Issue 39, March 2006 www.nesc.ac.uk
The ONDEX Framework
NGS Application Survey
For more information on anything mentioned in the newsletter, please contact
Alison McCall alison@nesc.ac.uk
Telephone 0131 651 4783
Newsletter produced by:
Alison McCall and Jennifer Hurst
The decision by Research Councils UK that they will continue to fund the e-Science Institute through an
Engineering and Physical Sciences
Research Council grant for a further fi ve years post July 2006 marks a signifi cant investment in the continuation of the UK e Science Programme which commenced in 2001. Over £2.7 Million has been awarded to the Institute at the University of Edinburgh, to continue its programme of support for the UK e-Science community by providing a focus and meeting place for researchers.
The e-Science Institute (eSI) situated near to the centre of Edinburgh is the national UK centre and the meeting place for e-researchers. It already responds to current issues and community needs by running a programme of workshops, lectures, conferences and tutorials with hands-on training. There, researchers can share knowledge and ideas about their particular research projects, forge new interdisciplinary activities and investigate ways in which distributed computing can advance their research.
They have the opportunity to recognise new challenges and invent new research strategies to address them, and to explore emerging issues in depth.
The eSI also runs a visitor programme, in which researchers can focus on their research with like-minded experts and enthusiasts, and summer schools intended to seed the UK with highly motivated young researchers with well advanced e-Science research skills. In this new phase, the Institute will concentrate on developing a more thematic approach to its programme, enabling particular areas to be investigated in depth and over an extended period of time.
are extremely fortunate to have this opportunity in Edinburgh and look forward to stimulating signifi cant innovation. In this new phase, the Institute will be focussing on the research challenges of further developing e Science and in helping researchers in all disciplines to take advantage of e-Science methods.”
Professor Timothy O’Shea, Principal and Vice-Chancellor of the University of
Edinburgh, said: “We very much welcome this award. The University of Edinburgh deservedly has a world-wide reputation in e-Science - an exciting fi eld of research that extends beyond the sciences.
E-Science includes all areas of research which will benefi t from the latest advances in computing science, and indeed it has applicability in other areas of human endeavour including business, education, healthcare and libraries. This additional funding will enable us to continue our very strong commitment to e-Science and to support the most advanced possible research which delivers academic, economic and scientifi c benefi t.”
Dr Anne Trefethen, Director of the
e-Science Core Programme, said: “The eSI plays a fundamental role in continuing e-Science activities. It will help to set the directions and agenda for e-Science research across the disciplines. Providing support for the eSI to enable it to sustain its activity at least until 2011, means that there will be a continuing forum for researchers, national and international, to address and develop the research agenda within e-Science.”
Professor Malcolm Atkinson, Director of the e-Science Institute, said: “The e-Science Institute is an international focus where leading researchers meet to pursue advanced research. We

Issue 39, March 2006
The UK e-Science Programme is entering a new phase with the appointment of its first envoy and the award of continued funding to eight e-Science centres.
After five years, the UK e-Science Programme, one of the first coordinated national e-Science programmes in the world, is entering a new phase during which a national e-Infrastructure for research and innovation will be established.
Professor Malcolm Atkinson, Director of the
National e-Science Centre (NeSC) and the e-Science
Institute (eSI) in Edinburgh, takes up the new post of
UK e-Science Envoy on 1 April. “I am delighted to have the opportunity to help more people benefit from e-Science and to help steer the future development of e-Infrastructure,” he says.
E-Science centres in Belfast, Lancaster, Leeds,
Manchester, Newcastle, Oxford and the
National e-Science Centre in Edinburgh and Glasgow has been awarded £1.5m to continue work for a further two years. The centres support e-Science projects with researchers from local industry and universities.
The e-Science Institute in Edinburgh is to receive an additional £2.5 million over five years to run workshops and conferences and so continue its role as an international focus for e-Science research.
In the first five years, the UK e-Science Programme has funded more than 100 projects to develop e-Science techniques for a diverse range of applications. The emerging e-Infrastructure incorporates the networks, services and software needed to do e-Science.
By working closely with JISC which provides IT infrastructure and services to UK higher education and research, the future e-Science programme will help to establish a fully-fledged e-Infrastructure that meets the requirements of the government’s Investment
Framework for Science and Innovation 2004-2014.
