The monthly newsletter from the National e-Science Centre
Issue 69 May 2009
www.nesc.ac.uk
By Iain Coleman
2.0
It’s said that obscenity is impossible to define, but easy to recognise. Web 2.0 is much the same. It is a manyfaceted concept that encompasses sharing and combining data and services on the web, user-generated content and structure, and the creation of virtual communities. Many aspects of Web 2.0 are now part of daily life for untold millions of people who have never even heard the term, but happily combine Twitter, Facebook and Google Maps to organise a night out on the town.
Now data sharing and collaboration are crucial to modern science. They are also at the heart of the e-Science agenda. So it seems only natural to ask how Web 2.0 can help scientists do their research. The workshop on “The
Influence and Impact of Web 2.0 on e-Research Infrastructure, Applications and Users”, held at the e-Science Institute on 23-27 March, posed exactly this question, in preparation for an eSI research theme on the same topic.
That Web 2.0 has had a substantial social impact is undeniable. How revolutionary it is in technological terms is more open to question.
As eSI Director Malcolm Atkinson pointed out in his opening address, computing has always been about combining components to build useful systems, and has entailed moving work onto other people ever since the job of building compilers and operating systems stopped being done by users and became the work of communities and companies.
Image: A ‘wordle’ of Iain Coleman’s notes from the Web 2.0 conference (www.wordle.net)
Still, there is a new energy and vibrancy about Web 2.0. It’s to do with speed – shallow learning curves and instant gratification.
Lightweight protocols make it easy to combine unrelated resources to do something new and unexpected: mashups are the epitome of Web 2.0. This encourages fast exploration and fast discovery, and has led to the distinctive Web
2.0 philosophy of the “perpetual beta”, as outlined by Mark Borkum (Southampton). Nothing is ever really finished, in this worldview: instead, tools and services that more or less work are released to general use. As problems crop up or improvements are suggested, the software is modified promptly behind the scenes, without all the fanfare of a new release.
It’s faster for users, too. The Web 2.0 platform is the web browser itself, comfortable and familiar through daily use.
This convenience comes at a cost, however, as Mark Baker (Reading) explained. Web browsers have significant security vulnerabilities, which can be a problem in any research project where personal privacy or commercial confidentiality are important.
A similar trade-off can be seen in cloud computing, another new trend with close connections to Web 2.0. Just as Web
2.0 features disparate software and dispersed data that can be grabbed from the web and put together ad hoc, so cloud computing is all about taking remote computing power as and when you need it, without worrying about where or precisely how the computing is being performed. It’s computing as a pay-as-you-go service: effectively infinite resources with no up-front cost and no need to maintain the IT system yourself. Like Web 2.0, it’s about moving work on to other people, so that you can do what you really want to do quicker and more flexibly.

Issue 69, May 2009
Continued.
The great advantage is in instant scalability. As Ian Osborne (Grid Computing Now) pointed out, Amazon built its whole business on meeting the peak demand a week before Christmas. Their cloud computing service is just a way of putting that expertise to wider use. This scalability isn’t trivial to achieve, however, as Paul Watson (Newcastle) warned. There are a range of different cloud computing providers, from Amazon EC2 to Microsoft Azure to Google
Docs, occupying different points along a spectrum of complexity. To fully exploit the most flexible systems requires expertise in writing distributed systems: simpler cloud services are available, but they come with more restrictions.
The more fundamental trade-off is in security. If your data and your software are on a computer that you control, you can in principle make it as secure as you need. When it’s all being handled by a cloud provider, on who knows what machines, being administered by persons unknown, there is a real limit to the security level you can achieve. Indeed, cloud computing terms and conditions are typically hedged with caveats disclaiming responsibility for keeping your data secure. In many cases this doesn’t matter, but for researchers like Richard Sinnott (Glasgow) who work with sensitive NHS medical records, cloud computing is simply not an option.
