A new era for the post EMI: all together for MeDIA

The European Middleware Initiative (EMI) presented a new initiative for a long-term, open, lightweight collaboration on the coordination of distributed middleware technologies: the Middleware Development and Innovation Alliance (MeDIA). The goal of the initiative is to facilitate the future development and evolution of middleware solutions beyond the current short-term project limits. The event launch took place last week in one of the most ancient places of the world, Rome, just remembering what Roman poet Ovid said in his Metamorphoses: omnia mutatur; nihil interit, that is everything changes, nothing perishes. The place was indeed the right stepping stone to open a new era for the EMI project, which achieved many important results in the design and implementation of common services and technical agreements in several areas.

As EMI has shown the importance of coordination and iterative practical implementation and validation, MeDIA would like to provide this same highly qualified cooperation mechanism through the definition of dedicated working groups based on contributions from several development teams. The workshop represented a truly open kick-start meeting to summarise three years of work and achievements of the EMI project and to discuss about future goals, scope, activities finalised to setting up new technical collaborations among team leaders, members of middleware development teams and other interested parties, such as technical experts from the user communities, infrastructure providers, application developers, and commercial companies.

During the entire event, the heated discussions put the spotlight on an effective and sustainable continuation of the key activities. In substance, MeDIA plans to provide a forum for coordinating the innovation and development of middleware services across academic and scientific research infrastructures based on the members’ interests and priorities. The members’ participation is voluntary and bottom-up and relies on an active sharing of information, proposals and ideas from members to members.

The participants were very proactive in all debates and, after fruitful exchanges, have outlined the following goals for the MeDIA initiative:

·         To provide a forum for synchronization of technical development roadmaps;

·         To concretely act upon the actions identified during the roadmap discussions;

·         To build the bases for a solid collaboration platform on distributed computing and data management;

·         To enhance the relationships among all partners using modern social networking techniques.

In conclusion, MeDIA is intended to be not only a coordination initiative to give software developers from existing EMI product teams, but also a place where the technical collaboration can continue and expand to include other development teams worldwide. Last, but not least, this initiative aims to outline future technical roadmaps for the European research infrastructures, promote interoperability and common development work, and put in place all the necessary activities to continue the success of EMI.

Wrapping up at CAPRI – beers, bikes and brainstorming

At the end of a long day at the CAPRI meeting, the sessions closed with a brainstorming discussion on the present and future of CAPRI. Which targets should be in the frame for the next phase? Before the discussions got underway though there were a series of lightning talks from early stage researchers – great to see them brought into the spotlight. A session on docking methodology and servers followed. Paul Bates of Cancer Research UK focused on the SwarmDock server, a webservice for generating 3D structures of protein-protein complexes, by looking for the lowest energy solutions. He described the swarming process as a bit like wandering around Utrecht after a few beers – you might end up in the canal, get lost down a cobbled street or “be run over by one of these high speed cyclists.” There was a big laugh of recognition from the delegates for that one.

Anisah Ghoorah from the University of Lorraine, INRIA, pointed out that, “Docking is difficult, but that also makes it interesting.”  Ab initio techniques i.e. starting from scratch are too difficult, so there’s a need to use templates and knowledge based approaches. “CAPRI should focus on the difficult cases – leave Google for the simple ones,” he said.

ClusPro was the first fully automated, web based program for computational docking of protein structures. It has been around for 10 years, and has about 3000 users. Sandor Vajda of Boston University had been looking at usage of the server over the course of the year.  “First of all you can see that dockers don’t work on the weekend – and they go on holiday in August,” he pointed out. “And no one cares about Christmas!”

Martin Zacharias of TU Munchen wound up the session by presenting protein-protein docking and refinement with a coarse-grained protein model. The computing needed seems very efficient. “It’s possible to do 10,000 docking simulations on a single core in an hour,” said Zacharias. “These happen much faster in reality than they do in silico.”