In its next phase, the UK e-Science Programme will aim to make the techniques developed so far easier to use and encourage their uptake across a broader spectrum of users. The vision is to provide computing resources to the user in a similar way to the electric power grid: the user accesses electric or computing power without knowing which power station or computer it is coming from. “The fledgling e-Infrastructure also needs to be as flexible as the modern telephone service. This means it must be able to adapt to changing demands and advances in technology seamlessly, so that the service to users is always maintained,” says Professor Atkinson.
The UK e-Science Programme is a coordinated initiative involving all the research councils. It consists of an e-Science Core Programme, operated by the EPSRC to serve the communities of all the research councils, and e-Science programmes run by each of the eight individual research councils. The Department of Trade and Industry (DTI) supports e-Science-related projects under its technology programme.
The e-Science Core Programme funds the development of generic technologies, such as the software known as middleware that is needed to enable very different resources to work together seamlessly across networks and create computing Grids. The Core Programme also supports the e-Science Institute and regional e-Science Centres to engage and support a wide spectrum of academic, industrial and commercial users in e-Science projects.
The individual research councils fund projects to develop e-Science techniques and undertake a broad range of research. Some successful applications include:
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• monitoring the health of aircraft engines remotely; moving very large files between BBC stations and accessing editing facilities remotely; investigating the contribution neighbourhoods make to crime rates; selecting a handful from millions of molecules as promising candidates for new drugs; discovering a new fault line associated with an earthquake; identifying genes associated with disease; building an e-Infrastructure to manage the vast amount of data expected from the next major particle physics experiment at CERN; simulating bigger and more complex molecular processes than possible before; building an e-infrastructure to enable astronomers to find new discoveries in the wealth of data held in astronomical databases worldwide.
Judy Redfearn, e-Science Communications Officer
Further information about the UK e-Science Programme is available at: http://www.rcuk.ac.uk/escience
NeSC News 2 www.nesc.ac.uk

NeSC News
Issue 39, March 2006
The Fifth UK e-Science All Hands Meeting (AHM 2006) will be held from 18-21st September 2006 at the
East Midlands Conference Centre in Nottingham, UK.
The aim of the meeting is to provide a forum in which e-Science projects from all disciplines can be discussed, and where the results from projects can be demonstrated. The conference will therefore feature presentations by groups from throughout the UK who are active in e-Science projects, in addition to poster sessions, miniworkshop sessions, project demonstrations, and birds-of-a-feather sessions. The schedule will also include a number of invited Keynote speakers involved in leading Grid and e-Science activities.
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There are several options for participation (please note that to reflect the increasing quality of the submissions, this year we are asking for full papers to be submitted for review, rather than abstracts):
Regular paper. These will be presented in a parallel session, with 25 minutes allocated to each paper.
Each paper can be up to 8 pages in length. Full papers (not abstracts) should be submitted. The deadline is the 1st May 2006.
Presentation in a mini-workshop (25 mins). The mini-workshops are sessions organised by individuals to bring together a number of presenters for a particular theme. The call for mini-workshops has already gone out, with a deadline of 20th February 2006. The proposals will be reviewed and up to ten selected.
There will then be a call for papers for those workshops (published 1st March 2006) with the same format and deadline as for regular papers (1st May 2006).
Poster Presentation. There will be a poster session where colleagues will have the opportunity to explain projects to the conference delegates. Please submit up to four pages for review by 1st May 2006.
Birds-of-a-Feather. Up to five, two-hour Birds-of-a-Feather sessions will be organised. These are sessions that do not have the normal session format; for example tutorials, panel sessions, discussions etc. If you wish to organise one of these then please submit a 2 page summary describing the aims, schedule and intended audience by 1st April 2006 .
A full review process will be managed by the AHM Programme Committee.
Details of the format required for the papers, and how to submit will be available shortly at: http://www.allhands.org.uk/
There will be proceedings for the conference, which will be provided in CD format with an ISBN number. As in previous years we are aiming to have the best papers published in special issues of at least one journal.
This year, for the first time, the Programme Committee will present a best paper award, and that paper will be presented in a plenary session. There will also be a Best Student Paper award. For a paper to qualify, it must have a student as the lead author, and the PC chair must be e-mailed to inform him of this once the paper has been submitted. This paper will also be presented in a plenary session.