Even if security is not a big issue, there are still some applications for which cloud computing is fundamentally unsuitable. Jeremy Cohen (Imperial College London) explained that an application where latency has to be kept low is unlikely to benefit from being put out in the cloud where different processes might well end up running on machines half a world apart. But academic research that is able to be performed in the cloud experiences significant advantages.
In research, or in scientific commercial start-ups, the process of obtaining funding then buying and installing computers can open up a big delay between having a clever idea and being able to start implementing it. Commercial clouds can short-circuit this path: as soon as you’ve had your idea you can grab computing power from a cloud provider and start work, paying only for what you use. If the project is successful and accumulates users, the requisite scaling up is straightforward: if unsuccessful, the investment of time and resources was much less, and you can more quickly move on to something new.
Of course, research isn’t all about lone geniuses fizzing with inspiration. It’s about collaboration and communities. And that’s where Web 2.0 is at its strongest. Blogs, filesharing and social networking sites have enabled communities to grow up around the most obscure interests, from Renaissance poetry to pictures of cats with bacon taped to them. So why not science? Do we need a “Facebook for Scientists”?
Dave de Roure (Southampton) thinks so, and his myExperiment project is designed to enable scientists to share their workflows freely. Ian Frame (Cambridge) agrees, although his SciSpace.net project emphasises collaborative working among well-defined groups of researchers. In both cases, the distinctions between general social networking sites and these more specialised services for scientists reflect the differences between scientists and teenagers. While scientists will share the fruits of their labours, myExperiment has found that maintaining proper credit and attribution is essential, and the mechanisms have to allow scientists to control security and licensing of their work. The SciSpace working environment, where scientists use tools like wikis, blogs and filesharing to develop projects and write papers, has also required very fine-grained access controls. This isn’t just about keeping data secure: it’s also about giving scientists a safe discussion space in which they can say things that might be wrong without having their mistakes publicly recorded for anybody to see.
Building these services isn’t enough. You need to build the community – and that’s the hard part. Giving scientists the incentive to contribute is a big challenge, and social networking for scientists only works if the scientists get involved.
Users create the value, as Cameron Neylon (Southampton) explained, not just by contributing information, but by creating the network effects that make new science happen. To get them involved, you need to solve a pressing problem that they have, or give them something they understand and want to contribute to. It takes time, effort and resources to build the community, and this is both more difficult and more important than building the service itself.
It may seem ironic that Web 2.0 and cloud computing, with their promises of simplicity and flexibility, should pose such difficulties in being used effectively by researchers. What this workshop showed, however, is how much potential there is in these diverse and powerful technologies, and how keen the research community is to exploit them to their fullest potential. If Web 2.0 lives up to the expectations of its enthusiasts, it may do as much to change the way we do research as the founding of scientific journals once did.
Slides and other material from this event can be downloaded from http://www.nesc.ac.uk/esi/events/968/
NeSC News 2 www.nesc.ac.uk
www.nesc.ac.uk

NeSC News 2
Issue 69, May 2009
A two-day event at the National e-Science Centre in April proved that the e-Science community is “bubbling with ideas and energy,” and that there is “extensive penetration of the effects of e-Science,” says e-Science Envoy Professor
Malcolm Atkinson.
The E-Science: The Changing Landscape event was held on April 16 and 17, and attracted the biggest names from across UK e-Science.
The first day was mainly a meeting for e-Science directors, getting together to assess how well e-Science is embedding into the research culture in Universities.
“The overall impression was that there is a remarkable and deep impact of e-Science on many aspects of research life from the provision of computing and data resources to the methods used in research,” says Atkinson. “There were plenty of examples of research results and spin off companies or research projects. This was well illustrated by the cascade of follow on projects from DAME, with one grant of over £9 million and with at least three major
UK companies engaged, that was reported by Prof. Jie
Xu when talking about the White Rose Grid. That was also remarkable for the multi-level network of human communication which kept it progressing over the last eight years,” he says.
