transferring the
results of e-Science
research into
everyday practice in
higher education.
We look forward to welcoming you
to this year’s All Hands Conference
which remains the key event in
the e-Science calendar. We are
fortunate to have an excellent set of
invited speakers:
The packed programme reports
the latest results in e-Science
as papers, posters, workshops
and BoFs – plus an exhibition
demonstrating practical
achievements.
You will also find the Provisional
Programme online at http://www.
allhands.org.uk/programme/index.
cfm
Remember to register before
1 August to ensure the lower
registration rate.
Grid Computing and the
National Grid Service Induction
e-Science Institute, Edinburgh, 26
- 27 July, 2007
This course will introduce
participants to the concepts of
Grid Computing and then give a
practically oriented introduction to
the middleware and services of the
National Grid Service.
FOr information, go via http://www.
nesc.ac.uk/training/events/
Call for Participation: A
Plenary Session on the
Authentication Levels of
Assurance (LoA)
August 29, 2007,
Manchester, UK
http://www.ias07.org
The event will be hosted in
conjunction with the Third
International Symposium on
Information Assurance and
Security that aims to bring
together researchers, practitioners,
developers, and policy makers
involved in multiple disciplines of
information security and assurance
to exchange ideas and to learn the
latest development in this important
field. For more details, please visit
the conference website at http://
www.ias07.org.
Call for Papers
Third EELA Conference
Catania (Italy)
3-5 December 2007
More information can currently be
found at:
http://indico.eu-eela.org/
conferenceDisplay.py?confId=96
The NeSC Newsletter produced by:
Alison McCall and Jennifer Hurst,
email alison@nesc.ac.uk,
Telephone 0131 651 4783
The deadline for the August/
September Newsletter is: 31st August
2007
www.nesc.ac.uk
Issue 52, July 2007
Forthcoming Events Timetable
July
23-24
AHRC ICT Methods Network Workshop
on Space and Time: Methods of
Geospatial Computing for Mapping the
Past
e-Science Institute http://www.nesc.ac.uk/esi/events/772/
26-27
Grid Computing and the National Grid
Service - Induction
e-Science Institute http://www.nesc.ac.uk/esi/events/810/
30-31
Collaborative Knowledge Extraction
(CoKE): Sequencing Animal Behaviour
e-Science Instiute
http://www.nesc.ac.uk/esi/events/807/
16-18
Grid and Co-operative Computing (GCC)
Urumchi, Xinjiang,
China
http://vega.ict.ac.cn/gcc2007/
27-28
CoreGRID Symposium
IRISA, Rennes,
France
http://www.coregrid.net/mambo/content/view/358/330
28-31
Euro-Par 2007
IRISA, Rennes,
France
http://europar2007.irisa.fr/
3-7
LAnguages, methodologies and
Development tools for multi-agent
systemS (LADS007)
Durham, UK
http://lia.deis.unibo.it/confs/lads/
3-7
Parallel Computing Technologies
Pereslavl-Zalessky, Russia
5
Distributed Programming Abstractions
- Workshop II
e-Science Institute http://www.nesc.ac.uk/esi/events/815/
6-7
The Fourth International Conference on
Life Science Grids 2007 (LSGrid 2007)
National e-Science Centre,
Glasgow
http://www.nesc.ac.uk/events/
lsgrid2007/
10 - 13
UK e-Science All Hands Meeting Registration Now Open!
East Midlands
Conference
Centre,
Nottingham
http://www.allhands.org.uk/
10 - 14
5th International GridKa School
15
HiPerGRID
Brasov. Romania
http://pact07.cs.tamu.edu/
19-21
The 8th IEEE/ACM International
Conference on Grid Computing (Grid
2007)
Austin, Texas
http://www.grid2007.org/
20 -21
Computational Methods in Systems
Biology (CMSB 2007)
e-Science Institute
http://www.nesc.ac.uk/esi/events/749/
1-5
EGEE07 Conference
Budapest
http://www.eu-egee.org/egee07/
registration
7-9
Third International Conference on eSocial Science
Ann Arbor,
Michigan, US
http://ess.si.umich.edu/
22-24
PhyloInformatics Workshop
e-Science Institute
http://www.nesc.ac.uk/esi/events/710/
August
September
http://www.ssd.sscc.ru/conference/
pact2007/
http://www.fzk.de/gks07.
October
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
NeSC News
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
www.nesc.ac.uk