Programme Committee:
Chair, Professor Paul Watson, Newcastle University ( paul.watson@ncl.ac.uk
).
Deputy Chair, Professor Jie Xu, Leeds University ( jxu@comp.leeds.ac.uk)
The IECnet Knowledge Transfer Network is pleased to announce the second Grid Computing Now! event. This will be a halfday meeting on Virtualisation and Grids, to be held in London on the 22 March. Delegates will be presented with the business advantages of virtualisation and its relationship to Grid computing. Case studies will show how these have been put into practice. A panel session will allow delegates to ask questions of vendors and existing users.
Vendors represented on the panel will include Intel, Oracle, Platform, DataSynapse, and IBM. Presentations will be given by speakers from the Enterprise Grid Alliance and the 451 Group, along with users from Trader Media and a large US investment bank. Delegates will be welcome to join the speakers and panellists afterwards for an informal lunch. Grid Computing Now! technology events are aimed at commercial IT staff with a technical responsibility, who want to learn how Grid solutions are appropriate for their business and how to understand the supplier landscape.
To find out more about Grid Computing Now!, visit http;//www.gridcomputingnow.org
Pre-registration is required for the event and a small fee will be required. To register for the event, which will be held at
Intellect’s offices, please contact Rebecca Straker (020 7331 2037, rebecca.straker@intellectuk.org).
NeSC News 3 www.nesc.ac.uk

Issue 39, March 2006
The e-Science Institute invites proposals for meetings and workshops to be run over the next twelve months commencing in June 2006.
The e-Science Institute (eSI), situated in Edinburgh, is the UK’s Centre for e Science Meetings. Funded by the e-Science Core Programme, it has been operating since
August 2001, during which time it has had a very lively programme running over 360 meetings attended by some
11,500 delegates and has hosted 43 visitors who have stayed for varying periods from one day to a year.
The Institute has been funded for a further five years to
August 2011. We have split our budget to support both themes (the subject of a separate call) and ‘responsive mode’ meetings. About 80% of the meetings budget has been allocated to planned events and we are now seeking proposals for future meetings and workshops to be run over the next year. These will be considered by our Programme
Committee when it convenes at the end of May 2006. Only a small amount will be set aside for urgent requests and members of the e-Science community who plan to run meetings in the next year should not rely on this source.
There will be a further call in 6 months time.
Under the new scheme, eSI will pay for 1 or 2 speakers a day and will provide the usual support in the form of experienced staff, organisation and facilities. Researchers who want to organise a workshop to engage in collaborative work (e.g. ‘hackathons’) should also consider applying to the visitor programme for additional funds to enable them to engage a larger group of participants.
Proposals for meetings will have to show a clear link with e-Science – whether with well developed existing communities or new communities in the early stages of applying e-Science techniques to their research. eSI is actively looking to support activities across all academic disciplines and encourages new communities to take advantage of the significant expertise we can offer, in particular in putting them in touch with technical experts and computational scientists already engaged in e Science.
Initial enquiries should be made by emailing lee@nesc.
ac.uk to check on availability. Proposals will be reviewed by the eSI Programme Committee which convenes in late
May 2006, and should be submitted no later than 19th April
2006 for initial consideration by that committee. Further information on the eSI responsive mode is available at: http://www.nesc.ac.uk/esi/arranging_events.html
NeSC News 4
e
The e-Science Institute invites proposals for new themes to be run over the next two years. Theme topics, as well as being interesting in their own right, should address issues that are relevant to applications researchers and be able to demonstrate significant buy in from both the applications and computational scientist communities. It is not intended that they address only the sciences – all areas of academic research present opportunities for the application of e-Science techniques.
To continue our rolling thematic programme, we are now calling for proposals for topics for future themes to start August 2006 or later. These will be reviewed by the eSI Science Advisory Board which will meet in early
June 2006, and should be submitted no later than 19th
April 2006 for initial consideration by the Programme
Committee. Proposals for theme topics can be made either by the research community in which case eSI will undertake to try to find an appropriate leader, or potential theme leaders may put themselves forward along with the theme they wish to develop.
