The monthly newsletter from the National e-Science Centre
NeSC News
Issue 61 June 2008 www.nesc.ac.uk
The New Republic
By Iain Coleman
We are all heirs to the
Enlightenment ideal of the
Republic of Scholars, that used
learned journals – the advanced
communications technology of the
time – to share new ideas and new
information, and to refine knowledge
in the crucible of criticism.
Now, new technology has brought
about the new republic of
e-Science. But this revolution isn’t
just about doing the same old things
faster and cheaper. It is enabling
scholars, scientists and artists to
work in new ways, and to achieve
things that were simply not possible
before.
Some of these new opportunities
could be seen at the Arts and
Humanities e-Science Projects
Meeting, held at the e-Science
Institute on 6-7 May as part of
the “e-Science in the Arts and
Humanities” theme. The theme
leaders, Stuart Dunn and Tobias
Blanke of the Arts and Humanities
e-Science Support Centre, hosted a
gathering of researchers, students
and representatives of funding
bodies. It was an opportunity to see
presentations on a striking variety
of projects, and to participate in the
wide-ranging discussions that they
engendered.
The e-Dance presentation by
Helen Bailey (Bedfordshire)
and Simon Buckingham-Shum
(Open University) asked: what
can e-Science offer as a novel
environment for creating new kinds
of choreography?
In exploring the creative potential of
the AccessGrid as a performance
environment, they have developed
new concepts and social
formulations of space. And this has
led to significant developments in
the technology, with new ways to
Assumed route of Byzantine army to Manzikert
display and manipulate AccessGrid
windows.
New technology is also enabling
innovative ways of doing history,
as Vince Gaffney (Birmingham)
explained. Taking as a case
study the Battle of Manzikert, the
Byzantine army’s epic march to
its defeat at the distant edge of
Anatolia, Gaffney showed how
long-standing questions about the
size of this great army and how it
was supplied can be addressed with
agent-based modelling.
There is no new data on this event,
from a conventional historical
point of view – the existing written
records, patchy as they are, are
all we have. But simulating the
behaviour of the people who made
up this army, building up a largescale picture from the ground up,
can give new insights into the most
probable ways this event might
have played out in reality.
It is possible to obtain genuinely
new historical data with e-Science
technologies. Ségolène Tarte
(Oxford) presented a system for
helping classicists to decipher and
transcribe ancient texts. These
documents can be difficult to read,
being composed of hand-made
incisions on stone, lead or wood,
covered by the stains of time and
set within the natural textures of
the material. Advanced image
acquisition techniques are enabling
the letters to be more readily
picked out from their surroundings,
and classicists are participating in
reading sessions to improve the
algorithms.
(continued on page 2)
**********************
AHM 2008
Early Bird Registration
for AHM 2008 is now
open and available till
13th July 2008.
For more information,
see page 3.
*************************
Issue 61, June 2008
The New Republic
By Iain Coleman
(continued)
Once data is gathered, of course, it
must be documented and archived,
to serve as the base material for
a thousand scholarly arguments.
This is one of the most important
applications for e-Science in the
arts and humanities.
As Stuart Dunn pointed out, the
arts and humanities do not have a
data deluge like the hard science,
they have a complexity deluge.
New systems for handling complex
information, myriad forms of data
annotated and cross-referenced,
are beginning to revolutionise
the time-honed techniques of
scholarship.
Henry Purcell
In music, too, there are new ways
of organising knowledge: the
Musicspace project (MC Schraefel,
Southhampton) employs semantic
web technology to integrate
information for researchers,
while Purcell Plus (Tim Crawford,
Goldsmiths College, University of
London) combines original scores,
NeSC News
published scores, recording and
commentaries to locate and store
the semiotic signs that manifest in
different forms in each domains.
A tempo marking in a score, for
example, might make the music
go slowly in a recording, which is
remarked upon in a commentary.
Sally Macdonald (UCL) and her
colleagues are developing
e-Curator, a system for recording
three-dimensional laser scans of
museum artefacts. Not only will
this dataset contain much more
information than catalogue entries
and photographs, it will also allow
researchers to do much more
with the objects without having to
physically travel to the museum,
and without exposing the objects to
potential wear and damage.
