The monthly newsletter from the National e-Science Centre NeSC News Issue 71 July 2009 www.nesc.ac.uk Trust Me, I’m A Computer By Iain Coleman Nostalgics will speak wistfully of the days when people could go out for the day without needing to lock their doors. A cynic might respond that this only worked when people didn’t have anything worth stealing. They would both have a point. We only need security because we don’t have trust. Why bother with a door lock, if you know your neighbours are honest? But even if trust is absent, the level of security we need depends on the risks. Why get a lock that is more expensive than anything behind the door? So trust and security are two sides of the same coin. Both are long standing human and technical problems, and both present new and pressing problems for the digital age. The e-Science Institute research theme “Trust and Security in Virtual Communities” aims to address these problems, and is currently hosting a visit by the distinguished trust and security expert Prof Vijay Varadharajan, Microsoft Chair in Innovation in Computing at Macquarie University. As the scale and pervasiveness of computing increases, so the trust and security problems become more complex and more pressing. As new kinds of computing emerge, these problems continue to multiply. Prof Varadharajan’s Visitor Seminar, held at eSI on 15 June, detailed the issues that will be facing trust and security researchers over the coming years, and gave some pointers towards the solutions they may use. Every year brings cheaper embedded computing, more pervasive networking and greater mobility. Computing is also expanding in its geographical and social reach, and the user base is becoming more global and more diverse. So more and more people are using computing for more and more things, with their financial, social and family relationships increasingly mediated through digital technology. The future promises a continued dramatic growth in computing power, storage and bandwith. The era of petabyte personal computing, though distant, is approaching. When you consider that everything you say from the time you are born till the time you die would fill less than one percent of a petabyte, and that your entire life experience can be captured in colour with just a few petabytes, then the question of who you trust with this information, and how you safeguard it, comes into sharp relief. Large-scale computing brings security challenges of its own. How can we provide secure information to billions of users? And how do we counteract epidemic-style attacks, from spam and phishing to worms and denial of service? Mobility introduces two new problems. If you don’t know where a program is coming from, it’s hard to be sure what level of trust and privileges to assign it. Programs are also able to cross administrative domains, which may have different levels of trust. Distributed computing also complicates the security picture. Systems have to be designed to deal with dynamic changes in security policies, and with self-organisation and management in dynamic networks where ad hoc entities form and dissolve on short time scales. Professor Vijay Varadharajan Further, there is the question of where the security services should be placed in a distributed system. The operating system? The middleware? The hardware? The application? All of the above? These are hard questions, but what makes them harder is the fragmentation of the security world. There are multiple security models, on multiple platforms, from multiple vendors. Policies proliferate, and there are far too many different security standards, many of them incompatible with one another. If security is becoming increasingly complex, can a closer look at trust help us to solve some of these problems from a different direction? Trust has been studied for many decades, if not centuries, in different disciplines, and is generally better understood by philosophers, sociologists and psychologists than by technologists. It can be a slippery notion. Trust depends on a context, and is not necessarily transitive. Just because I trust you and you trust her, doesn’t mean that I trust her. Trust can increase or decrease through time. Issue 71, July 2009 Trust me, I’m a computer Continued Generally speaking, trust takes a long time to establish but can be lost very quickly. It is important to distinguish between trust and trustworthiness. A secret service employee may be trusted with restricted information, but if she illicitly sells it to a foreign power she is not trustworthy. Misplaced trust – when trust is greater than trustworthiness – leads to increased risk of harm. Misplaced distrust – when trustworthiness is greater than trust – leads to loss of opportunities. The trick is to match trust and trustworthiness as closely as possible. So how does this translate into computing? Well, a trusted computing platform has a trusted component in the form of built-in hardware, and it uses this to create a foundation of trust for software packages. Essentially, the