The monthly newsletter from the National e-Science Centre
NeSC News
Issue 75 November 2009 www.nesc.ac.uk
Mapping Meaning
By Iain Coleman
Maps are all about what you choose
to display, and what you leave out.
Street maps are more useful than
satellite photographs if you want to
find your way around a city, while you
want much more information about
the steepness of a slope if you’re
hiking than if you’re driving a car.
The digital age offers boundless
possibilities for making maps that
illuminate key facts about a given
set of data. The e-Science Institute
workshop on “Mapping Information
with and without Geography:
Approaches to Data Visualization
and Structure in the Arts, Humanities
and Social Sciences”, held at eSI
on 30 September – 1 October, set
out to explore the different ways
that mapping and visualisation can
provide new insights in the arts,
humanities and social sciences.
An overview of the diverse ways
maps can be used in geography
was provided by Martin Turner
(Manchester). He showed how
different the world looks if it is
visualised such that each country’s
size is proportional to its population
rather than its land area, and how
adding time as the third dimension on
a map can show not only the routes
of Napoleon’s armies but also how
long they spent in particular battles
– and how quickly they died off in
the bitter Russian snows. Maps can
also play a role in political decision
making – showing population
densities or poverty indices across a
city – and in oil drilling, showing 3-d
clusters of heavy metals found in drill
cores.
A reconstruction of the inhabited world as described by Herodotus
The Strategic Environmental
Archaeological Database (SEAD)
project, introduced by Fredrik Palm
(University of Umeå), demonstrated
how mapping can be used to shed
light on the past. With spatially and
chronologically referenced data from
excavations, including pollen, insects
and soil chemistry that act as proxies
for environmental parameters, SEAD
allows researchers to explore the
ways the environment has varied
throughout the past.
Mapping can do more than depict
the relationships between objects
and places in the world. It can also
connect the different ways that
human beings relate to them. As Jo
Walsh (EDINA) explained, extracting
place names from literature and
documents, attaching them to maps
and annotating them can provide
new ways to travel through the data,
revealing new insights along the way.
This kind of georeferencing can allow
data to be reused in interesting ways
that the creator never thought of,
such as the map of the Lake District
that shows which places have the
most photos posted on the image
sharing website Flickr.
But georeferencing can be a
problematic business. We are
accustomed to thinking of place
names as approximations to
geographic coordinates, but it’s
really the other way round. A given
town can be represented in different
databases by coordinates that
differ by several kilometres, but
that doesn’t stop the town being a
well-defined geographical entity. On
the other hand, some quite distinct
hills share the same name, but
have different coordinates. Creating
a system that can automatically
Issue 75, November 2009
Mapping Meaning
Continued
By Iain Coleman
understand both these types of
ambiguity is a difficult challenge.
And what about a name like
“Camelot”? It definitely refers to a
place somewhere in Britain, so it is
geographically meaningful – but it is
also very vague.
of Herodotus, and arguably of his
Greek contemporaries. Drawing
out the real networks in the ancient
world is a task for historians and
archaeologists, and may well prove
quite different from the worldview that
Herodotus expressed.
From this perspective, mapping is as
much about how we conceptualise
information as it is about displaying
objective facts. The Herodotus
Encoded Space-Text-Image Archive
(HESTIA) is taking this approach
to the way space is represented in
the writings of Herodotus, as Elton
Barker (Open University) explained.
Yet another worldview can be seen
in the sacred maps created by
Aborigines in the Northern Territories
of Australia. Julie Tolmie (King’s
College London) showed how these
are highly abstract representations
of objects and places in a landscape,
connected by the routes taken to
reach them in a particular order.
This abstract approach is similar to
the classic London Underground
map – but the sacred map encodes
mythical meaning and history as well
as geography.
Herodotus was one of the first
historians. His histories, written
around 430 BC, take in the whole
Mediterranean and beyond as he
tries to explain why the Greeks and
the Persians came into conflict. This
project uses a database to develop
a model of how places come in and
out of focus as Herodotus moves
through his narrative. It’s a way of
discerning the relative importance
of different places at different
times, and of mapping the network
of connections between them. It’s
important, however, to appreciate
that this is only giving us a picture
of the world from the perspective
This points the way to another use of
maps – divorcing them from the need
to represent any physical place at all,
and instead using them to express
connections between concepts,
capturing and displaying information
that is relevant to a particular
audience. These kinds of maps are
valuable in depicting interacting
hierarchical systems, from university
funding structures to game design
components.