One relatively long-standing use of
e-Science for organising knowledge
is the archaeological work at the
Silchester Roman excavation.
Michael Rains (York Archaeological
Trust) gave a candid account of the
ups and downs of this technological
testbed project, and of the lessons
that can be more widely applied.
Simple, robust and familiar
interfaces proved to be the key.
Researchers recorded information
in situ with digital pens that write on
a surface similar to normal paper:
this data was then uploaded from
the pens to the project database.
This approach was successful
in speeding up and enhancing
the post-excavation work, and
it meant a paper back-up was
always there in case of computerrelated disaster. Other technologies
were less successful, particularly
relatively fragile machines such as
PDAs that have a screen-based
interface. These are fine in the lab,
but fail in the field. While learning
new technology on the job is not
ideal, specialists will be open to new
technology if they can see a clear
benefit from it, if it is reliable and
easy to use, and if it is suitable for
their working environment.
This digital pen and paper system
is a rare example of an interface
that in no way resembles a web
browser. Most demonstration
projects use web-like interfaces,
but as discussion at this workshop
showed, rectangular boxes on
screens are not necessarily the
best way of working with and
thinking about e-Science tools. The
e-Dance project will be going on
to look at some of these issues
– scale and immersiveness, and
the degree to which technology is
made transparent or obvious – in a
performance context, but the results
could spin out to wider technological
development. The big barrier,
though, is the fact that new types
of interfaces can be very expensive
to develop to the point of pervasive
availability: the money that has
been put into developing Windows
and MacOS dwarfs the budget of
any e-Science project.
Despite limited resources, the
arts and humanities are doing
impressive work in e-Science.
That was Malcolm Atkinson’s
assessment in his closing remarks,
when he described the great
variety and complexity of the data
that arts and humanities projects
are successfully dealing with.
This eSI theme is a first step on
an adventure that has its share
of risks, but that can lead to
immense opportunities. Working
together, with a shared vision and
shared agendas, researchers
and practitioners in the arts and
humanities can achieve a decisive
cultural change.
Slides from this event can be
accessed from
http://www.nesc.ac.uk/esi/
events/879/
www.nesc.ac.uk
Issue 61, June 2008
Crossing Boundaries: Computational Science, E-Science
and Global E-Infrastructures
8th – 11th September 2008 in Edinburgh, Scotland
http://www.allhands.org.uk/2008/conference/venue.cfm
Early Bird Registration is now open until: 13th July 2008. Any registrations received from 14th July 2008 will
incur a late fee of £50.
AHM 2008 is the principal e-Science meeting in the UK and brings together researchers from all disciplines,
computer scientists and developers to meet and exchange ideas. The theme for this year’s meeting is Crossing
Boundaries: Computational Science, E-Science and Global E-Infrastructures. Professor Peter Coveney (UCL) has
been appointed as Programme Chair.
For more details about the event, see:
http://www.allhands.org.uk/
The general format of the meeting will include cross-community symposia (kicked off by invited key speakers) and
workshops. For more details about the workshops, see:
http://www.allhands.org.uk/2008/programme/call.cfm
Applying e-Science to Environmental Problems
The Cardiff School of Computer Science is taking on a key role in a European initiative to combat human-induced
extinction of plant and animal species the world over.
Some estimates put the rate of loss of species due to man-made habitat destruction at tens of thousands per year.
Named the “sixth extinction crisis”, it follows five earlier mass extinction events, including extinction of the dinosaurs,
that have occurred during the course of the Earth’s 4.5 billion year history. It is not only species loss that causes a
problem. Invading species, such as Rhododendron and Japanese Knotweed, introduced by the Victorians, and the
more recent American Crayfish, are also having an impact on biodiversity. The consequences are serious for the
environment, for the economic and social aspects of sustainable development, and ultimately for human quality of
life.
The Cardiff School of Computer Science has now become a key executive partner in the planning for Lifewatch – an
ambitious 15-20 year programme to construct and operate a Europe-wide infrastructure for biodiversity research,
supporting policy and decision-making in all member States. The School was selected for its reputation gained in
e-Science, the BioDiversity World project and several European Framework Programme projects in biodiversity
informatics.