The e-Science Institute (eSI), situated in Edinburgh, is the UK’s Centre for e Science Meetings. Funded by the e-Science Core Programme, it has been operating since August 2001, during which time it has run over 360 meetings attended by some 11,000 delegates and hosted
46 visitors who have stayed for varying periods from one day to a year.
As well as hosting meetings and the visitors’ programme, the Institute recently instigated a thematic mode, which concentrates on in-depth and sustained investigation of a topic by a series of linked talks, workshops and conferences over a period of six months to a year. Such themes are led by a theme leader who is a long-term funded visitor to the Institute. To date, eSI has had two themes: Information Services for Smart Decision Making
(now complete) which was led by Dr Jennifer Schopf from Argonne National Laboratory and the current topic
Exploiting Diverse Sources of Scientific Data led by Prof
Jessie Kennedy of Napier University.
Further information on eSI themes is available at: http://www.nesc.ac.uk/esi/themes/index.htm
To propose a theme or if you have any questions on
Themes or Meetings and Workshops, please contact
Anna Kenway by email anna@nesc.ac.uk or 
+44 (0)131 650 9818 www.nesc.ac.uk

NeSC News
Issue 39, March 2006
The NeSC training team has begun a new series of events to introduce researchers to e-Infrastructure. These are run in association with a host organisation to help to expand their communities of those engaging in e-research. The fi rst event was at the Welsh e-Science Centre on 14 February, and the second at UCL on 22 February. The NeSC team introduces concepts of e-Infrastructure (networks + grids + supporting organisations to enable collaborative research), with reference to campus, national and international scales. The hosting organisation describes their points of contact and the support available for those wishing to engage with the technologies. In the events to date there have also been talks by researchers in the host organisations, including case studies and outlines of developments they have undertaken.
The presentations from these events can be accessed via the training team’s page for UK events: http://www.nesc.ac.uk/training/events/ . Future events will be with MIMAS at the University of Manchester (20-21 March) and with the White Rose Grid at the University of Leeds on 28 March.
There is a 2-day course, “Induction to Grid Computing and the National Grid Service” at the e-Science Institute, Edinburgh on
13-14 March. There are a few vacancies on this course - if you are interested please register as soon as possible via:
http://www.nesc.ac.uk/esi/events/671/ .
GGF is now accepted proposals for the GGF17 program to be held on 10-12 May in Tokyo, Japan. This event is collocated with the 3rd Grid World Exhibition being held on 11-12 May in the Tokyo International Forum. For more information on the call for participation, visit: http://www.ggf.org/GGF17/ggf_events_cfp_ggf17.htm. The deadline for proposal submission is 24
March.
GGF17 Registration Open
Advanced registration for GGF17 in Tokyo (10-12 May) is now open. To take advantage of the lowest rates, please sign-up today at: http://www.ggf.org/GGF17/ggf_events_regstrtn_ggf17.htm.
GGF17 Student Scholar Applications Accepted Applications are now being accepted for GGF’s student scholars at GGF17 in Tokyo, 10-12 May. To submit an application or for more information, please visit: http://www.ggf.org/GGF17/ggf_events_ student_ggf17.htm.
Several NeSC and EPCC staff played leading roles in the 16th meeting of the Global Grid Forum in Athens last month.
Three of the groups that we co-chair or otherwise engage heavily in - JSDL, DAIS and ByteIO - have submitted proposed recommendations to the GGF editor, which starts their path to becoming recognised international standards. The meeting was also a good source of information about developments in the Grid world, as summarised in articles for the Grid Computing
Now! website which is jointly run by our IECnet project.
Malcolm Atkinson was our representative on the GGF Steering Group and, as onen of the two data area directors, oversaw the running of the working groups in his remit. These included the OGSA Data WG, co-chaired by Dave Berry, and the OGSA
ByteIO WG, co-chaired by Neil Chue Hong. Dave Berry also attended the day-long meeting of the OGSA working group on the Friday following GGF. Stephen Davey led the charge from the other end of tne week, attending the two-day meeting of the Information Dissemination WG over the weekend before GGF, as well as attending GGF itself, where he also gave a presentation in the OGSA Data WG sessions.
