The monthly newsletter from the National e-Science Centre
Issue 68 April 2009
www.nesc.ac.uk
The last week of March saw a packed lecture theatre at the e-Science
Institute, with over 100 people attending a five day workshop on ‘The
Influence and Impact of Web 2.0 on e-Research Infrastructure, Applications and Users’.
Run by Professor Mark Baker, a research professor of computer science at the University of Reading, the workshop looked at the rapid growth in Web
2.0 services, the ways these are used, and at the impact such tools have on infrastructure, applications and users.
A full report on the conference will be included in the May issue of NeSC news.
In the meantime, slides and other material can be downloaded from www.
nesc.ac.uk/action/esi/contribution.cfm?Title=968, and a Twitter feed, as attendees ‘tweeted’ live from the conference, can be found under Twitter search feed #research3 (http://search.twitter.com/search?q=%23research3).
Prof. Mark Baker
Two Theme Issues of Philosophical
Transactions of the Royal Society of
London (Series A), to be published on May 15 and June 1, 2009, will contain the proceedings of the UK e-
Science All Hands Meeting 2008.
The meeting was held in Edinburgh on September 8-11, 2008, attracting
250 contributions (a record number) and 527 participants.
Professor Peter Coveney, director of the Centre for Computational
Science at UCL, was chair of the conference in 2008, under the theme
“Crossing Boundaries: Computational
Science, e-Science and Global e-
Infrastructure”. The title emphasised the intended interdisciplinarity of the meeting, as well as the nature of its principal technical challenges.
“A major goal of the meeting was to ensure we realised a good balance between scientific (‘applications’) and computer science aspects of e-
Science. (We use the word ‘scientific’ here in the widest sense, embracing digitally enabled activities in the Arts
& Humanities.) We sought to foster a genuine synergy between computer scientists, computational scientists and researchers in all domains, achievable by facilitating access to, and exploitation of, all kinds of distinct resources across disparate administrative boundaries,” say
Professor Coveney, and e-Science
Envoy Professor Malcolm Atkinson, in a joint introduction to the themed issues.
“The resources required to change the scientific game are extremely heterogeneous -- they include software, middleware, compute, data, storage, visualisation, networks, information, digital sensors and digital communication – and are geographically widely distributed, generally residing within diverse administrative domains: all need to be made available to users transparently and on demand if e-
Science is to have its much heralded impact. The outcome from such an undertaking is clear and substantial: new, faster, better and different science than has been possible before,” say Coveney and Atkinson.
Reviewing the vast number of submitted papers took place in two phases: initially, the papers submitted as extended abstracts to the Conference itself were reviewed, on the basis of which a selection of fifty-four full contributions was invited; those manuscripts were then subjected to rigorous peer review, leading to the set of 30 articles which are being published in the two backto-back Theme Issues.
“Only just over ten per cent of the papers originally submitted to conference made it through to the proceedings which, by itself is indicative of the quality of the manuscripts to be found within these pages,” say Coveney and Atkinson.
A list of the papers and abstracts can be seen here: http://www.allhands.
org.uk/archive/2008/programme/ proceedings.html

Issue 68, April 2009
By Iain Coleman
Medical imaging – MR scans, CT scans and so on – is incredibly valuable to doctors trying to treat serious illnesses, from cancer to strokes. It also enables medical researchers to understand the inner workings of our bodies in much more detail and certainty than ever before.
The problems arise when these two ways of working collide. In an ideal world, the clinicians’ priority of treating the patient in front of them, and the researchers’ need to amass patient data for statistical studies would mesh smoothly together. In practice, formidable obstacles can appear, from data infrastructure issues to the need to preserve patients’ privacy. train imaging researchers for the future and rationalise data management. Its main investment is in people rather than machines, providing academics and research students to meet the shortfall in skilled researchers.
The NHS has also been investing in people, but in data managers rather than researchers. Hamish McRitchie
(NHS Scotland) explained that the
The MIDAS - SINAPSE Meeting on
Research Medical Imaging Data in the University and the NHS, held at the e-Science Institute on 18 March, brought together specialists from the worlds of healthcare and academic research to make links across their respective boundaries, in the hope of exploiting the possibilities of medical imaging to the full.
The massive expansion in the use of medical imaging in recent years has occasioned a serious shortage of scientific specialists, as Joanna
Wardlaw (Edinburgh) explained.
The technology was seen as a very attractive clinical tool, but the investment in equipment was not matched by an investment in people.