A three year preparatory project to establish the necessary financial and legal frameworks and to undertake the
technical planning of the construction was launched recently at the Nemo Science Centre in Amsterdam. Staff
from the School of Computer Science will play key roles in setting the technical strategy and planning for the
infrastructure, ensuring service relevance and technical interoperability across national borders and compatibility
with the emerging European Grid and with other major biodiversity information facilities.
Alex Hardisty, Manager of the Welsh e-Science Centre in the School of Computer Science, said:
“Joining the Lifewatch consortium is well-deserved recognition of Cardiff’s collective expertise in e-Science as
applied to problems in biodiversity. We have the opportunity to play a substantial role and look forward to working
closely with our European partners to bring the Lifewatch vision to fruition.”
For more information about Lifewatch, see: http://www.lifewatch.eu/
NeSC News
www.nesc.ac.uk
Issue 61, June 2008
e-Science
Institute
NGS Wants You!
The NGS has just launched a user
survey to which everyone who has
ever used the NGS is invited to take
part. The survey is quite short and
will only take around 5 minutes to
complete. We would like to find out
what users think of the services we
currently offer, how frequently they
use them and what improvements
we could make to the current service.
A report will be produced from the
results of the survey and it will be
available from the NGS website in
due course.
ClearSpeed Cluster
at the NGS
If you would like to take part in the
Serving your NGS
survey please go to:
http://www.zoomerang.com/Survey/?p=WEB227TRL65SMP
The NGS will soon be offering a
ClearSpeed 4-node cluster which
will be based at the University of
Oxford core node. There will be
extensive support for the LAPACK
(Linear Algebra Package) and BLAS
(Basic Linear Algebra Subprograms)
mathematical libraries, making it
ideal for Monte Carlo simulations.
There will be dedicated support to
help NGS users get up and running
on this node.
If you are interested in being one
of the first to use the cluster, then
please contact the helpdesk:
support@grid-support.ac.uk
NGS Roadshows
A quick reminder that the NGS is still keen to hear from people who would
like a NGS roadshow at their institution. The roadshows consist of a series
of short presentations, followed by lunch (provided by the NGS) and an
exhibition of NGS demos. NGS certificates can also be distributed at these
events enabling people to leave and access the NGS resources straight
away.
If you are interested in hosting a workshop, please contact:
Gillian.sinclair@manchester.ac.uk
NGS Upcoming Diary
The 4th international conference on e-Social Science, organized by the
ESRC National Centre for e-Social Science (http://www.ncess.ac.uk), is
taking place on the 18th – 20th of June and the NGS will be exhibiting. We
will hopefully be able to offer people NGS certificates to “take away” at the
conference so if you are planning on attending, please bring photographic ID
and USB pen with you.
The NGS will also be exhibiting at the 26th Eurographics UK conference
(http://www.eguk.org.uk/) where again we hope to be able to give out
certificates to those people who are interested in trying the NGS for the first
time.
NeSC News
NGS at OGF
OGF23, OGF-Europe’s first
international event was held in
Barcelona, Spain from the 2nd
– 6th of June. The NGS was well
represented at OGF, with NGS staff
present in the security, accounting
and data working groups and
research groups. David Wallom,
technical director of the NGS,
represented the NGS at the Grid
Interoperability NOW sessions and
gave a presentation at a workshop
on energy efficiency and Grid.
More information on the conference
can be found at:
http://www.ogf.org/OGF23/.
www.nesc.ac.uk
Issue 61, June 2008
e-Science
Institute
Take up Thy Data Grid and Walk
By Iain Coleman
“If you build it, they will come.” But what if they don’t? e-Science is hardly the first new technology movement to face
the challenge of achieving widespread adoption, but the defining characteristics of e-Science make the path to wider
uptake particularly treacherous.
The e-Science Institute theme on Adoption of e-Research Technologies is dedicated to understanding how
e-Science can become a pervasive infrastructure that researchers take for granted. The latest workshop in the
theme, “Fostering e-Infrastructure: from user-designer relations to community engagement”, held at eSI on 8-9 May,
brought together researchers with representatives of current initiatives aimed at improving the uptake of e-Science.