trusted platform vouches for the state of the machine to a third party. For instance, before sending out a movie to your PC, Disney might check that your PC has a particular application that lets you view the movie without being able to cut-and-paste or copy it. Or, if you take a laptop to another organisation, they might use the trusted platform module to check the state of your laptop before allowing it to connect to their network. Grid Computing Now! annual report But this is just the first step in implementing trust in computing systems. The ultimate aim is to create a “trusted stack”, consisting not only of trusted hardware, but also of a trusted operating system, middleware and applications – not to mention trusted users. Today’s security problems are formidable, but tomorrow’s will be tougher still. The more skill and imagination we apply now, the more likely it is that the distributed computing systems of the future will be built on secure foundations. A webcast and slides from this event can be downloaded from http://www. nesc.ac.uk/esi/events/998/ The Grid Computing Now! knowledge transfer network has released its 2009 annual report. It can be downloaded here: http://grid.globalwatchonline. com/epicentric_portal/binary/com. epicentric.contentmanagement. servlet.ContentDeliveryServlet/GRID/ About%20Us/GCN!_Annual_Rep_ 2009.pdf NeSC-based students come out on top Two undergraduates who have been working with the National e-Science Centre have won awards recently. Andrei Lyashko, a graduate student from Minsk, Belarus, has been awarded the Microsoft Prize for the best undergraduate honours project. Andrei achieved a mark of 91% for his project on ‘Association Rules Applied to Microarray Results from a Cystic Fibrosis Study’. The project involved data mining in the form of association rules and frequent patterns on scientific data from a microarray study on Cystic Fibrosis by the Molecular Medicine Centre of the University of Edinburgh, with the objective of identifying correlations between differentially expressed genes. He will continue to work on the project at NeSC until the middle of August, under the supervision of Dr Jano van Hemert, Dr Varrie Ogilvie and Rob Kitchen. “I am hoping to finalise what I achieved in my project and release a stand-alone application for mass gene expression analysis using the methodology I have developed,” he says.“I am very happy about the award, as I have put so much work and effort into the project and it’s such a rewarding feeling when your work is recognised by others,” he says. The second student, Carl Orebäck, was awarded both the Agilent Prize and the Class Medal for best performance in the BEng Electronics and Computer Science degree His project aimed to investigated the use of graphical user interface languages and their generators and use these in conjunction with the Rapid Development Tool for Job Submission Portlets (Rapid), which is being developed at the National e-Science Centre. NeSC News 2 www.nesc.ac.uk Issue 71, July 2009 A SLiM chance for viruses By Simon Hettrick, OMII-UK Viruses have evolved a clever way of reproducing. They hijack the signalling pathways used to instruct cells, and fool them into producing copies of the virus. If we could understand these signalling pathways, we could develop treatments for viruses and for the many diseases that operate in a similar way. This is a massive task which, in the human body, requires an understanding of the interactions between about 20,000 proteins. A team of biologists from the University of Southampton have teamed up with OMII-UK, the UK’s e-Research software provider, to try to better understand viruses using the latest e-Research techniques. a complex problem, which would often require a single computer to run for many days. By executing the program on many computers at the same time, the execution time can be significantly decreased. Richard could take advantage of a cluster of computers within Southampton University, or even the colossal computing power provided by the National Grid Service. Richard Edwards is the head of the Bioinformatics and Molecular Evolution group at the University of Southampton. He studies how proteins interact, and is particularly interested in short, linear motifs – known as SLiMs. “A protein can be thought of as a sequence of amino acids, like beads on a string” explains Richard “[SLiMs] consist of about three-to-five specific amino acids in the protein”. SLiMs could be responsible for the signalling pathways between many proteins, because they control the ways in which proteins interact. They are potentially useful to viruses too. SLiMs are small so it is relatively easy for a virus to evolve a structure that mimics them, and hijack the signalling pathway controlled by the SLiM. A variety of diseases occur due to problems with signalling pathways, which means that a better understanding of SLiMs could be vital to the development of new treatments for ailments such as heart disease. Being one of a rare breed of