As a result, a lot of imaging research is being carried out by people who are not trained to do it properly, and is performed on data sets that are too small for reliable statistics. This kind of work is unlikely to be effective.
national PACS (Picture Archiving and
Communications System) project is all about improving the efficiency of clinical care, upgrading infrastructure to deal with ever-increasing data volumes from medical imaging. Each image is currently retained for the life of the patient, plus three years.
With more and more use of imaging technology, the demands on data storage have increased much more quickly than was anticipated, and the cost of management and security is rising fast.
It was to solve these problems that
SINAPSE (Scottish Imaging Network
- A Platform for Scientific Excellence) was set up. This consortium of six
Scottish universities – Edinburgh,
Glasgow, Aberdeen, Dundee, St
Andrews and Stirling – is intended to bring together a critical mass of researchers and staff to conduct large-scale studies across multiple centres, disseminate best practice,
NeSC News
Crucially, this PACS project has no academic input, and its remit does not run to considering research requirements. It’s not unreasonable for an NHS project to focus on delivering patient care, but the accumulated mass of data is a
2 goldmine for researchers, and they can hardly be blamed for wanting to get hold of it.
Elizabeth McDowell (Edinburgh) presented a case study of how this can be done. The Clinical Research
Imaging Centre (CRIC) is a joint partnership between the NHS and the University of Edinburgh. This is being set up through the course of this year, and will feature a suite of scanners and analysis tools, with
NHS and university IT specialists working together to create a stateof-the-art facility for clinical and research work.
Working in partnership is far from easy. There are significant technical constraints, not just because of data volume, but also because different centres have different network models. A further problem is the need to respect the privacy of patients. Research data should be anonymised so that it cannot be used to identify individuals, which is easy to say, but not always easy to do. Some personal information is essential for research purposes, to see the effects of home location, lifestyle or genetics on particular illnesses – and sometimes the medical images themselves can be used to identify the patient. There is still a lot of work to do in agreeing data protection standards, either at a local or a national level.
Getting things done can be achieved in two ways: top down, or bottom up. If solutions to these problems are found at a local level, such as at
CRIC in Edinburgh, then these can be extended nationally. However, this approach can falter due to the need to overcome institutional inertia every time the scheme expands. The top down approach has its limitations too – the history of projects driven by political pressure to solve problems before clear solutions are available is littered with costly failures – but a high-level champion for the cause of data sharing can wield enough authority to sweep away barriers that would otherwise be insurmountable.
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NeSC News 2
Issue 68, April 2009
Cont.
The problems of data sharing between healthcare and academic research are substantial, but the will to make it happen is manifest.
By bringing researchers into NHS policymaking in this area, by identifying and disseminating best practice in the SINAPSE centres across Scotland, and by developing case studies of important research that is stymied by data sharing problems, the full potential of medical imaging can be realised. And that’s something we’ll all benefit from.
The DEISA Extreme Computing Initiative, or DECI, is an excellent way to gain access to a large amount of HPC cycles, for projects which are too large to run on a single National Resource.
DEISA, or the Distributed European Infrastructure for Supercomputing
Applications, consists of 11 HPC Centres across Europe, providing a pan-
European Grid of HPC resources. HPCx has been a platform within DEISA for the last 4 years and HECToR joined DEISA in May, 2008.
The DECI is a scheme through which European computational scientists can apply for single-project access to world-leading computational resources in the European HPC infrastructure, operated by DEISA, for up to 12 months.
Slides and other material from this event can be downloaded from http:// www.nesc.ac.uk/esi/events/954/
A number of capability computing projects will be selected on the basis of innovation and scientific excellence. These projects 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. DEISA also offers applications-enabling assistance from experts at the leading European HPC centres to enable projects to be run on the most appropriate platforms in the DEISA consortium.
Projects supported by DECI will be chosen on the basis of innovation potential, scientific excellence and relevance criteria. Priority will be given to proposals that promote collaborative research, either at a cross- national or crossdisciplinary level. Further, proposals from PIs that have yet to benefit from DECI compute and applications enabling resources may be given preference. Proposals selected under this call will be given access to the infrastructure for applications enabling from 1 October 2009 and for production runs from 1 November 2009 to 30 September 2010.
The following applications 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 on more than one platform.
Submission Deadline: 4th May 2009: www.deisa.eu/science/deci/deci-call-for-proposals2009
For the second year running, OMII-UK will mentor student participants in the Google Summer of Code (GSoC) programme. GSoC provides students all over the world with a stipend to spend three months of their summertime writing code for open source projects. In its 5-year history, the GSoC has helped nearly 2,500 students work on more than 180 open source projects, creating millions of lines of code.