Neil Chue Hong gave presentations at the Globus Toolkit and OMII tutorials. Ali Anjomshoaa, co-chair of the JSDL group and organiser of a oneday JSDL workshop, was another member of the substantial EPCC team, which also included Amy Krause and Tom Sugden, who ran a successful OGSA-DAI Technology Update session, Mark Parsons and Maureen Wilkinson, who ran a Grid Architecture Experts seminar, and Malcolm Illingworth who presented work from the DEISA project at the SAGA group.
Malcolm Atkinson and David Fergusson organised a three-hour workshop on Grid Education and Training which was enthusiastically attended. We hope it will lead to a Community Group on Grid Education and Training as well as furthering the cause of training in EGEE and education in ICEAGE. We also participated in workshops: announcing OMII-UK’s work, reviewing GT4’s latest technology and a NextGRID initiated discussion of grid architectures. This was a very vigorous and enthusiastic GGF with many exciting signs of progress in standards, in grid research and in production grids, including the dynamic mechanisms in Ian Foster’s keynote and the plans for a merger between GGF and EGA.
NeSC News 5 www.nesc.ac.uk

Issue 39, March 2006
Condor Week 2006 takes place on April 24-27 in Madison,
WI. It will include talks on the state of Condor, reports from users, discussions about the future of Condor, tutorials, demonstrations, and more. The schedule is not fi nalized yet, but the web site will be updated as the details become known. Learn more online: ht tp://www.cs.wisc.edu/condor/CondorWeek2006/
Note that the schedule is different than last year: tutorials have their own day now, the day before the technical talks.
This will mean more tutorials and relax the pace of the talks.
Registration is open and available from the web page. The deadline for registration is March 13th, 2006.
We are looking for members of the Condor community that would like to give a talk about how they use Condor, what they use Condor for, or other topics the Condor community would fi nd interesting. If you are interested, please contact
Alain Roy roy@cs.wisc.edu
by March 1st.
Note that there will be a birds of a feather session for the
Condor Enterprise Users Group this year. More information is on the web page.
The offi cial kick-off meeting of the EUMEDGRID Project took place in Malta on the 6 February 2006 with the aim of empowering e-Science across the Mediterranean.
Funded by the European Commission, the EUMEDGRID project will over the next two years, collaborate to develop a Grid e-Infrastructure for e-Science across the
Mediterranean: a concrete initiative aiming at bridging the
Digital Divide and fostering collaboration between Europe and its Mediterranean neighbours.
The Project will exploit the existing e-Infrastructures, i.e. the pan-European high bandwidth backbone GEANT2
(Gigabit Pan-European Research & Education Network) and the Mediterranean EUMEDCONNECT Network.
Furthermore, EUMEDGRID will actively collaborate with the EU EGEE project and its regional extensions (the
Projects: BalticGrid, EELA, EUChinaGRID, SEEGRID, etc), using common guidelines to encourage the porting of new applications on the pilot e-Infrastructure, thus promoting the growth of new user communities and the adoption of new powerful Grid tools and services.
The EUMEDGRID project is coordinated by INFN, the
Italian National Institute of Nuclear, Particle and High
Energy Physics and involves several partners and thirdparty
For further information about EUMEDGRID please visit: http://www.eumedgrid.org
or contact the Project Offi ce po@eumedgrid.org
.
http://www.dcc.ac.uk/events/dcc-2006/
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The 2nd International Digital Curation Conference will be held on 21 - 22 November 2006 at the City Centre Hilton,
Glasgow, UK
The Digital Curation Centre welcomes contribution and participation from individuals, organisations and institutions interested in the curation of data and the management of repositories for science and scholarship. This would include all disciplines and domains that are engaged in the creation, use, re-use and long-term management of digital data from researchers and curators, through to policy makers and funders. All proposals will be considered for papers, workshops, demonstrations and posters with both a practical and a research focus.
The Programme Committee will be chaired by: Chris
Rusbridge, Director of the Digital Curation Centre and
Professor Tony Hey, Vice President of Technical Computing
Initiative (TCI), Microsoft
For further info on the Call for Papers, a list of the main conference topics and submission dates see: http://www.dcc.ac.uk/events/dcc-2006/call-for-papers/
For further information about the venue see: http://www.dcc.ac.uk/events/dcc-2006/venue/
NeSC News
2pm, 17th March, 2006, Lecture Theatre E7, Renold
Building 8, University of Manchester.