Finally, the community took at look at some new areas proposed for CAPRI. These include interface predictions, useful for cancer studies and interface water predictions, which are potentially very challenging and are currently underrepresented. Also floated were protein-peptide interactions, protein-oligosaccharides, protein-RNA and even protein-DNA (with a question mark). For affinity challenges, it’s a question of what they both can and want to evaluate. From the discussion, it was clear that they are looking for a mix of easy and difficult targets, as well as having lots of targets to choose from. However, cooperation from the structural community is essential – they need to submit their structures to compare with the predictions. “They won’t solve the targets just to be nice to us!” it was pointed out. So it’s not just protein-protein interactions that are important in the end, but those between the structural biologists and modellers as well.

Proteins by design – expanding on nature

Yesterday at the CAPRI meeting,  a heartfelt plea from Dr Ilya Vakser of the University of Kansas really caught my ear. “There’s so much data and so few people to dig into it!” he cried.

Dr David Baker of Washington University, Seattle introduced the CAPRI meeting to the design of proteins, and how they interact with each other. It could all have been different though – first Baker polled the audience to see whether they would prefer to hear about structural modelling with sparse data instead.  That’s the first time I’ve ever seen audience participation in a talk at that level – it was practically the conference equivalent of X Factor.

Once he had the correct set of slides cued up, Baker started out by praising the excellent job that Mother Nature’s naturally occurring proteins do. They solve the challenges that biological evolution presents perfectly, such as capturing and storing energy, making and breaking down molecules. However, thanks to modern life we now find ourselves faced with challenges that are not thrown at us by nature alone, such as global warming and living longer. The question for protein designers is can they design a whole new world of synthetic proteins to address these challenges? “Ideally we should take less than 2 billion years to figure out how to do it,” said Baker.

There are a number of areas to focus on, including designing the next generation of therapeutic proteins, building scaffolds for enzyme reactions, and self assembling cages to carry drugs and vaccines into the body. The process starts by calculating a sequence of biological building blocks known as amino acids that might give the desired protein structure and function. You read off the sequence, and translate that back into a DNA sequence that would encode the synthetic protein. Once you have a DNA sequence, you can then make the gene that will then build the protein you want. As a non-biologist, this was the part that I found like an extract from a sci-fi novel – you can now buy a custom gene over the internet, and then back comes the DNA encoder that you need. Build your protein, then see if it does what you want.

But the process starts with finding the sequence with the lowest energy configuration – because molecules like to exist at the lowest possible energy. It’s difficult to know whether the structure you have found is the lowest possible however and this is where non-scientists can get involved. Rosetta@home is a volunteer computing project which uses spare computer time donated by volunteers to look for the lowest energy versions of protein sequences and send back the solutions. Luckily the synthetic protein structures are somewhat easier to predict than naturally evolved proteins.

Baker ran through some more key challenges for protein builders, such as designing binding between proteins when looking for ways to treat Spanish flu, and finding methods to inhibit intracellular interactions when you need to target just one black sheep out of a whole family of proteins, for example the Epstein-Barr virus. 

FoldIt puzzle screenshot

One question Baker asked is, "Why are the enzymes we design ourselves so lousy?" Here he turned to the FoldIt volunteer community. FoldIt was dreamed up in response to Rossetta@home users who wanted a bit more of a challenge. FoldIt poses protein folding puzzles to users, to check protein design sequences and see if in silico folding predications are accurate.

One example is the de novo designed Diels-Alderase, an enzyme for forming carbon-carbon bonds.  "Can we improve activity by remodelling active site loops?" asked Baker. "Let’s ask the Foldit community!" He gave them a solve it game for FoldIt players and one successful player increased the interaction 20 fold. When the crystal structure was solved, it was found to be very similar to the prediction. ”Now I’ve come to be a big believer in the concept that if you don’t know the answer, ask more people until you do!” said Baker. A response to Vaksar’s plea earlier perhaps – the people to analyse your data are out there, you just need to give them the tools to do it.