researchers who is adept in his chosen field and in computer science, Richard wrote SLiMFinder: a program which investigates whether the properties of a protein are caused by SLiMs. Discovering SLiMs is NeSC News SLiMFinder’s interface also needed some work. The early version required scientists to learn the correct commands to run SLiMFinder. This interface may be familiar to Unix users (and anyone who used a PC in the 70s or 80s), but it is something that many scientists – in this pointand-click age – find difficult to use “It’s one of those Catch-22 situations” says Richard. “The kind of people who are able to download and run [the early version of SLiMFinder] are the kind of people who are likely to develop their own software”. OMII-UK develops free and opensource software for e-Research, and helps researchers benefit from the technology. Helping researchers get started with e-Research is the role of Engage – a joint project between OMII-UK and other partners in the UK. After meeting with Richard, Engage began a collaboration during which OMII-UK experts were commissioned 3 to develop SLiMFinder into a more user-friendly and powerful software package. Development focused on the creation of a workflow for SLiMFinder, which used OMII-UK’s very successful Taverna software. This allows the automation of repetitive tasks, such as data collection from databases, or data manipulation. ‘Data management is a non-insignificant part of the work’ explains Richard. ‘The time-saving potential is more than [SLiMFinder] now runs in a day, it also didn’t need someone to spend a day setting everything up’. OMIIUK developers also developed one of SLiMFinder’s sub-programs so that it could execute on distributed resources, such as the clusters at the University of Southampton, which significantly reduced execution time. By developing SliMFinder into a Taverna workflow, the software was given a user-friendly interface. Rather than having to learn and type commands, scientists can now use Taverna’s intuitive, pointand-click interface. This opens up SLiMFinder to a much wider audience. The use of Taverna also allows scientists to share their experiences and their work through Taverna’s myExperiment website – which was described by New Scientist as MySpace for scientists. Richard believes that this user friendliness will lead to the real benefit of the new SLiMFinder: any biologists could use it, regardless of their computing experience. This superior ease of use, combined with the faster execution times, has made SLiMFinder into a tool that could be of great interest throughout biological sciences, as Richard explains: ‘It’s made the difference between a tool that people would think “that’d be interesting, but I’m never going to use it” and something that people could try out to see if it’s interesting’. For further information about this article, please contact: Simon Hettrick (tel. 023 8059 8871, email: publicity@omii.ac.uk) www.nesc.ac.uk Issue 71, July 2009 The Art of Community Building By Iain Coleman E-Science may have originated in the hard sciences, but it wasn’t long before some enterprising scholars in the arts and humanities saw the potential to revolutionise their own research practices with distributed computing. A community of digital pioneers grew up, crystallising around the Arts and Humanities Data Service (AHDS), finding new ways of using e-Science techniques in disciplines as diverse as history, literature, and the performing arts. But funding for AHDS came to an end, and the digital arts and humanities community might have crumbled had it not managed to rally around new forms of organisation. One of these is arts-humanities. net, a community web resource developed by Torsten Reimer and his colleagues at Kings College London. It was designed as a living site to support research activities and virtual communities, encouraging networking and promoting community events. And community is at the heart of the project. Users build up the extensive knowledge base of digital arts and humanities projects, tagging their information so that it can be browsed by subject, method and output type. The events calendar can also be tagged, and users can discuss arts and humanities events in the hosted discussion forums and blogs. The result is an extensive and rich resource of information and social connections, sustaining the digital arts and humanities as a coherent research community and giving scholars new to e-Research a way to learn about new methods and possibilities. For all the importance of user contributions, the key to a thriving and useful web resource is enlightened editorial control. This means it is not strictly a Web 2.0 project, even though it uses a lot of Web 2.0 tools such as tagging, NeSC News arts-humanities.net aggregation and syndication. But it does allow the kind of quality control that is needed to keep the site usable and reliable, whether that involves ensuring that a project description is complete and well-structured, or performing some discreet pruning