Among the possibilities raised by this
kind of thinking is an interdisciplinary
crossover between the very different
fields of archaeology and dance.
Archaeologists have two main ways
of visualising information: spatial
and temporal. Stuart Dunn (King’s
College London) explained how
modern technology is allowing
archaeologists to integrate these two,
visualising space and time together.
The e-Dance project, meanwhile, is
working on capturing the movement
of the human body in performance
and visualising it as a spatio-temporal
structure. This results in maps that
don’t make sense in space alone, but
need the time dimension if they are
to be meaningful.
It’s a far cry from the A-to-Z, but eScience is now allowing researchers
to capture the ephemeral and map
the intangible in ways that could
not previously have been dreamed
of. As mapping, visualising and
georeferencing become more flexible
and more ubiquitous, the full power of
maps to enhance our understanding
of the world and of ourselves is just
beginning to be tapped.
Slides from this event can be
downloaded from http://www.nesc.
ac.uk/esi/events/1005/
DPA Theme Team wins Best Paper Award at Grid2009
The Distributed Programming Abstractions paper, Critical Perspectives on Large-Scale Distributed Applications and
Production Grids was awarded the Best Paper at IEEE Grid 2009.
Authors Shantenu Jha, Daniel S. Katz, Manish Parashar, Omer Rana and Jon Weissman are all members of the team
researching this topic as part of the Distributed Programming Abstractions theme.
NeSC News
www.nesc.ac.uk
Issue 75, November 2009
ESRC appoint National Strategic Director and
Deputy Director of e-Social Science
Professor David De Roure of University of Southampton has been appointed
to the new role of Economic and Social Research Council’s (ESRC) National
Strategic Director of e-Social Science, with Dr Marina Jirotka of the Oxford
e-Research Centre as Deputy Director. Both are part of the e-Research South
consortium.
The appointments, which begin this month and run for three years, mean that
Professor De Roure and Dr Jirotka will take a key strategic role in maximising
the uptake, use and impact of new e-technologies across the Social Science
community. They will also develop a coherent inter-agency approach drawing
on various national and international e-Social Science initiatives.
‘In the past five years, the National Centre for e-Social Science (NCeSS) has
made excellent progress towards establishing powerful new research tools
and methods,’ said Professor De Roure who directs e-Research activities at
the University of Southampton’s School of Electronics and Computer Science
(ECS).
Professor David De Roure
‘Our experience in e-Research, coupled with the fact that Southampton is
the home of the National Centre for Research Methods (NCRM), puts us in
a great position to build on the achievements of NCeSS and communicate
these new approaches to the broader research community and the next
generation of researchers.’
Dr Jirotka, Associate Director of the Oxford e-Research Centre, added ‘My
background in both social and computer science will enable me to assist in
the coordination of training and capacity building activities to embed e-Social
Science techniques in research practice and make effective use of emerging
infrastructure.’
Professor Ian Diamond, Chief Executive at ESRC said: ‘ESRC is pleased
Dr Marina Jirotka
to announce the appointment of Professor De Roure and Dr Jirotka,
who combined will provide an ideal leadership team , bringing extensive
experience and expertise to the NCeSS research programme to enable social
scientists to harness the wealth of digital technologies in undertaking innovative world leading research.’
Professor De Roure has just returned from an intensive tour of the US with Professor Malcolm Atkinson, UK e-Science
Envoy, on a fact-finding mission which is set to inform UK strategy and develop international collaborations.
‘e-Science and e-Social Science are very highly thought of internationally,’ he said. ‘We are establishing a terrific
network of advisors and collaborators to ensure that e-Social Science goes
from strength to strength’.
The National e-Science Centre congratulates Professor de Roure and Dr Jirotka on their new appointments.
NeSC News
www.nesc.ac.uk
Issue 75, November 2009
A magical time with the NGS
By Gillian Sinclair
The second NGS Innovation Forum
was recently held in London at
The Magic Circle Headquarters in
London. An interesting venue for a
very interesting event!
The event was nominally divided to
appeal to two main audiences – the
first day was targeted more at users
and potential users with the second
day containing talks of relevance for
IT and research support staff.
Many of the attendees on the first
day were new to the NGS and so the
introduction the services provided
by the NGS by the NGS Executive
Director, Dr Andrew Richards,
proved invaluable. Some interesting
analogies concerning the London
underground and shipping containers
were to describe the past, present
and future of the NGS. In a natural
progression, the next presentation
concerned actually using the
resources. It’s all very well telling
people what the NGS offers but it can
still seem intimidating to someone
who hasn’t used it before. Dr David
Fergusson from the NeSC training
team talked the audience through
the life cycle of a job on the NGS
including birth, mating and death
accompanied by some of his own
great photos– very interesting!