(For more information about volunteer computing, read the e-ScienceBriefing at http://www.e-sciencetalk.org/briefings/19/ESTB-19-Desktop-grids-Connecting-everyone-to-science.html)

Combining and conquering at the CAPRI 5th evaluation meeting

After the beer and curry-fest of Manchester and the EGI Community Forum last week, e-ScienceTalk is taking a more leisurely sojourn in a sunny, cobbled Utrecht for the CAPRI 5th Evaluation Meeting. The strapline for the event is ‘Combine and Conquer'. Many processes in the body’s cells are driven by large, complex molecular networks of proteins. The 3D structures of these combined complexes are often the key to their function. But deciphering their detailed structure is difficult, because you need access to large pieces of kit such as X-ray synchrotrons or  nuclear magnetic resonance machines, plus these protein complexes can be fiendishly tricky to crystallise. Lower resolution techniques such as small angle X-ray scattering can give clues and increasingly this data is being used as a starting point for computational modelling. Predicting, modelling and understanding these large complexes is making an important  contribution to drug and protein design – but how confident can you be that the models are correct? CAPRI (Critical Assessment of Predicted Interaction) is an international effort to assess the performance of these methods, by inviting developers to test their algorithms on the same protein targets. This week’s meeting focuses on assessing the performance of docking methods in predicting the 3D structure of complexes and is extending the challenge to predicting binding and de novo interface design.

The opening keynote was by Piet Gros of Utrecht University and winner of the prestigious Dutch Spinoza research prize in 2010. Actually, Gros comes from Dokkum in North Holland, a neat coincidence with the focus on ‘docking’ interactions between proteins at the event. “Although if you think Utrecht is flat, it’s a hill compared to Dokkum,” he remarked.

Gros’s talk highlighted the complement system, which is an ancient part of our immune defence found in the blood. The complement system is formed by around 30 large plasma proteins and cell surface receptors. This system then recognises and eliminates bacteria, viruses and altered host cells, while protecting healthy cells. It links our inbuilt and acquired immunity. “Essentially, it cleans the garbage,” said Gros.

You won’t see a ‘complementology’ department in a hospital, but disruptions in this systems can lead to a range of health problems. It is linked to auto immune conditions such as rheumatoid arthritis, stroke and heart attacks and injuries due to a loss in blood supply, for example to the brain. Genetic changes in complement proteins can lead to kidney conditions and eye problems, such as age related macular degeneration (AMD).  They even have a role in infections, such as EHEC a type of E.coli bacteria, which led to the most expensive drug on the planet being used 2 years ago in Germany during an outbreak.

Using structural studies, Gros’s team has revealed the molecular mechanisms responsible for their functions, such as central amplification, protection of the host body and what happens at the start when a membrane-attack complex forms. In molecular terms, the structural re-arrangements involved are large – about 100 A when a typical atom is a few Angstroms in size (one angstrom is one ten billionth of a metre).

Alexandre Bonvin of the WeNMR project asked Gros to tell the computational modellers in the room what might be lacking from the toolkit he needs for his work. Gros didn’t pinpoint an example, but agreed that the docking modelling and structural work with X-ray crystallography were indeed complementary fields (no pun intended I guess). “In the end we should be able to model everything,” he said, “because otherwise it means we still don’t understand it.”

Over the classic local 'borrel' later, I asked Dr Gros about the computing he uses to support his structural work. Essentially he uses an in-house computing cluster, and does not foresee a need for expanding out to grid computing or the cloud at the moment. This makes an interesting contrast with the WeNMR project community, which relies heavily on grid portals to help them to work on NMR structural data. This presents a challenge for e-Infrastructure providers such as EGI.eu when reaching out to the ‘long tail’ of science – how to engage users with international federated resources when increases in computing power make home grown resources so attractively simple, but maybe not scalable? Does this mean that the long tail has no need of scalable solutions to solve their questions – or can the questions themselves scale up?

SCI-BUS update brings clouds to scientific gateways

On Friday morning, we had the chance to catch up with Zoltan Farkas from SCI-BUS and Pamela Greenwell from the University of Westminster, UK, to talk to them about the new development in SCI-BUS which is bringing clouds to the platform – and the new science this enables.

Tom Morrison from STFC: EGI Training Marketplace

Tom Morrison from STFC is the developer of EGI Training Marketplace. Here he shows us a demo of how it works:




Tom also had time to talk to us about his highlights of the Community Forum:

Thomas Kulhanek: EGI Champion!

