The monthly newsletter from the National e-Science Centre
NeSC News
Issue 67 March 2009 www.nesc.ac.uk
UK e-Researchers aid efforts to understand climate change
By Simon Hettrick, OMII-UK and Phil Kershaw, NERC DataGrid.
Providing decision makers with information about the potentially disastrous effects of climate change is the role of the
IPCC (Intergovernmental Panel on Climate Change). Attaining new levels of detail and precision in their predictions
requires access to ever greater volumes of data. This challenge is being aided by expertise developed by the Natural
Environment Research Council Datagrid (NDG) during an OMII-UK funded project.
The IPCC would like researchers to have access to fifteen-hundred terabytes of data – fifty-times more than previously
available. Storing this data volume using conventional methods would be difficult, so e-Research solutions are being
exploited. Namely, a distributed archive based on the pooled resources of the British Atmospheric Data Centre,
the World Data Centre for Climate in Germany and a US federation led by the PCMDI (Program for Climate Model
Diagnosis and Intercomparison). Fifteen-hundred terabytes of data represents a substantial amount of research and
funding. It is no surprise then, that the
data producers and funding agencies
want some oversight over who is using
the data, and for what purpose.
Securing access across organisational
boundaries in a way that is transparent
to users presents many significant
Muir Glacier, Alaska, in 1941 and 2004. Images
courtesy of National Snow and Ice Data Center/World
Data Center for Glaciology, Boulder, Colorado
challenges. The NDG project has already addressed these
challenges in its OMII-UK funded security solution: NDG
Security. This software provides authentication of a user’s
identity and authorisation of their rights over distributed
resources. The NDG Security team are now applying their
expertise in a collaboration with the US Earth System
Grid (ESG)—the team responsible for developing the IPCC’s distributed archive. The collaboration has agreed
on a standards-based approach for secure distributed access. ESG software will form the heart of the distributed
archive, and the ESG group of Earth Science research centres will form a natural extension of the core data archive.
The security solution adopted for the NDG/ESG collaboration will facilitate the inclusion of other institutions into the
consortium, whether they are from Europe, the US or elsewhere.
NDG enables scientists to discover, access and visualise data that spans data-provider organisations. Secure
access is key: without it, some providers would not publish their data. NDG Security is easy to deploy and maintain,
and flexible so that partner organisations do not have to change their pre-existing infrastructures. It supports Single
Sign On, and a system of access-role mapping, which enables federated access to data whilst respecting existing
role structures at individual sites. Use of the Python programming language provides a familiar and easy-to-use
environment for the user base. NDG is used by some of the major UK data centres, such as the British Atmospheric
Data Centre and the British Oceanographic Data Centre. Recent funding from OMII-UK has greatly enhanced the
interoperability of NDG Security, perfectly placeing it for the current interoperability work with the Earth System Grid.
This is an example of what e-Research does well: complex problems, huge data sets and multiple users all dealt with
efficiently. It is also a vindication of the open-source model for funding, with money invested in one project creating
expertise that can be re-used in others. If we are to prepare for climate change, it is vital that we have accurate
information about the potential changes that we may encounter—e-Research may be the key to that information.
Issue 67, March 2009
Electronic pioneers of the ancient world
By Iain Coleman
It was the edge of the world. To
the ancient Greeks, the Black Sea
coast was as far east as you could
go without meeting the sunrise. A
land of amazons and sorceror-kings,
the mysterious home of the Golden
Fleece.
In time, they colonised the region,
establishing settlements all round the
Black Sea coast and encountering
the nomadic population of the
Eurasian steppes. Unfortunately
for historians, they left behind few
written records.
That’s where epigraphy comes in
– the study of stone inscriptions. It’s
an important tool for archaeologists
in general, but particularly here
where the inscriptions form the bulk
of the evidence about how people
lived their lives. Thanks to extensive
excavation by Russian and Ukrainian
archaeologists, more inscriptions
are being discovered every year.