A new addition to the Innovation
Forum this year was break out
sessions to enable participants and
communities to meet and discuss the
major challenges in their area, issues
that the NGS can help with etc. The
break out sessions were a mix of
research communities (molecular
modelling, bioinformatics and social
sciences) and more general topics
(data handling, site integration,
NeSC News
Dr Steven Newhouse,
Acting EGI Director
(above) and Dr Andrew
Richards, NGS Executive
Director (left) speak at
the NGS Innovation
Forum
software, user support). The breakout sessions were lively affairs with a
great deal of discussion and debate.
Each break-out group reported back
in the afternoon to allow for more
debate and discussion.
One of the highlights (amongst
many!) from the event was the series
of presentations by NGS users and
community representatives. There
were four in total: Bioinformatics data
challenges - Henning Hermjakob,
European Bioinformatics Institute:
The NGS and me: from protein
free energies to protein free energy
profiles - Philip Fowler, University
of Oxford; Exploring the locomotor
dynamics of large animals using
Evolutionary Robotics - Karl Bates,
University of Manchester; and
Using in-silico computer models of
the heart to optimize therapies for
cardiovascular diseases - Gernot
Plank, University of Oxford
An excellent set of presentations
which highlighted some of the
amazing research taking place in
the UK which makes use of NGS
resources.
The first day ended with a drinks
reception to allow conversation and
www.nesc.ac.uk
Issue 75, November 2009
A magical time
with the NGS
Magic Circle theatre
Continued
debate to continue. Obviously given
our surroundings the entertainment
was provided by a magician
specialising in close up magic
resulting in a large number of people
scratching their heads in amazement!
The second day focused more on
the “nuts and bolts” of the NGS
services. There were presentations
on why institutes should think
about joining the NGS, the process
involved in becoming a member
and the technologies available from
the NGS as well as a discussion on
cloud computing. While having more
institutions joining the NGS is good
we also need to reach the potential
end users at these institutions. A
presentation from Dr David Wallom,
NGS Technical Director, focused
on the NGS Campus Champions
scheme which aims to have a single
point of contact for the NGS at
each institution to liaise with users
and also to liaise with the NGS.
Following this was a presentation on
the outreach services available from
the NGS by Dr Gillian Sinclair, the
NGS Liaison Officer.
Overall the event was a great
success judging by the feedback
received verbally at the event and
from the feedback sheets received at
the end. Discussions have already
started for the third NGS Innovation
forum in 2010 so watch this space!
NeSC News
OGSA-DAI 3.2 released
The OGSA-DAI project, a partner in OMII-UK, and in which EPCC plays
a significant role, has released version 3.2 of its database access and
integration software.
OGSA-DAI is an extensible framework for the access and management of
distributed heterogeneous data resources - whether these be databases,
files or other types of data - via web services. OGSA-DAI provides a workflow
engine for the execution of workflows implementing data access, update,
transformation, federation and delivery scenarios.
The main features of OGSA-DAI 3.2 are: OGSA-DAI 3.2 now includes
Distributed Query Processing (DQP).
DQP allows the tables from multiple distributed relational databases to be
queried, using SQL, as if there were multiple tables in a single database.
These databases are exposed via OGSA-DAI servers.
DQP was originally designed and developed by at the University of
Manchester and the University of Newcastle upon Tyne. Previous versions of
DQP were released as a separate product - OGSA-DQP.
DQP has now been rewritten and is now simply an extension to OGSA- DAI.
DQP’s functionality is now exposed as OGSA-DAI resources and activities
and accessed via OGSA-DAI’s standard services. This greatly simplifies
deployment and enables extensibility within a single framework.
Non-blocking data sinks that allow data pushed to OGSA-DAI from a client to
be cached until it’s ready to be processed.
A new monitoring framework which tracks the data blocks produced and
consumed by each activity in a workflow.
Support for relational database-specific meta-data extractors and mappers
from JDBC column types to OGSA-DAI tuple types.
New security activities for passing client credentials through workflows and
retrieving credentials from a Globus Delegation Service.
More efficient GridFTP activities.
A number of bugs have been fixed, components made more efficient or
robust.