Tomas Kulhanek talks to us about integrative physiology and his role as an EGI Champion:

Getting citizen scientists on your team

There are currently four million volunteer computers searching for new pulsars for the Einstein@Home. This sleepy distributed team has so far collectively processed over 1 petaflops. 46 individual pulsars have been discovered this way. Dr Ad Emmen (AlmereGrid) introduced a session yesterday, 'Getting citizens scientist on your team'. Ad roughly calculated that in Greater Manchester alone there could be over 2.5 million computer sitting idly. It is now estimated that there could up anyway up to 2 billion computers worldwide.  The potential growth of this computing capacity is enormous.

One project, International Desktop Grid Federation (IDGF), has been harnessing this processing power.  IDGF brings together those interested in desktop grids including 50 different desktop grids, 50 member orgnisations, and over 240 individual members. 

As an IDGF member, institutes have access to high level science gateways with a host of applications for end users. There is also certification support, a roadmap for guiding the management of desktop grids for administrators, plus a vimeo training channel and a technical wiki.

In June 2012, the monthly performance of the desktop grid virtual organisation (VO) in the EGI portal was an impressive 1,051,051 CPU hours.  It basically held the 10th spot for a while. However, this number fluctuates and IDGF have ambitions to capture more processing power for scientific research. By contrast, the ATLAS experiment uses 100,000,000 CPU hours.

Dr Robert Lovas from MTA SZTAKI introduced IDGF-SP . The idea behind this support programme is to gather experiences, promote success stories and set up a coordinated campaign to boost uptake of desktop grids by institutes, universities and researchers across the globe. It also hopes to encourage the growth of a network of citizen scientists.


What IDGF-SP is currently looking for are ambassadors to bridge the gap between scientists and citizens. Similar to the EGI champions programme, IDGF-SP are hoping to encourage the promotion of desktop grids usage inside and outside scientific organsitions. One of their current ambassadors is Professor Stephen Winter from the University of Westminster. Last year, the university saved £500,000 from deploying a desktop grid (DG).

IDGF-SP was launched in December 2012. Another aim is to build a desktop grid virtual team by:

• Promoting the technology in the EGI communities
• Adding DG resources to more virtual organisations (VOs)
• Collecting spare capacities from VOs
• Running new applications on the integrated infrastructure
• Finding EGI champion/IDGF ambassadors

The project will collect data in an application super-repository where users can see existing applications and associated metadata (i.e. attributes and implementations etc) and administrators have access to SZDG technical wiki (a consolidated knowledge base for DG related technologies).

Check out our educational website, Volunteer Garage (www.volunteer-garage.org). 

More than just computers: it's science! Meryam Tahar talks to e-ScienceTalk

Meryam Tahar is a year in industry student at the STFC. She tells us about her perspective on the Community Forum and why more young people should consider science and technology careers:

Another EGI Champion interview: Fotis Psomopoulos

Fotis Psomopoulos develops data-mining algorithms for genomic research and protein modelling, and he is talking about life sciences:

Climate modelling on the grid: Eleni Katragkou, EGI Champion

Eleni Katragkou is a climate scientist from the University of Thessaloniki in Greece. She uses the grid to build more accurate climate models that integrate data at different scales, and is an EGI Champion. We managed to catch her during a break and this is what she had to say:

Using the grid to help make decisions in water network engineering

It's been unusually dry, for the first half of the week at least, for a conference in Manchester. There wasn't much water falling from the sky.

The community forum is here for people doing scientific computations, or computational science. Computer networks rely on infrastructure and network engineers are the experts in setting them up.

What about water distribution networks? (See what I did there? – a somewhat obtuse segueway, I grant you.) These marvels of 19th century engineering in the UK can present a challenge when it comes to managing them, mainly because you can't actually put sensors everywhere you might need them to figure out how flows can be regulated. Could you use grid computing and the information from sensors you can access to predict how the network is operating in places where sensing is impossible?

Well, yes!