Last year OMII-UK hosted six students working on four projects: taverna, OGSA-DAI, AVATS and SAGA. An ideas page lists some projects that mentors would be willing to supervise (see below) but students should not be restricted to these ideas because OMII-UK will consider any projects related to its work.
Finally, it’s not all about money or CVs. All participants involved in GSoC - whether admin, mentor or student - are entitled to one of the much-coveted GSoC T-shirts.
OMII-UK: www.epcc.ed.ac.uk/projects/omii-uk
GSoC Ideas page: www.omii.ac.uk/wiki/GoogleSummerOfCode
GSoC student applications will be accepted from 19:00 UTC on 23rd March, 2009 to 19:00 UTC on 3rd April, 2009.
Applications should be made through: http://socghop.appspot.com
NeSC News 3 www.nesc.ac.uk

Issue 68, April 2009
th
Moving to Multi-Scale Science: Managing Complexity and Diversity.
The Digital Curation Centre would like to announce the 5 th International Digital Curation Conference to be held 2 – 4
December 2009 at the Millennium Gloucester Hotel, London, UK. The conference will be held in partnership with the
Coalition for Networked Information (CNI).
The Programme Committee will be co-chaired by Chris Rusbridge, Director of the Digital Curation Centre, Liz Lyon,
Director of UKOLN and Clifford Lynch, Executive Director of CNI.
The first day of the conference will address development of data-driven infrastructure for science – looking at a wide range of issues including scale, discipline, skills, sectors, and funding.This part of the programme will include invited speakers in plenary sessions together with an interactive afternoon, including a “Community Space” for posters, demonstrations, informal meetings, a Symposium and an opportunity to attend clinics on aspects of curation.
The second day of the conference will be dedicated to practitioner approaches, solutions and models, with peerreviewed papers in themed parallel sessions.
Preliminary Call for Papers
The IDCC will shortly invite submission of full papers, posters, workshops and demos and will welcome contributions and participation from individuals, organisations and institutions across all disciplines and domains that are engaged in the creation, use, management and re-use of digital data, especially those involved in the challenge of curating data for e-science and e-research.
Proposals will be considered for short (6 pages) or long (maximum 12 pages) papers and also for demonstrations, workshops and posters. The full text of papers and abstracts for all posters, workshops and demos will be peerreviewed. Final copy of accepted contributions will be made available to conference delegates, and papers will be published in the International Journal of Digital Curation (see http://www.ijdc.net). Papers should be original and observational or textual) to support their conclusions.
original and innovative, probably analytical in approach, and will include or reference significant evidence (whether experimental,
Subject matter can be policy-oriented, strategic, operational, experimental, infrastructural, tool-based (etc) in nature, but submissions must display originality and evidence. Layout and structure should be appropriate for the disciplinary area. Research papers should not have been published in their current or a very similar form before, other than as a pre-print in a repository. Survey papers that summarise the current state of the art within a research area may also be considered.
29th April, 2009 09:30 - 17:00 WestPark Conference Centre, Dundee
This meeting is intended to bring together Scottish researchers who make heavy use of computational techniques, such as simulation, modelling or analysis to do research. This will allow an exchange of ideas and provide an opportunity to see how other scientists use resources to maximum benefit.
The day will be arranged into four sessions covering a wide range of computational research: Computational Chemistry, Cell Biology and
Bioinformatics, Medical Imaging, Computational Techniques. Speakers are from a range of Higher Educational Institutes around Scotland. In addition, a poster session will be held in the coffee and lunch breaks.
The symposium is free of charge and lunch and snacks are provided.
Registration is via the following website: http://www2.epcc.ed.ac.uk/~edikt2/
For more information on the edikt2 project or the symposium, please see the edikt2 website (http://www.edikt.org.uk/edikt2/edikt2009) or contact Jon Hill
(j.hill@epcc.ed.ac.uk, 0131 6506494).
We seek papers that respond to the main themes of the conference: multi-scale, multi-discipline, multi-skill and multi-sector, and that relate to the creation, curation, management and re-use of research data.
Research data should be interpreted broadly to include the digital subjects of all types of research (including
Arts and Humanities, and all the
Sciences).
We expect the paper submission date to be 24 July, 2009. The full announcement will be circulated to several email lists, and will be available at http://www.dcc.ac.uk/events/dcc-
2009/call-for-papers/
NeSC News 4 www.nesc.ac.uk
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NeSC News 4
Issue 68, April 2009
The NGS is pleased to announce that is has received continuation funding from
JISC and EPSRC for the next 2 years. A total of £3M has been awarded by the two funding organisations and will ensure that the NGS can continue to provide services and support to users from all research areas and also to drive forward the ongoing collaboration with Europe.