of taxonomies that might otherwise proliferate into ever-narrower subsub-classes. The biggest task is not the editing, or even the coding: it is encouraging contributions and user activity. Here, arts-humanities.net has been remarkably successful in soliciting a substantial amount of project information, even if a little polite pestering has sometimes been required. The team are still working on ways to increase activity, and this centres on ensuring that academics are able to gain credit for their contributions. There has to be a clear benefit to people who spend time adding information to the knowledge base or participating in discussions, 4 and enhanced visibility of individual members is a part of demonstrating to the community when someone adds value to the site. Ultimately, it is the ratio of benefit to effort that determines whether or not people will contribute, and the challenge to the arts-humanities.net team is to make that ratio as high as possible. Forced by circumstance, the digital arts and humanities has found itself taking a lead in establishing a research community with its base in the virtual world. It has not been easy, and there are still improvements to be made in the light of experience, but the success of this project may provide valuable lessons for other research communities in the digital age. For more information, see http://www. arts-humanities.net/ www.nesc.ac.uk Issue 71, July 2009 OGF appointments for NGS staff The NGS is pleased to announce that two members of staff have recently been appointed to the OGF board. Dr David Wallom, NGS technical director based at the University of Oxford, has been appointed VP of e-Research taking over from Geoffrey Fox. David’s responsibilities include co-ordinating and steering the interactions of the research communities and their participation in OGF with the other functions, including Enterprise and Standards. David stated that “since there are also significant situations where we are not seen as the natural place for these groups, they normally for example have a conference of their own, then it is important that OGF ‘goes on the road’ as it were”. Jens Jensen, based at RAL, was appointed Area Director for security. Jens explained that “this is an interesting challenge which I look forward to. For one thing, there are numerous security related projects building things for the NGS, and being able to chase them about using standards - or creating them when they don’t exist - will be useful”. RA training The NGS will be running a training course for new RA operators at RAL on the 21st of July. The short course (11am – 2pm) is designed for new RA managers and operators. It gives comprehensive training on the procedures and tasks that RAs will encounter. Items on the agenda include certificate security, how to authenticate users requesting certificates, how to approve and revoke certificates and operation of the RA web interface (https:// ca.grid-support.ac.uk). If you would like to attend the course please register your interest by emailing support@grid-support.ac.uk. David Wallom, VP of e-Research Upgrade to NGS P-Grade portal to make life easier for you! The NGS partner site, University of Westminster, is releasing a new workflow interoperability solution available through the NGS P-GRADE portal (http://ngs-portal.cpc.wmin. ac.uk) to support NGS users to run their applications. The latest edition of the quarterly newsletter from the NGS is out now. Featuring a host of articles on use cases, new technology and the grid community the newsletter can be downloaded from the NGS website at www. ngs.ac.uk/newsletter. P-GRADE portal has been extended with the capability of nesting heterogeneous sub-workflows and execute them on NGS resources. The solution, that currently supports the embedding of Taverna, Triana and Kepler workflows in PGRADE workflows, is based on the GEMLCA Grid application repository and submitter. Particular highlights are a report on the Protein Molecule Simulation workshop held at the NGS partner site, the University of Westminster as part of the Engage project (www.engage.ac.uk); ongoing collaboration between NGS, OMII-UK and the Australian DataMINX project; cloud computing and the NGS; the HARC scheduler and much more. Description of the workflow interoperability solution, manual and case study presenting this solution can be found on the wiki page of the NGS P-GRADE portal. NGS newsletter NeSC News 5 www.nesc.ac.uk Issue 71, July 2009 Oxford is the place to be this December... Photo courtesy of Freefoto.com Oxford’s the place to be this December - Two exciting conferences. One week. One location. Keep up with what’s happening in e-Science – two key events in the same week this December in Oxford. The 2009 UK e-Science All Hands Meeting takes place from Monday 7th - Wednesday 9th December, followed by the 5th IEEE International Conference on e-Science from Wednesday 9th - Friday 11th December. Paper submissions are open now for both conferences and we are pleased to announce that the