The question is, how best to
record, present and understand this
material?
The workshop on Enhancing
and Exploring Epigraphic and
Archaeological Data through eScience, held at the e-Science
Institute on 10 February, brought
researchers working on the
IOPSE project (Inscriptiones Orae
Septentrionalis Ponti Euxini: Ancient
Inscriptions of the Northern Black
Sea Coast) together with researchers
in related fields, both historical and
computational.
The first data sets of Greek
inscriptions from the northern Black
Sea region were established in
the late nineteenth century. Even
then, data volume was a problem.
No sooner had the first corpus
been published than a new edition
was needed, as so many new
inscriptions had been excavated
in the meantime. The problem has
only continued to grow, as Askold
Ivantchik (Russian Academy of
Sciences) explained. The next step
is to create a new corpus, building
on structures established in earlier
NeSC News
work, and to digitise it. This includes
re-examining the stones described
in earlier corpora, where possible.
Earlier descriptions often omitted
very small inscriptions, and graffiti.
Scholars now recognise these as
valuable sources of information in
themselves – although the sheer
quantity of graffiti can be intimidating.
This modern approach of recording
as much information as possible
makes publishing it in book form
prohibitively expensive. This is
where epigraphy meets e-Science.
Gabriel Bodard and Charlotte
Roueché (Kings College London)
showed how the EpiDoc project
allows epigraphers to use markup
languages such as XML to create
electronic editions with much more
content than can be included in a
printed edition. They emphasised
that scholars cannot simply hand
over the technical side of this work
to IT specialists: decisions about
how to mark up the text – this is a
word, this is a name, and so on – are
fundamentally academic decisions,
and scholars need to at least be
familiar enough with the markup
language to retain intellectual control
over the process.
In principle, this shouldn’t be too
much of a problem. Epigraphers have
already mastered ancient history,
Greek and Latin, palaeography,
multiple modern languages and
the scholarly conventions of their
field. Compared to all this, XML
should be no trouble. Still, many
epigraphers are reluctant to get
involved in computing. The biggest
stumbling block is not knowing other
people who are doing it – a problem
this workshop was intended to
overcome. There is also a tendency
in this and other fields of scholarship
towards working in solitude and
carefully guarding the results, quite
the opposite of the collaboration
and sharing that is at the heart
of e-Science. The ability to share
information and knowledge more
freely, with comment and annotation,
may bring about a change in the
working practices within epigraphy.
Creating a new, well structured and
annotated data set is one thing, but
what about all the information that
has already been collected and
catalogued over the past century
or more? Mike Jackson (EPCC)
introduced the LaQuAT project
– Linking and Querying Ancient Texts
– which aims to provide new tools
and layers in front of existing data
sets, so that scholars can easily run
queries across multiple databases in
a single operation. Integrating varied
databases with different structures,
different languages and even
different character sets poses many
technical challenges. The end result
will be complementary to the EpiDoc
approach of altering the underlying
data format, and the two approaches
can work together.
All of this work should enable
epigraphers to exploit fully the
advantages of electronic publication.
Books are limited in size, with
information limited or abbreviated
to fit a maximum page count, and
specialist texts may only exist in a
hundred large libraries across the
globe. An electronic version can hold
an effectively unlimited quantity of
data, and is accessible to scholars in
smaller or more remote institutions.
Electronic publishing also allows new
kinds of information and structure to
be used: multimedia presentations
and interactive images can give
scholars new ways of seeing the
objects in question, while hypertext
allows easy navigation within a text
and between different texts, which
can produce new connections and
insights.
This is a new way of working for
the epigraphy community, but this
meeting showed that many scholars
are seeing the ways e-Science can
enhance their work, and are willing,
like the Greek colonists on the Black
Sea coast, to take a bold move
into new and previously mysterious
territory.