Biological information can be found in experimental results, in hundreds of scientifi c databases/ontologies and in millions of scientifi c publications. Furthermore, sequence analysis methods are commonly used to predict the functional and structural properties of genes and gene products. Extracting and combining information from these very different sources has many potential applications from Bioinformatics, for example: supporting i) database and ontology curation, ii) gene annotation, iii) analysis and interpretation of experimental results and iv) modelling and simulation of biological systems.
ONDEX is an integration framework which aims to address these and similar applications by combining features of database integration, text mining and sequence analysis with methods for graph-based data analysis and visualisation.
This presentation gives an overview of the principles underlying the ONDEX framework, its ongoing development and future plans. Some example applications will also be presented. ONDEX can be found at:
http://ondex.sourceforge.net www.nesc.ac.uk

NeSC News
Issue 39, March 2006
March
9-10 Integrated Health Records (IHR) - Practice and Technology
13-14
13-14
16
20-21 and
28
23
23-24
25
28-30
Induction to Grid Computing & the National Grid service
DEISA Middleware and Security Technical Meeting
Service-Oriented Architecture: A “Grid Computing Now!”
Technology event
I ntroduction to e-Infrastructure: Enabling the Research of the
Future .
UKQCD Grid System Administration Training 2006
ICEAGE Kickoff Meeting
EGEE NA3 Wrap up Meeting
Hacklat06 e-Science Institute,
Edinburgh e-Science Institute,
Edinburgh e-Science Institute,
Edinburgh e-Science Institute,
Edinburgh
MIMAS, Manchester and Leeds e-Science Institute,
Edinburgh e-Science Institute,
Edinburgh e-Science Institute,
Edinburgh e-Science Institute,
Edinburgh http://www.nesc.ac.uk/esi/ events/648/ http://www.nesc.ac.uk/esi/ events/671/ http://www.nesc.ac.uk/esi/ events/643/ http://www.nesc.ac.uk/esi/ events/659/ http://homepages.nesc.ac.uk/
~mjm/training/roadshow.html
http://www.nesc.ac.uk/esi/ events/663/ http://www.nesc.ac.uk/esi/ events/656/ http://www.nesc.ac.uk/esi/ events/672/ http://www.nesc.ac.uk/esi/ events/662/
April
27 ATLAS e-Science Project - Introductory software training course e-Science Institute,
Edinburgh http://www.nesc.ac.uk/esi/ events/669/
May
27 Ontology Engineering & Automated Reasoning e-Science Institute,
Edinburgh http://www.nesc.ac.uk/esi/ events/668/
July
9-21 International Summer School on Grid Computing Jolly Hotel Delle
Terme, Ischia, Italy http://www.dma.unina.it/~murli/
ISSGC06/
September
18-21 All Hands Meeting 2006 East Midlands
Conference Centre http://www.allhands.org.uk/index.
html
For more events please look at the NeSC website: www.nesc.ac.uk/events
This month NeSC would like to welcome some new temporary staff members:
John Lyons is covering for Susan Andrews, our web and database developer, while she is on maternity leave.
John Scotland is a Data Resource Support Developer, working with The Training Team.
Yin Chen who is a Research Assistant, working on data replication management.
NeSC Project Manager (EGEE II Training Activity)
Fixed Term for 2 years £31-274 - £36,959.
NeSC is looking for a motivated project manager with expertise in computing and excellent communications skills to join an expanding and exceptionally successful team.
For further details and to apply please visit: www.jobs.ed.ac.uk
The National Grid Service is interested in hearing from current and prospective users as to the software that they would like to have available across the NGS sites.
The aim of this survey is to understand the requirements of all NGS users, to be able to assess what software can be provided and to facilitate the forward planning of future
NGS resource. The results of the survey do not guarantee that requested software will be made available at this time, but the requests will be used to determine the future software policy and priorities on the NGS.
We are interested in hearing of your interest in all areas such as (but not limited to) compilers, libraries, databases, specific scientific applications etc.
To send your list of desired software applications please email: support@grid-support.ac.uk
with the title
‘Application’ Survey’
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
NeSC News 7 www.nesc.ac.uk