The workshop kicked off with a wide-ranging discussion, led by theme leader Alex Voss. He highlighted a major
problem in the mismatch between traditional user engagement strategies and e-Science. The normal model
of engagement is based on well-described systems serving well-defined purposes, whose users are small,
homogeneous groups with closely aligned interests. This is a good model for industry, but not for research. While
cultures vary somewhat from one discipline to another, most research that might employ e-Infrastructures involves
loosely coupled groups of collaborators whose interests are only partially and temporarily aligned, and both the goals
of the work and the systems that are used can shift as the research agenda develops.
So e-Research challenges the traditional systems engineering approach to development and user engagement.
The question is: what to put in its place?
Paths to wider uptake can be plotted on two axes: Deepening and Widening. Deepening comprises the grand
research challenges, high performance computing, grids and custom-made applications for exceptional tasks.
Widening involves the widespread use of common tools for a variety of everyday uses, including the social grid and
the cluster of technologies that come under the heading of Web 2.0. Data analysis for the Large Hadron Collider sits
solidly on the Deepening axis, while geo-tagging photos on Flickr is a prime example of Widening. Historically,
e-Science began with a deepening approach, and is now being challenged by widening technologies.
The key point is that these are orthogonal concepts. Web 2.0 plus cloud computing is not going to solve the grand
challenges, any more than high performance computing will enable people to display wedding photos to their old
high school chums. The whole IT community is struggling with the divide between providing sophisticated tools for
specific purposes, and creating generic easy-to-use tools. Both approaches may have their place: a research group
might well do demanding calculations on the grid, and use Web 2.0 tools to communicate with one another.
But simply analysing all these possibilities doesn’t provide a concrete strategy for increasing uptake of e-Science.
For that, we need to look at the projects that are working right now to determine how more researchers can be
encouraged to get involved with these new technologies.
The National Grid Service (NGS) has been implementing its outreach plan for nearly a year now, following a multipronged strategy that runs from mailing lists to newsletter articles to conferences and roadshows. Gillian Sinclair,
NGS Liaison Officer, described how her work is evolving, from a public relations, profile-raising exercise to a more
targeted engagement programme aimed at specific communities and research groups. One successful tactic has
been generating NGS user certificates on the spot for interested parties at conferences, and handing it to them on a
memory stick. This helps to overcome one of the great hurdles: many people are interested in grid computing when
they hear about it, but then get back to the office and never get round to the process of applying for a certificate.
More barriers to entry have been identified in questionnaires run by the Joint Information Systems Committee
(JISC) e-Uptake Project. Elphini Fragkouli explained how responses from a wide range of researchers and service
providers have shown that lack of awareness is only one of the obstacles to wider use of e-Science. More training
and documentation are needed, tools need to be usable and well supported, and the technology needs to work with
existing systems: not just local infrastructure, but established disciplinary cultures and research practices. Finally,
users have to be confident that the technology is sustainable in the long term.
Sustainability also came up as a key issue for the OMII-UK ENGAGE Initiative, a project to develop better use
of e-Infrastructure through community engagement. Neil Chue Hong, the Director of OMII-UK, reported how a
programme of interviews with selected e-Science users and potential users brought up sustainability of software
and infrastructure, training, and dissemination of information as crucial common issues. Other questions also arose,
concerning the security of confidential data on the grid and how best to persuade people to make the shift from
desktop to grid infrastructure.
(continued on page 6)
NeSC News
www.nesc.ac.uk
Issue 61, June 2008
Take up Thy Data Grid and Walk
By Iain Coleman (continued)
One of the problems inherent in all this work is that the easiest people to interview are those who are already using
e-Science technologies. It is harder to get hold of people who are interested potential users, and even more difficult
to engage with those who are wholly unengaged with e-Science. Even if some of these researchers are inspired to
try out e-Science, it is not always clear how to transform that initial enthusiasm into sustained use of the technology.
While case studies and demonstrators are useful, tools have to be taken beyond the demonstrator stage if people
who are interested in using them in their own research are to be able to do so without becoming frustrated – and
perhaps giving up on e-Science as a bad job.