Slides and other material from this
event can be downloaded from http://
www.nesc.ac.uk/esi/events/964/
www.nesc.ac.uk
Issue 67, March 2009
£5M awarded to found the Numerical Algorithms and Intelligent
Software Centre (NAIS)
A new research centre will develop the mathematical foundations of innovative tools for scientific and engineering
computation on multiprocessing high-performance computers. The Numerical Algorithms and Intelligent Software
centre (NAIS) is a collaboration between Edinburgh, Heriot-Watt and Strathclyde universities. It is supported by a £5m
grant from EPSRC.
EPCC will play a crucial linking role in the centre, applying novel tools and techniques to real computational
applications. The combination of algorithmic advances and the massive computational power of parallel
supercomputers will allow simulations to be done at previously impossible levels of scale, complexity and accuracy.
NAIS aims to place UK researchers in an ideal position to fully exploit national supercomputer systems such as
HECToR.
NAIS’s expertise will be drawn from many areas of scientific computing and numerical analysis and will include 4
lectureships, 8 postdoctoral research fellowships and 24 postgraduate research studentships.
For more information on NAIS, see: www.nais.org.uk.
DCC Digital Curation
101 Workshop
10-12 March 2009, London
The majority of scientific research
is carried out through short-term,
funded projects. Accordingly,
principle investigators and
researchers are constantly on the
lookout for new funding opportunities
to continue their research activity.
This, coupled with often limited
staffing resources, has meant that
data management and curation
activities have not always been
given a high priority within research
projects. However, research councils
and funding bodies are becoming
increasingly aware of the value of
sharing and reusing data and now
require evidence of provision for data
management and curation in new
grant funding applications. To assist
researchers in developing sound
data management and curation
plans, we developed this workshop
to provide an introduction to digital
curation and the activities that should
be considered when planning and
implementing new projects.
Using our DCC Curation Lifecycle
Model [PDF] as a reference point,
this course will employ lectures
and practical exercises to equip
participants with both a theoretical
underpinning of digital curation
issues and hands-on experience in
applying the lessons learned.
NeSC News
EPCC Spring Training Courses
EPCC will be running a series of courses in various aspects of High
Performance Computing during April, May and June.
These courses are open to anyone at the University of Edinburgh, members
of the EUFORIA project (and researchers in Fusion Science) from anywhere
in Europe, and to visitors to EPCC through the HPC- Europa project. The
course timetable is given below. The course material is based around the
corresponding courses from our MSc in High Performance Computing.
21-23 April: Fundamental Concepts of HPC 28-30 April: Tools & Techniques
for HPC Programming
05-07 May: Shared Memory Programming
w/c 11 May: no courses
20-22 May: Message Passsing Programming
26-28 May: Practical Software Development
02-04 June: Applied Numerical Algorithms
The courses are free, but please note that attendees will be responsible for
their own travel, accommodation and meals.
To book, please send an email to epcc-support@epcc.ed.ac.uk which should
include your name, the course(s) you wish to attend and your affiliation (UoE
/ EUFORIA / HPC-Europa).
Participants will gain an
understanding of the range and
nature of data management and
curation activities that should be
considered when planning new
research projects, and will be better
equipped to develop and implement
sound data management and
curation plans for future research
funding bids.
The target audience for this
workshop is researchers with
funding body data management
and curation mandates to fulfil and
information management specialists.
A key goal is the integration of these
communities of practice to share
their experiences and to identify
where, when and how they could
best cooperate to meet data curation
challenges.
To register, please go to
http://www.dcc.ac.uk/events/digitalcuration-101-2009/.
www.nesc.ac.uk
Issue 67, March 2009
Coveney ‘makes it happen’
The IET Knowledge Network recently published a list of ‘The people who make it happen’, and included the following
piece on Professor Peter Coveney of UCL:
Among the many distinguished hats that Professor Peter Coveney dons for his work at University College London is
director of the Centre for Computational Science, where pioneering work is underway to use the combined processing
power of the US and UK supercomputer Grids to simulate the effect of drugs on human metabolisms.