Unlike previous versions of OGSA-DAI, OGSA-DAI 3.2 only compiles under
Java 1.5 and not Java 1.4. Apart from this, OGSA-DAI 3.2 is designed to be
backwards compatible with OGSA-DAI 3.1 without the need for recompilation
- data resource, activity and presentation layer APIs and service WSDLs
remain the same.
OGSA-DAI is a free, open source, 100% Java product and is released under
the Apache 2.0 licence. Downloads compatible with Apache Axis 1.4, Globus
4.0.8 and Globus 4.2.0, are available
OGSA-DAI 3.2 download: http://sourceforge.net/projects/ogsa-dai/files/
OGSA-DAI 3.2’s user doc: http://sourceforge.net/apps/trac/ogsa-dai/
wiki/UserDocumentation/ogsadai3.2
Release notes:http://ogsa-dai.sourceforge.net/documentation/ogsadai3.2/
ogsadai3.2-axis/Release.html
http://ogsa-dai.sourceforge.net/documentation/ogsadai3.2/ogsadai3.2gt/Release.html
OGSA-DAI project website: http://www.ogsadai.org.uk
OGSA-DAI’s open source project site: http://sourceforge.net/ projects/ ogsadai
OMII-UK: http://www.omii.ac.uk.
The OGSA-DAI project, which involves both EPCC and NeSC, is funded by
EPSRC through OMII-UK.
www.nesc.ac.uk
Issue 75, November 2009
Ay! dreich an’ dowie’s been oor lot, An’ fraught wi’ muckle pain...
T. Watts in Minstr. of the Merse (ed. Crockett 1893)
By Richard Sinnott
Consider a researcher who wants
to use digital resources in a
comparative investigation of the
development of the English language
in northern England and in southern
Scotland.
To undertake this research they
might use the Oxford English
Dictionary and the Dictionaries of the
Scots Language individually, record
the search results and compare
them manually. The lecturer may not
be aware of other relevant digital
resources such as the Historical
Thesaurus, the corpora of Scottish
English and of northern English,
collections of letters, wills and
charters.
Manually collecting and aggregating
data from numerous resources
is very time consuming and the
accuracy of the conclusions
cannot be guaranteed when so
much available data may not be
included. This problem is magnified
when these resources have rights
permissions from the digital objects
or collections and the researcher
must manually register for access
to each of them individually. In this
case, the researcher is expected to
remember lists of usernames and
passwords for access to various
collections, and abide by the
various copyright issues pertaining
to usage of the data resources. In
such circumstances, many users
simplify this by keeping the same
username/password across all sites
– thereby weakening the security
of all sites. The user interface to
NeSC News
these collections also changes and
users are advised to update their
subscriptions and adapt to the new
interfaces.
It is also the case that many
language and literature data sets (the
majority!) are held by individual
scholars and are inaccessible to
the community. Whilst many of
these are deposited in national or
local archives, many more remain
unknown and inaccessible to the
wider community. Publishing requires
technical expertise and funding that
is not always available.
An interactive, research
infrastructure providing
seamless access to major
repositories and exploitation
(where appropriate) of high
performance computing
facilities will help to solve
many of these problems for
users. This is the basis for
the Enhancing Repositories
for Language and Literature
Researchers (ENROLLER http://www.gla.ac.uk/enroller/) funded
by JISC.
Through ENROLLER we propose
to radically change the existing
language and literature researcher
modus operandi for language and
literature researchers by bringing
data resources into a seamless,
user-driven framework where access
to remote heterogeneous language
and literature resources is available
and augmented with tools targeted
to the specific needs of this underresourced research community.
The project is now up and running
with a portal that has been protected
through the UK Access Management
Federation and initial services and
data sets now deployed. These
include services that provide a
step change in the way in which
data querying and analysis is
now possible, e.g. using Googles
MapReduce algorithm for bulk
searching of data across resources
on the NGS.
For more information on the eInfrastructure developed through
ENROLLER please contact Prof.
Richard Sinnott (r.sinnott@nesc.gla.
ac.uk).
For more information on becoming
involved in the work, e.g. through
an associated Network of Scolars
please contact Jean Anderson
(J.Anderson@arts.gla.ac.uk).
www.nesc.ac.uk
Issue 75, November 2009
Virtual world predicts dire future for British cities
A SimCity-like computer simulation
that enables social scientists to
understand how real-life populations
react to change has predicted a
depressing future for British cities by
the year 2031.