Dr Andrew Richards, Executive Director of the NGS, explained that “the new funding will enable the NGS to move to being a sustainable service, underpinning the e-infrastructure within the UK, and continue to enable innovative research using e-science technologies. The continuing commitment to the NGS from both JISC and EPSRC, also facilitates ongoing closer engagements with
GridPP in the UK to facilitate common e-infrastructure services, and places the
NGS along with GridPP in a strong position interact with ongoing international developments in the areas of e-infrastructure development such as the EGI
(European Grid Initiative) and PRACE (Partnership for Advanced Computing in Europe)”.
By the time you read this newsletter the NGS will be in full swing preparing for two NGS roadshow events at the universities of Aston and Bath.
The Aston event is taking place over the 7 th and 8 th of April and involves a
NGS roadshow on the first day which will give a brief introduction to the NGS and will include presentations on how to get started with the NGS, using the
NGS portal and submitting jobs and a presentation from Sarah Harris from the University of Leeds on using the
NGS resources for understanding biomolecules and their interactions.
The second day of the Aston event is a “hands on” training session run by the TOE team at NeSC. Attendees will be taught how to submit jobs to the
NGS and be able to practice using the
NGS portal. Attendees are welcome to attend one or both days.
The Bath event will be a one day
NGS roadshow event featuring presentations from various NGS staff and an exhibition over lunch where
NGS staff will be on hand to answer questions from attendees as well as distributing grid certificates making it easier for people to get up and running on the NGS quicker.
Further details on both events can be found at www.ngs.ac.uk/events/ roadshows.
Paul Daniels © Getty Images.
Paul Daniels © Getty Images.
After the success of last years NGS innovation forum, we are pleased to announce the dates for the IF’09.
The event will take place on the 21 st – 22 nd October 2009 at the Magic Circle
Headquarters in London (http://www.themagiccircle.co.uk/) – literally a stone throw from Euston train station. There are sure to be a few surprises taking place due to the magical setting so be sure to put the dates in your diary now.
The event will be free to attend and registration will open in the late summer.
If you are interested in hosting a NGS roadshow event at your institution then please contact Gillian Sinclair (Gillian.
sinclair@manchester.ac.uk), the NGS
Liaison Officer who will be happy to discuss your requirements and to tailor the event to your institutions needs. The roadshows and training events are free, local organisers just need to book a room!
NeSC News 5 www.nesc.ac.uk

Issue 68, April 2009
The Eduserv Symposium 2009 will be held on Thursday 21st May 2009 at the Royal College of Physicians, London.
More details about the event are available from: http://www.eduserv.org.uk/events/esym09
This symposium will investigate the intersection between identity management, access management and scholarly research collaboration across institutional and geographical boundaries in a world in which the Web has become ubiquitous and in which we see both institution-centric and user-centric identity solutions competing for our attention.
The event is intended to appeal to policy makers and senior researchers within institutions, research councils and similar bodies, librarians, senior staff in computing facilities, as well as staff in organisations that provide researchrelated services to the UK higher education sector.
Confirmed presenters include: James Farnhill, Joint Information Systems Committee; Cameron Neylon, Science and
Technology Facilities Council; Mike Roch, University of Reading; David Smith, CABI; John Watt, National e-Science
Centre (Glasgow).
To register for the event please use our online registration form which can be accessed from the above URL.
All places for the previous two symposia have filled up within a couple of weeks so we recommend that you register early in order to avoid disappointment. If you have any questions about the Symposium, please contact us at symposium@eduserv.org.uk or phone 01225 474 328.
April
7
16-27
20
28
30-1
May
5-7
11-12
13-15 eSI Public Lecture - “Adding Semantics to
Geographic Data Models” e-Science: The changing landscape
Use cases for provenance eSI
NeSC eSI
Network Visualisation and Analysis of
Biological Systems eSI
OMII-UK Collaborations Workshop 2009 NeSC http://www.nesc.ac.uk/esi/events/981/ http://www.nesc.ac.uk/esi/events/965/ http://www.nesc.ac.uk/esi/events/983/ http://www.nesc.ac.uk/esi/events/984/ http://www.nesc.ac.uk/esi/events/958/
HackLatt 2009
Capturing e-Science Fundamentals
Provenance in Secure and Advanced
Computer Systems eSI
NeSC eSI http://www.nesc.ac.uk/esi/events/973/ http://www.nesc.ac.uk/esi/events/985/
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 April 17, 2009
NeSC News 6 www.nesc.ac.uk