Last year Coveney’s team in UCL’s Department of Chemistry tested the efficacy of an HIV drug in blocking a key
protein used by the virus, using the Virtual Physiological Human (VPH)
initiative, which aims to simulate patient profiles against drug options to
determine which treatment should prove most effective.
Nine drugs are currently available to inhibit HIV-1 protease, but with standard
procedures doctors have no way of matching a drug to the unique profile of
the virus as it mutates, and have to rely on trial-and-error methods to find the
best match to a patient’s genotype.
Using a sequence of simulation steps performed across multiple
supercomputers on the UK’s National Grid Service and the US TeraGrid, VPH
simulations were run to predict how strongly the drug Saquinavir – an HIVinhibitor – would bind to three resistant mutants of HIV-1 protease – a protein
produced by the virus to propagate itself. These protease mutations are
associated with the disease’s resistance to Saquinavir.
Peter Coveney
The VPH study is a first step towards the ultimate goal of ‘on-demand’
medical computing, where doctors could borrow supercomputing time from
Grids to make critical decisions on life-saving treatments.
More recently Coveney has been behind a group of projects generically based on ‘Genius’ – Grid-enabled
neurosurgical imaging simulation. One application of this system traffics brain scans to a network of supercomputers,
the combined processing power of which generate a 3D model of the blood flow patterns in a patient’s brain
vasculature.
Using software written by Coveney and UCL student Marco Mazzeo, the system then displays representations of
critical blood vessel parameters. These models, generated just before an operation, would also let doctors test the
outcome of an intervention before doing it.
IEEE International
Workshop on Security in
e-Science and e-Research
Chengdu and Jiuzhai Vally, China,
10-12 August 2009
In recent years, the influence of
e-Science and e-Research has
grown considerably and their scope
of application now covers many
research domains. Supporting eScience and e-Research often places
numerous demands on capabilities
associated with e-Infrastructures.
One key challenge is security.
This workshop will provide a forum
for people working on security issues
associated with e-Science and eResearch to exchange ideas and
share experiences. The workshop
has emphasis on establishing a
state of the art for security in e-
NeSC News
Influence and Impact of Web 2.0 on e-Research
Infrastructure, Applications & Users
NeSC, March 23-27.
The number of Web 2.0 services and applications in use by Internet users,
academics, industry and enterprise, is growing rapidly. These technologies
and services are based on the open standards that underpin the Internet
and Web, and are used in many forms, e.g. blogs, wikis, mashups, social
websites, podcasting and content tagging. This field is having a significant
impact on distributed infrastructure and applications, and on the way users
and developers interact. The area needs to be thoroughly investigated and
understood to encourage the development of new services and applications
for e-Research.
More information is available here: http://www.nesc.ac.uk/esi/events/968/
Science and e-Research, identifying
challenges and discussing solutions
for successfully enabling security for
e-Science and e-Research.
the practical application of security
models and solutions in e-Science
and e-Research. The deadline for
submissions is 5 April 2009.
We invite original papers on a wide
spectrums of topics as well as reports
of experiences and case studies on
For further details and the CFP
please see: http://personalpages.
manchester.ac.uk/staff/wei.jie/
conference/issr2009
www.nesc.ac.uk
Issue 67, March 2009
Hardware updates at Glasgow
The NGS partner site, the University
of Glasgow, has recently updated
its hardware. The site now has
Supermicro servers which are
configured as Grid worker nodes.
Each server has two motherboards
(i.e. 2 worker nodes) with 2 Quadcore, 64bit CPUs (running at 2.5GHz)
per motherboard to give a total of
1360 cores.
In terms of Grid storage, they have
20 Supermicro disk servers, each
hosting 20TB of useable storage
in a RAID 6 configuration, to give a
total of 400TB space. This recent
upgrade means that Glasgow is now
the largest GridPP facility in terms of
raw computing power (measured in
kSI2K) available to the Grid.