Atkinson says, while the e-Scientists could see these significant changes, they would have liked to see even greater progress and embedding.
“But in fact, standing back it was obvious that since the start of the e-Science campaign in 2001 a great deal had been achieved and the community should be proud of that achievement and do more to convince others of its significance. The prospects were also good. In the past year the EPSRC research facilities programme has committed more than £8 million to e-Science and many e-Scientists had been successful in gaining responsive mode funding, or funding from other programmes that will deliver more e-Science progress and capabilities. Universities, such as Newcastle with its new
Informatics Research Institute and Manchester with its new
Scenes from the Village Market demos
Manchester Informatics initiative, are continuing to invest in facilitating and leading e-Science. The break-out groups came up with many good ideas on how to continue the good work,” he says.
The second day started with a series of talks about ways in which services for e-Science were developing to match the changing requirements. This led to a vigorous discussion about how they should change and at the same time provide sustained facilities researchers could commit to without risking their research. The following Village Market research fair provided exciting demonstrations of a number of new and emerging tools for researchers to use and illustrations of the ways in which they were changing research methods.
A report on the workshop will be produced this summer.
NeSC News www.nesc.ac.uk

Issue 69, May 2009
By Florance Kennedy
The DCC had a stand at the JISC
Conference held in the Edinburgh
International Conference Centre on
24 March. As well as launching the revised version of our brochure ‘What the Digital Curation Centre can do for you’ http://www.dcc.ac.uk/docs/ publications/What_the_DCC_can_ do_for_you.pd
f (copies available on request), we also held a crossword puzzle competition with the answers aligned to the information in our brochure.
Dr Jano van Hemert, a Research leader and CoTheme Leader at the
National e-Science Centre, has been awarded one of 0 places on the
Scottish Crucible 2009.
Crucible is an attempt to being together intelligent thinkers from a broad range of different areas, in the hope that they will talk to and spark off one another and, ideally, come up with some fresh ideas. Run by
NESTA (National Endowment for
Science, Technology and the Arts),
Crucible focuses on experienced post-doctoral researchers and those in their first academic position.
There was not much time in which to complete the puzzle but a hardy dozen or so managed to get their entries back in time to be considered for the prize. Thanks to an unexpectedly tricky question
(who expected the answer to be
‘duty’ rather than ‘data’?), there were only two correctly completed entries, and we decided to award a prize to both entrants. John Robertson of CAPLE at Strathclyde University was presented with his prize by
Chris Rusbridge, Director of the
DCC (photo attached). The second prizewinner, Amanda Hill of MIMAS, now living in Canada, had already returned home by the time the winners were announced but thanks to the wonders of modern technology has now also received her prize.
She plans to use it it as a back-up for the images she is digitising at
Deseronto Archives (http://www.flickr.
com/photos/deserontoarchives/).
This has a budget of next-to-nothing, so Amanda says “this is a real bonus for us.”
In 2009, it has come to Scotland, and chosen 0 people from the research community to take part.
Jano van Hemert
“I hope to discuss challenging problems with the other participants that are of direct relevance to society now and in the immediate future. I am confident computer science can provide a vital supportive role in solving challenges faced by our modern society,” says van Hemert.
The organisers say: “Scottish Crucible 2009 is all about helping bright thinkers to see the bigger picture. It aims to help researchers think differently and send participants back to your work inspired. The programme has been put together with the express goal of helping participants discover skills and attitudes likely to make your research more innovative. We want participants to return armed with a greater understanding of how science can benefit society and how thinking creatively can really make a difference to your work and your career.”
A second meeting on wave-flow interactions will be run at the National e-
Science Centre on May 25-29, 2009.
The Network on wave-flow interaction, funded by EPSRC (Engineering and Physical Sciences Research Council), brings together around 20 UK researchers working in various aspects of the interactions between flows and waves in fluids.