Ultimately, though, the real key to increased uptake is having researchers who exploit the full potential of e-Science
to do new, exciting research that couldn’t be done without this technology, and who then tell their colleagues and
peers that they used e-Science to do it. This needn’t mean active proselytising: it can simply involve the researchers
mentioning in their papers that they used, say, NGS, or putting the appropriate logos onto the posters and
presentations that show the results of their e-Science based research. Even achieving this takes considerable effort
on the part of those involved in outreach and engagement, but the more e-Science is seen to lead to real results and
real papers on the cutting edge of research, the more researchers will be eager to try it out for themselves.
Slides from this event can be accessed from http://www.nesc.ac.uk/esi/events/880/
Data Sharing in the Biosciences: A Sociological Perspective
Date: 26th June 2008, 10:00 am – 5:00 pm
Location: National e-Science Centre, Edinburgh
Web page: http://www.genomicsnetwork.ac.uk/innogen/events/workshops/title,3589,en.html
The aims of this workshop are: to explore the changes in the generation, utilisation and governance of information in
the biosciences; to consider the implications of these changes; and to provide advice as appropriate. The workshop
will bring together scientists who deal with data sharing issues in their own research (in biology and other relevant
disciplines), and social scientists who are studying the impacts of data sharing on scientific practices.
The last decade has seen the generation of increasing quantities of biological data, driven in part by large-scale
research efforts such as the human genome project and assisted by advances in automated analysis. Researchers
are increasingly likely to be utilising datasets produced elsewhere. These developments mean that life scientists
must develop new rules and governance procedures to do with the release and sharing of information, and with the
standardisation of data, models and experimental protocols. Additionally, public funders of research have introduced
data sharing policies that scientists are obliged to follow. These changes have consequences for research practices
and for the knowledge that is produced. This workshop will explore these issues by addressing questions such as:
•
What have been the major developments in the role of information technology and data sharing in the biosciences over the last decade?
•
What examples are there of emerging experience in working with biological data, and what changes has this brought about?
•
What implications do these changes have for scientific practice, community behaviour and associated infrastructures? (For example, will we see the dominance of ‘dry’ over ‘wet’ biology?)
•
Can experiences in other research sectors (e.g. cosmology, particle physics and climatology) throw light on potential upcoming challenges for the biosciences? Do they have useful experiences or tools that could be translated into bioscience?
This workshop is sponsored by the Biotechnology and Biological Sciences Research Council, in collaboration with
ESRC Centre for Social and Economic Research on Innovation in Genomics (Innogen).
There is no charge for this workshop, but places at the workshop are limited. Please send expressions of interest to
Robin Williams, Jane Calvert or Jef Grainger using this email address: research-data-workshop@lists.ed.ac.uk
NeSC News
www.nesc.ac.uk
Issue 61, June 2008
Calls for Proposals for the 4th DEISA Extreme Computing
Initiative
The DEISA Extreme Computing Initiative (DECI) is an
excellent way to gain access to a large amount of HPC
cycles. Last year’s call saw seven UK DECI projects
granted a total of over 3.2 million hours on a variety of
platforms spread across Europe. Indeed, the DECI not
only gives you cycles but has people available to help
you exploit the DEISA infrastructure.
The DEISA infrastructure results from the integration
of national HPC infrastructures employing modern
Grid technologies. DEISA contributes to a significant
enhancement of HPC capability and capacity in Europe.
The purpose of the DECI is to enhance the impact of
the DEISA research infrastructure on leading European
science and technology.
This initiative consists of the identification, enabling,
deploying and operating of Flagship Applications in
selected areas of science and technology. These leading,
ground-breaking applications must deal with complex,
demanding, innovative simulations that would not be
possible without the DEISA infrastructure, and which
would benefit from the exceptional resources of the
Consortium.
The DECI has now been expanded to include medium
to long term support for the enabling of important and
complex applications. The DEISA Infrastructure is
therefore ready to provide more sustained application,
enabling support to specific projects,, and to be involved
more deeply in the design of leading and innovative
complex simulations.