Photograph: Andy Elwell (Formerly at Glasgow as Data Management Expert); Mike Kenyon (ScotGrid Systems
Manager); Prof. Tony Doyle (Physics & Astronomy at Glasgow University); Dave Power (Viglen Engineer)
Computational Carbohydrate Chemistry workshop
The NGS is pleased to be one of the supporters of a week long workshop
organised by the University of Westminster who are a NGS partner site.
Organised by the ProSim project, (a project funded through the JISC Engage
initiative; www.engage.ac.uk), the workshop aims to train participants on
how to run in silico experiments using AMBER, CHARMM and AutoDock.
More importunately, from the NGS view point, it will also teach bioscientists
how to model carbohydrate binding proteins and their ligands on the NGS to
decrease execution times of experiments using a web-based graphical user
interface (GUI), which was developed within the framework of the ProSim
project.
The event will take place from the 20th – 24th April 2009 at the Cavendish
Campus of the University of Westminster, London. The training will be led
by Dr. Ross Walker, SDSC, USA and Dr. Michael Crowley, NREL, USA who
are both members of the development team for AMBER and CHARMM and
Dr. Martin Frank, GCRC, Germany who has experience of using AutoDock in
modelling protein-carbohydrate recognition.
For further details, including how to apply for a place at the workshop, please
visit the event website at https://engage.cpc.wmin.ac.uk/workshop
NeSC News
NGS User Survey Report
Over the summer of 2008, NGS
users were invited to participate
in the first ever user survey.
The survey was carried out on
the recommendation of the NGS
Review Board users in order to
ascertain the usage, type of usage
and feedback about the NGS in
general.
The results of this survey are now
available from the NGS website. If
you have any comments or queries
regarding the survey then please
contact the NGS Liaison Officer
through the NGS helpdesk.
www.nesc.ac.uk
Issue 67, March 2009
2nd BELIEF-II international symposium - 16th & 17th July 2009,
São Paulo, Brazil
Future trends and e-Infrastructures application: towards sustainable development
e-Infrastructures are always about development of new knowledge, but the impact of this to the development of
economies and societies in emerging economies is potentially a much steeper growth curve.
Education or health applications may need to be more targeted towards ensuring primary care or education in rural
areas for example, rather than collaborating with developed world researchers in pioneering new drugs, or analysing
patient data. In a sense, the benefits of adopting e-Infrastructures are whatever we want them to be. Each region will
have a different strategic priority for e-Infrastructures applications, but the result will always be - if the planning and
implementation is effective – societal and economic development.
For the aforementioned reasons the 2nd BELIEF International symposium will focus on “e-Infrastructures and
Sustainable Development”. The event will be opened by representatives from the Government of São Paulo and from
the EC Delegation to Brazil. It will engage experts from the areas of eHealth, eEducation, and eScience in order to
discuss and understand in deeper detail what has already been done in terms of sustainable development by adopting
e-Infrastructures and the necessary future steps to be addressed and taken into account by policy makers and
decisions makers.
Participation is free of charge. For more information please contact info@beliefproject.org
Forthcoming Events Timetable
March
18
MIDAS - SINAPSE Meeting
eSI
http://www.nesc.ac.uk/esi/events/954/
23-27
Influence & Impact of Web 2.0 on eResearch Infrastructure, Applications and
Users
NeSC
http://www.nesc.ac.uk/esi/events/968/
30-3 April
Symposium on Provenance in Software
Systems
eSI
http://www.nesc.ac.uk/esi/events/955/
2
OGSA-DAI-4 Kick Off Meeting
NeSC
http://www.nesc.ac.uk/esi/events/977/
7
eSI public lecture: “Adding Semantics to
Geographic Data Models”
eSI
http://www.nesc.ac.uk/esi/events/981/
16-17
e-Science - The changing landscape
NeSC
http://www.nesc.ac.uk/esi/events/965/
20
Use cases for provenance
eSI
http://www.nesc.ac.uk/esi/events/983/
April
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
The deadline for the April 2009 issue is March 20, 2009
NeSC News
www.nesc.ac.uk