The crossword was so well-received that we are planning a second version of that, too, as part of the fifth International Digital Curation
Conference in London from 2 -
December 2009 http://www.dcc.
ac.uk/events/dcc-2009/ The Call for
Papers has recently been launched http://www.dcc.ac.uk/events/dcc-
2009/call-for-papers/
A copy of the planned programme can be seen here: http://www.maths.ed.ac.uk/waveflow/edinburghmeeting/programme.shtm
l
The meeting will be organised with the support of the International Centre for
Mathematical Sciences (ICMS).
The first Wave-flow interaction meeting was held on June 26-27, 2008, at the University of Keele.
NeSC News www.nesc.ac.uk
www.nesc.ac.uk

NeSC News
Issue 69, May 2009
The NGS has recently hosted two roadshows at the Universities of
Aston and Bath. Both roadshows were a great success judging by the feedback received and the high number of attendees taking advantage of the Roaming RA certification facility.
Both roadshows featured presentations by David Wallom,
Technical Director of the NGS, who introduced the service followed by the Training, Outreach and Education team from NeSC who gave presentations on getting started with the NGS, the NGS Portal and job submission and training and outreach at the NGS.
resources to enhance and speed up their research. The topics covered were varied. Jonathan Mitchell from the University of Leeds gave a presentation at the Aston event and explained how high performance computing was the ideal tool for understanding biomolecules and their interactions. At the Bath event there were two presentations from users, both from the University of Leeds again. Andrew Turner demonstrated how he was using NGS resources for geodemographic modelling while
Narcis Fernandez-Fuentes explained how he performed in-silico drug screening on the NGS.
Users of NGS resources were invited along to the roadshows to demonstrate how they use NGS
The Roaming RA facility was also in attendance at both events. This allows attendees to leave the event with a fully functioning grid certificate meaning they only have to complete
the short NGS application form to be able to access NGS resources.
The Aston roadshow event also featured a full day of hands on training the day after the roadshow to enable attendees to put into practice some of the information they had received the day before at the roadshow.
Presentations from both events are now available from the NGS website
– please follow the events link on the homepage.
We are currently looking for more hosts for NGS roadshows for June and for the start of the new academic year. If you are interested in hosting a roadshow then please contact the
NGS Liaison Officer (Gillian.sinclair@ manchester.ac.uk
).
The more eagle eyed amongst you may have noticed the new banner adorning the top of the regular
NGS page in the NeSC newsletter.
The NGS logo has been updated to coincide with our new funding allocation which officially started on the 1st of April.
Over the forthcoming weeks and months you will see the new logo being implemented on all the NGS outreach mechanisms such as our Facebook group, blog (http:// nationalgridservice.blogspot.co
m /), Twitter (http://twitter.com/uk_ngs) etc not to mention NGS literature which is also undergoing a revamp. The NGS website has already been updated with our new banner logo. The NGS will also be phasing out use of our full title (National Grid Service) so you will see the acronym used more and more over the forthcoming months.
If you need the new logo for use in presentations, posters etc then please visit the logo webpage (http://www.gridsupport.ac.uk/content/view/176/118/) where you can find all versions of the new logo. We hope you like the new logo
– feedback is welcome!
NeSC News www.nesc.ac.uk

Issue 69, May 2009
By Simon Hettrick, OMII-UK
It’s risky to double-guess your users.
There can be a difference between what we think our users need, and what they actually need. This is especially the case in e-Research: it is a young technology with a multidisciplinary research base that can change focus with lightning speed.
To counter this problem, two of the UK’s foremost e-Research organisations began the JISC-funded
Engage project. The goal was to create a picture of the e-Research community through a series of interviews that would include everyone from old hands, to users who were only contemplating e-Research’s potential. Information culled from over 50 research groups has led to Engage’s latest phase: the funding of 14 cutting-edge projects that could, amongst other things, improve cancer treatment and help researchers understand climate change.
Researchers from the University of Oxford (David Wallom and Segolene Tarte) using image-processing tools to study ancient documents. Engage funding is allowing the image-processing tools to be developed.