DEISA
relevance criteria. Priority will be given to proposals that
benefit from an excellence label from more than one
partner organisation. Proposals from PIs that have yet
to benefit from DECI compute resources will be given
preference.
Projects supported by DECI will be chosen on the
basis of innovation potential, scientific excellence and
Application Profiles Support
The following application profiles are particularly suited to the DECI:
•
Large, highly-scalable parallel applications requiring exceptional computational resources
•
Data-intensive applications requiring access to distributed data repositories
•
Workflow simulations: managing simulation chains that access more than one computing platform
•
Distributed applications that need to run loosely synchronously on more than one platform
DEISA is ready to provide support for the design and enabling of these applications. In some cases, this support can
entail a medium-term commitment of human resources for the application design and enabling work (i.e. an engineer
for several months).
Call for Proposals
The 4th DECI Call for Proposals is now open. The deadline for submissions is the 30th of June, 2008. The
application form is available via the DEISA website at www.deisa.eu.
Contact the Applications Task Force for support in the preparation of the proposal (email to: ataskf@deisa.org).
Upon submission, the proposals will first be technically evaluated by the Applications Task Force, who will determine
the technical requirements, the allocation of computational resources and the human resources required for the
long-term application enabling. The scientific evaluation of the proposals will be done by a number of National
Scientific Evaluation Committees, and they will provide recommendations to the Consortium on the proposal’s
scientific importance.
NeSC News
www.nesc.ac.uk
Issue 61, June 2008
e-Science
Institute
Forthcoming Events Timetable
June
17
HPCx 6th Annual Seminar
eSI
http://www.nesc.ac.uk/esi/events/891/
18
Novel Parallel Programming Languages
for HPC
eSI
http://www.nesc.ac.uk/esi/events/892/
19
Modelling and Climate Change research
Workshop
eSI
http://www.hss.ed.ac.uk/
climatechange/
26
Data Sharing in the BioSciences: A
Sociological Perspective
eSI
http://www.nesc.ac.uk/esi/events/899/
2
e-Science Directors’ Forum
NeSC
http://www.nesc.ac.uk/esi/events/870/
8-9
Third Workshop: Trusted Services:
Requirements and Prospects
eSI
http://www.nesc.ac.uk/esi/events/902/
17
EPSRC/TSB e-Science Projects Meeting
NeSC
http://www.nesc.ac.uk/esi/events/888/
31
PASTA Workshop 2008
eSI
http://www.nesc.ac.uk/esi/events/889/
July
Data Preservation Costs
The online executive summary and full report (pdf file) of the JISC-funded research data preservation costs study
titled “Keeping Research Data Safe: a cost model and guidance for UK Universities” is now published and can be
downloaded from the JISC website at:
http://www.jisc.ac.uk/publications/publications/keepingresearchdatasafe.aspx
The study has investigated the medium to long term costs to Higher Education Institutions (HEIs) of the preservation
of research data, and developed guidance to HEFCE and institutions on these issues.
The study uncovered a lot of valuable data and approaches and we hope this can be built on by future studies and
implementation and testing. The study makes 10 recommendations on future work and implementation. For further
information, see the Executive Summary online.
The report itself has chapters covering the Introduction, Methodology, Benefits of Research Data Preservation,
Describing the Cost Framework and its Use, Key Cost Variables and Units, the Activity Model and Resources
Template, Overviews of the Case Studies, Issues Universities Need to Consider, Different Service Models and
Structures, Conclusions and Recommendations. There are also four detailed case studies covering the Universities
of Cambridge, King’s College London, Southampton, and the Archaeology Data Service (University of York).
Although focused on UK universities in particular, it should be of interest to anyone involved with research data or
interested generally in the costs of digital preservation.
Comments and feedback via the blog at:
http://blog.beagrie.com/archives/2008/05/14/just-published-research-data-preservation-costs-report/
Comments are also welcome via email to: info@beagrie.com
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 Katharine Woods. Layout by Jennifer Hurst.
email kwoods1@nesc.ac.uk
The deadline for the July 2008 Newsletter is: 24th June 2008
NeSC News
www.nesc.ac.uk