Researchers at The Universities of
Leeds and Manchester used new,
powerful simulation software to
create a virtual Leeds, revealing a
worrying picture of how the city’s
congestion and deprivation could
mushroom over 30 years.
Researchers from the MoSeS
project, part of the ESRC funded
National Centre for e- Social Science
(NCeSS) coordinated by University
of Manchester, also showed how codependent couples (two adults in a
single household, both aged over 65)
become hugely prevalent across the
Yorkshire City by 2031.
A new £1.4 million project at NCeSS
funded by the Joint Information
Systems Committee (JISC) will take
the MoSeS project a stage further
by creating video simulation for any
British city. It is launched this month.
According to geographer and project
leader Professor Mark Birkin from
the University of Leeds, the worrying
scenario for Leeds would almost
certainly be repeated across the
United Kingdom.
an even spread across the whole city
by 2031.
Professor Birkin said: “I think these
trends are very likely to be repeated
across the UK – but our task now
is to prove it conclusively. “Our new
project, the National e-Infrastructure
for Social Simulation (Ne-ISS), will do
just that.”
He added: “Ne-ISS means planners
have the potential to use a real
life version of ‘SimCity’ to test the
consequences of their policies.
“It use data from censuses, British
Household Panel Survey, Birth
and Death rates from ONS and
Health survey for England and
makes realistic assumptions about
demographic patterns at certain
intervals over the next 30 years.
“We are confident that Ne-ISS will
provide valuable material for planners
in local authorities across the UK.
“They will be able to use the tools to
look at a range of issues - including,
for example, crime.”
“In this way, Ne-ISS could have
a major impact: if planners and
policymakers were able to rigorously
compare the potential impacts of
different policies and decisions –it
would surely improve the quality of
their work.
“For this to be achieved, the Ne-ISS
project team must work closely with
users from start to finish. The aim is
to build up a community of users who
can contribute to the development of
these tools and thereby ensure that
their potential is fully realised.
“In the longer term, we anticipate that
Ne-ISS will provide a blueprint for the
provision of social simulation tools
to planners and policymakers on a
European scale.”
The Fourth Paradigm
Data-intensive science is dramatically
changing the way research is done.
Among the data produced by MoSeS
is a series of maps showing most of
Leeds in gridlock by 2031. Whereas
Citizens defined as “deprived”
–people with poor housing, health,
and access to transport t-are
currently concentrated in the Centre
of Leeds, the problems could engulf
a third of the city by 2031.
This book, dedicated to Jim Gray,
is a comprehensive compendium
of progress in this new approach. It
has several connections with UK eScience, Tony Hey being the Editor
and with contributions from Carole
Goble and Dave De Roure.
The book will be available for
free download from the website:
http://research.microsoft.com/
fourthparadigm.
The simulation also found that
contrary to the claims of some
commentators, the ghettoisation
of ethnic groups is decreasing
– dispersing from central locations to
NeSC News
Professor Rob Procter from The
University of Manchester said: “The
Ne-ISS project will make social
simulation tools available for planners
and policymakers to use as part of
the normal course of their work.
www.nesc.ac.uk
Issue 75, November 2009
Call for proposals to run eSI themes in late 2010
and early 2011
The closing date for submitting new theme proposals is 11
March 2010 . For further details and how to apply, follow this
link: http://www.nesc.ac.uk/esi/themes/index.htm
Note that this will be the last opportunity to apply in this round
of funding
Forthcoming Events Timetable
November
5-6
Eurosystem Workshop on Quantitative
Omics Technologies
eSI
http://www.nesc.ac.uk/esi/events/1018/
18
Mathematical Physics Group
eSI
30
OMII-UK Operations face-to-face meeting NeSC
http://www.nesc.ac.uk/esi/events/1039/
30-2
Next Generation Sequence Assembly
eSI
http://www.nesc.ac.uk/esi/events/1020/
1
Lecture Series: Next Generation
Bioinformatics User Group’ NGBug Event
eSI
http://www.nesc.ac.uk/esi/events/1022/
3
HUWY: Young people’s experience and
advice on Internet Policies
eSI
http://www.nesc.ac.uk/esi/events/1021/
15
JISC Winter Fayre
NeSC
http://www.nesc.ac.uk/esi/events/1006/
16
Improving Cancer Care for Children and
Teenagers in Scotland
eSI
http://www.nesc.ac.uk/esi/events/1012/
December
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
This NeSC Newsletter was edited by Gillian Law.
Email: glaw@nesc.ac.uk
NeSC News
www.nesc.ac.uk