OMII-UK and the NGS (National
Grid Service) are both interested in the same market and both invest a lot of effort in determining the needs of their users. This motivated them to join forces to discover the e-Research requirements of the research community. ‘It was an ambitious idea’ says original
Engage project leader, Chris
Brown, ‘trying to interview a range of people across a whole range of institutions was going to be difficult.’ The plan was ambitious: to include the views of established e-
Researchers, researchers who were only contemplating e-Research, and even those who knew nothing about e-Research but whose research was suited to the technology. To contact these new users, Chris relied on a viral campaign ‘We started locally and then asked each interviewee for recommendations of who to talk to next’. This strategy led to fiftythree interviews across the country with everyone from chemists to criminologists and performing artists to physicists.
NeSC News
Engage generated hundreds of hours of recorded interviews, which were assessed by a team of experts from
OMII-UK and the NGS. The result was a picture of the e-Research requirements in the UK. ‘Once we had the picture’ says Steve Brewer, current Engage project leader,
‘the next stage was to review best practices and the lessons learned from the interviews, and take forward the most promising technologies through a collection of Engagefunded projects’. Fourteen projects have been funded so far. They cover number-crunching applications conventionally associated with e-Research, such as crystallography, and projects that rely on the other strengths of e-Research, such as the image-processing of ancient documents. All of the software generated by the projects will be open-source and will adhere to opendevelopment practices: ‘anyone will be able to track the development of the software on the Engage website’ says Steve Brewer.
Engage funding for the Monte Carlo
Treatment Planning (MCTP) project will allow researchers from the Cardiff
School of Computer Science and the
6
Department of Medical Physics at the Velindre Cancer Centre to widen the availability of new, dose-planning techniques for radiotherapy. Dose planning is fundamentally important to radiotherapy. Get the dose too low, and the tumour will be unharmed; get the dose too high, and healthy tissue will be damaged. Monte
Carlo techniques help to accurately determine the radiation dose, but each calculation can take days to run using standard equipment, which can make the treatment cost prohibitive.
The MCTP project will use e-
Research techniques to increase the computational power available for dose planning, which reduces the computation time and the treatment cost.
Funding for the Aladin2 project will mean that a simple, fast-running model of the Earth’s climate system will be made available to a diverse research community. This project builds on the GENIE, which constructed a climate model that could be used over long timeframes.
Aladin2 will provide software that will help set-up and launch the
GENIE climate-modelling system, which will make it very easy to use www.nesc.ac.uk
www.nesc.ac.uk

NeSC News 6
Issue 69, May 2009
Continued and enable its uptake by a wide community of researchers. The
Aladin2 software has already found a market with training workshops for
PhD students and other researchers, and in Masters-level teaching units at the Universities of East Anglia and
Bristol.
By building a picture of the e-
Research community, the Engage project eliminates the risks in double-guessing the community’s needs and ensures that researchers get what they want. The final part of the project is now underway.
It will see the release of the new software that has been tailor-made for the community. As summarised by Steve Brewer ‘The first stage of
Engage identified the projects that could benefit from funding. The future stages will see the community benefitting from software that will be developed to meet their needs.’
More information can be found on the Engage website at www.engage.
ac.uk.
Edinburgh e-Science Training, Outreach and Education (TOE) and the
National Grid Service (NGS) will jointly run an Advanced Services Summer
School between the 7 - 11th September 2009 at Cosener’s House near
Oxford.
The school is a chance for attendees to not only get an excellent grounding in the current state of the art of advanced distributed computing in the
UK and internationally but also to spend a week in a small group getting to know both their peers and the leaders in the field. More information is available at: http://www.iceage-eu.org/adsss09/index.cf
m
“The idea is to build on our experience in running the highly successful
Deputy Director
Training, Outreach and Education
This year’s summer school will be in Sophia Antipolis, near Nice in France on the 5 - 17th July. Registration for this school is still open at - http://www.
iceage-eu.org/issgc09/index.cf
m )
The aim of the Advanced Services Summer School is to help develop the skills of those involved in providing computational support for research in a wide range of disciplines. In particular the school will focus on the use of, provision of interfaces to and the development of services based on employing the composition or aggregation of computational or data services.