first Tony Hey student essay prize will be awarded at the All Hands Meeting. Registration opens soon and we are already accepting declarations of interest from organisations interested in having a display booth at one (or both!) of the events so make sure to keep the dates clear in your diary. To find out more please visit the conference websites at: www.allhands.org.uk <http://www. allhands.org.uk> & www.escience2009.org <http://www. escience2009.org> Workshop Programme to Open the 5th International Digital Curation Conference The 5th International Digital Curation Conference will open its doors on Wednesday 2 December at the Millennium Gloucester Hotel in London with a day of workshops covering different aspects of digital curation that will vary in style and content from discussion and discourse through to tools and training, followed by an evening drinks reception at the Natural History Museum in London. The following four workshops have been confirmed so far: New Perspectives on Research Data: How and why is digital curation shaped by disciplinary dimensions? The SCARP Project case studies have explored data curation practice across a variety of clinical, life, social, humanities, physical and engineering research communities. This workshop will look at selected examples, considering the lifecycle of different data assemblages, and NeSC News the risks and benefits encountered in curating them with the aim of stimulating discussion on the practical steps needed to manage this lifecycle and to translate approaches across communities. Digital Curation 101 Lite Research councils and funding bodies are increasingly requiring evidence of adequate and appropriate provisions for data management and curation in new grant funding applications. This one-day workshop is aimed at researchers and those who support researchers and want to learn more about how to develop sound data management and curation plans. The workshop will provide an introduction to digital curation, the range of activities and roles that should be considered when planning and implementing new projects, and an overview of tools that can assist with curation activities. Citability of Research Data 6 Citable datasets are accessible and can be integrated into existing catalogues and infrastructures. A citable datasets furthermore rewards scientists for their extra-work in storage and quality control of data by granting scientific reputation through cite-counts. The workshop will examine the different methods for the enabling of citable datasets and discuss common best practices and challenges for the future.This will be a half-day workshop Repository Preservation Infrastructure (REPRISE) The workshop will discuss digital repositories and their specific requirements for/as preservation infrastructure, as well as their role within a preservation environment. Further details are available at http:// www.dcc.ac.uk/events/dcc-2009/ programme/ Booking for the workshops and conference will open in July 2009. www.nesc.ac.uk Issue 71, July 2009 e-Science 2009 call for papers Scientific research is increasingly carried out by communities of researchers that span disciplines, laboratories, organizations, and national boundaries. The e-Science 2009 conference is designed to bring together leading international and interdisciplinary research communities, developers, and users of e-Science applications and enabling technologies. The conference serves as a forum to present the results of the latest research and product/tool developments and to highlight related activities from around the world. The sixth IEEE e-Science conference will be held in Oxford, UK from Dec 9-11. The meeting coincides with the UK e-Science All Hands Meeting that will be held from Dec 7-9th, 2009. Building on the successes of previous meetings, we would like to develop some themes at the conference. These include: Arts and Humanities and e-Social Science, Bioinformatics and Health, Climate and Earth Sciences, Digital Repositories and Data Management, eScience Practice and Education, Physical Sciences and Engineering and Research Tools, Workflow and Systems There is also the opportunity to submit a workshop programme that is focussed on newer and less well developed areas of research. conforming to the above guidelines can be submitted through the eScience 2009 paper submission system (see URL below). It is expected that the proceedings will be published by the IEEE CS Press, USA and will be made available online through the IEEE Digital Library. All papers will be peer-reviewed. Accepted papers from both the main track and the workshops will be published in pre-conference proceedings published by IEEE. Selected excellent work may be eligible for additional post-conference publication as extended papers in selected journals, such as FGCS ( http://www.elsevier.com/locate/fgcs ) Papers Due: Friday 31st July, 2009 Notification of Acceptance: Tuesday 1st September, 2009 Camera Ready Papers Due: Friday 18th September, 2009 Websites http://www.escience-meeting.org/ eScience2006/instructions.html https://cmt.research.microsoft.com/ ESCIENCE2009/Default.aspx DCC releases draft checklist The Digital Curation Centre (DCC) is delighted to announce the release for public comment of its draft content checklist for a data management plan. For more information on the DCC, please see http://www.dcc.ac.uk. In addition to our recent summary of main UK research funders’ policies and the support infrastructure they provide (http://www.dcc.ac.uk/ resource/curation-policies/indexnew), the checklist is intended to act as an aide when producing data management plans as part of new research projects. Following the public consultation, the content checklist will be developed into an interactive, web-based tool into which researchers can insert their own information and automatically generate customised data management plans. To view the draft checklist, please see http://www.dcc.ac.uk/docs/templates/ DMP_checklist.pdf. Comments and suggestions on the draft checklist and/or desired functionality for the online tool are invited at http://www.dcc.ac.uk/ feedback-dmp-checklist/. The deadline for submitting feedback is July 3rd 2009. As well as the vibrant research agenda the meeting will offer the opportunity to meet socially with colleagues in the some of the UK’s most spectacular University venues. Authors are invited to submit papers with unpublished, original work of not more than eight pages of double column text using single spaced 10 point size on 8.5 x 11 inch pages, as per IEEE 8.5 x 11 manuscript guidelines (see website list below). Authors should submit a PDF or PostScript (level 2) file that will print on a PostScript printer. Papers NeSC News A new issue of Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences is available online, containing selected papers from the UK e-Science All Hands Meeting 2008. The Table of Contents is available online at: http://rsta.royalsocietypublishing. org/content/vol367/issue1897/?etoc Print copies of the document are available at the special price of £47.50, reduced from £58. To place an order at this price, please enter the code TA 1897 for vol. 1 or TA 1898 for vol. 2 at http://rsta.royalsocietypublishing.org/ site/issues/computational_eScience.xhtml 7 www.nesc.ac.uk Issue 71, July 2009 e-Social Science at the University of Manchester The University of Manchester is re-vitalising its e-social science research programme with the launch of the Manchester eResearch Centre (MeRC) under the directorship of Professor Rob Procter. The Centre will pursue two related strands of work. Its applications strand seeks to develop an enabling infrastructure (e-infrastructure) – comprising advanced information and communication technologies – that will support social scientists in their pursuit of new solutions to their substantive research problems. The social shaping strand adopts a social studies of science and technology approach to understand how e-science, including e-social science, is being developed, how it is being used and what its implications are for scientific practices and research outcomes. MeRC builds on Manchester’s five years of highly successful operation as the coordinating Hub of the National Centre for e-Social Science (NCeSS), responsible for the strategic management of the Centre’s seven research projects (‘Nodes’) at universities across the UK. The Hub is widely recognised to have played the key part in establishing NCeSS internationally as the world-leading centre of e-social science, and its success has influenced analogous developments in other countries. From October 2009, the ESRC plans to use a different model for coordinating the final phase of NCeSS and the key research work of the Hub will be carried forward by MeRC. MeRC will enable Manchester to retain its major role in UK e-social science. It will continue to collaborate closely with other researchers in e-social science across the UK and beyond. It will take forward several existing projects and it will continue its impressive record of attracting funding (20 awards over the past five years) to extend both strands of its work. For further information, contact Professor Rob Procter: rob.procter@manchester.ac.uk. Forthcoming Events Timetable July 13-16 StoMP2009: Noisy Bugs: Modelling and Microbiology eSI http://www.nesc.ac.uk/esi/events/962/ 20-24 Emerging Modelling Methodologies in Medicine and Biology ICMS http://www.icms.org.uk/workshops/ modellingmethodologies 22-23 Developers and Architects Meeting for Arts and Humanities Research Infrastructures eSI http://www.nesc.ac.uk/esi/events/1004/ 22-24 ADMIRE Consortium Meeting #6 NeSC http://www.nesc.ac.uk/esi/events/982/ 27-28 Developing Shared Resources for Digital Research in the Arts and Humanities eSI http://www.nesc.ac.uk/esi/events/1002/ 27-31 Kinetic and Mean-field models in the Socio-Economic Sciences ICMS http://www.icms.org.uk/workshops/ kinetic 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 August 2009 issue is July 17, 2009 NeSC News 8 www.nesc.ac.uk