For instance the school will show how to compose a variety of services into bioinformatics work flows which can be used to support biomedical research processes, how to use and develop lab or department scale clusters of computers to run simulations, how to work with the National Grid Service to compose protein simulation models for running on UK or international super computers, developing a portal to support legacy applications.
The cost is £276 per student, including accommodation and meals. Further information is available here: http://www.iceage-eu.org/adsss09/index.cf
m
24 – 26 June 2009
Maternushaus, Cologne
REGISTRATION NOW OPEN: http://www.ncess.ac.uk/conference-09/registration/
Early bird registration rates are available until 26 April. For full details on fees, please visit http://www.ncess.ac.uk/ conference-09/conferencefees/ . Special Conference rates on accommodation at selected hotels are also available until 24 April. Details of these offers can be found at http://www.ncess.ac.uk/conference-09/accommodation/
The aim of the annual international conference on e-Social Science is to bring together leading representatives of the social science, e-Infrastructure, cyberinfrastructure and e-Research communities in order to improve mutual awareness and promote coordinated activities to accelerate research, development and deployment of powerful, new methods and tools for the social sciences and beyond.
The full programme for the conference will be announced shortly.
For further information on the conference, and to register, please visit http://www.ncess.ac.uk/conference-09/
NeSC News www.nesc.ac.uk

Issue 69, May 2009
15
20
May
-
11-12
13-15
13-14
nd
“The BELIEF-II symposia constitute the principal ‘international dissemination’ dimension of the project and serve to reinforce the relevance of Europe’s e-Infrastructures globally. The symposia will offer a platform to EU projects and activities in key regions, connecting with EU e-Infrastructures where user communities can benefit hugely from adoption of these research technologies.” Stephen Benians, BELIEF II project coordinator
The second BELIEF international symposium will be held at the Escola Politécnica of the Universidade of São Paulo,
Brazil on 16-17 July. The event will focus on the theme of Future trends in e-Infrastructures applications: towards sustainable development.
The Symposium, organised with the support of the GLOBAL project, will revolve around the question of how existing
EU-Latin American e-Infrastructure links should evolve in a way that will bring benefits to Latin American development and to the e-Infrastructure cooperation between the regions. The symposium’s discussions will shape a position paper to be sent to key stakeholders and decision makers.
Thanks to the support of the GLOBAL consortium, remote participation is welcome. Those who wish to give a presentation via the Internet (as a remote site via ISABEL) should contact Juan Quemada (jquemada@dit.upm.e
s ) of the GLOBAL consortium.
The deadline for abstract presentation submission is May 15, 2009. www.beliefproject.org
2-29
HackLatt 2009
Capturing e-Science Fundamentals
Provenance in Secure and Advanced
Computer Systems
The Influence and Impact of Web 2.0 on e-Research Infrastructure, Applications and Users Workshop eSI Public Lecture: “The Future of
Provenance” by James Cheney
High-throughput Approaches and
Bioinformatics for Breast Cancer
Research
Waveflow interactions: second meeting eSI
NeSC eSI eSI eSI
NeSC
ICMS http://www.nesc.ac.uk/esi/events/973/ http://www.nesc.ac.uk/esi/events/985/ http://www.nesc.ac.uk/esi/events/986/ http://www.nesc.ac.uk/esi/events/969/ http://www.nesc.ac.uk/esi/events/987/ http://www.nesc.ac.uk/esi/events/980/ http://www.icms.org.uk/workshops/ waveflo w
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 June 2009 issue is May 16, 2009
NeSC News 8 www.nesc.ac.uk