John Brooke from Manchester University spoke to us about his work developing the architecture to enable this kind of prediction:

Silvia Olabarriaga discusses bioscience gateways

Silvia Olabarriaga accepted to talk about setting up a gateway for bioscience

Matteo Turilli and Federated Cloud Taskforce

Matteo Turilli from the Oxford e-Science Research Centre tells us about the EGI Federated Cloud Taskforce:

Knowledge and Technology Transfer on the EMI (or better SciencePAD) spot

EGI Community Forum 2013, at its second day in the University of Manchester: EMI, more precisely SciencePAD (Platforms, Applications, Data), keeps focussing on sustainability. This time the curtains opened the scene on Knowledge and Technology Transfer (KTT).

It seems indeed to be one of the best approaches. Why? Let’s consider…Have you ever considered how technology affects our everyday lives, so much so that we don’t even think about it? Just consider what each day will be without technology. You wake up to an electronic alarm; brush your teeth with an electric toothbrush while the coffee is getting ready and the television is on with the last news. What is the first thing you do at work? Sit in front of the computer and read e-mails from anywhere in the world.

Directly or indirectly, technologies can have a significant impact, sometimes less evident, in every aspect of your life. Even though we can easily access them, this is not for granted but it is the results of a long process. For centuries, in the quest to find out responses to its major queries, fundamental research developed very sophisticated instruments using cutting-edge technologies and requiring performance that often exceeds the available industrial know-how. Technology has promoted and still promotes on all levels the injection of science into daily life in many different ways. For example, nobody would ever have thought that a phenomenon based on the theory of quantum mechanics – quantum entanglement – would find practical applications in the fields of cryptography, computing and, who knows even teleportation in the future, leading to the creation of new companies to secure information sharing. Moreover, technological developments most often require the involvement and interaction of experts in a large variety of domains, such as IT and derivatives, thereby resulting in technological cross-fertilization and knowledge transfer.

“SciencePAD allows decisions to be taken based on knowledge shared and verified by a large community of experts, for developers to share their software, researchers to get the needed support, companies to offer services, and sponsors to assess the projects’ impact. – Says Alberto Di Meglio, EMI project director and chair of the SciencePAD collaboration. –– Just as today, the EMI project is able to help the complex relationship among experts (developers, users, service providers, research communities, commercial companies, etc.) working in the different data environments (Cloud, desktop, stand-alone, High-Performance Computing, etc.).”

So, let’s see more specifically what the SciencePAD KTT future requirements are:

1.      To understand how to manage software information within scientific communities

2.      To formalise such information and its integration with the other digital entities

3.      To guarantee the long-term preservation and re-use of software, especially related to data

4.      To realise a data-driven Software as a Service prototype platform for research.

Last, but not least:

5.      To investigate the constraints, conditions and tools required to promote the transfer of ideas and people from academic research to commercial endeavours.

Thanks to the technologies developed for the purpose of research activities, scientific laboratories have produced improvements in many fields (beyond their specific domains), making our daily environment more functional, practical and comfortable. Researchers are continually working to find better solutions for technical and scientific problems from which the entire humanity profits. Even being aware, they know what Winston Churchill meant when saying: “Success is never final, and failure is never fatal”.

So, EMI (or better SciencePAD) must go on…

Malaysian masks and oral history: digital cultural preservation at the EGI Community Forum

Earlier today I had the chance to chat to Dr. Farridah Mohd Noor fron the University of Malaya about her work on digital cultural preservation:

Facilitating the discovery and uptake of software: EMI, DCore, SciencePad

Beyond European Middleware Initiative (EMI) was the subject of a popular EGI session yesterday afternoon. Robert Harakaly spoke about some of the developments with DCore data and knowledge platforms and software, which are rooted in EMI technologies. One solution addresses the need for match-making for scientists with similar issues building an automatic ontology collaboration platforms. Robert is also currently piloting a platform for internal secure enterprise storage system at his own campus at Safarik University Slovakia. There has also been interest outside the academic world from the banking sector in Switzerland, and a new technology project is in preparation examining security in medical data management again also based on EMI services. 

Another project from EMI, addresses another important issue. How do developers really know who is using their software? EMI is very good at developing software but perhaps not as good at advertising or finding out how their middleware has been used. This was a previous concern of EMI Project Director, Alberto Di Meglio.  Last year, EMI set up SciencePad (formerly known as ScienceSoft). This project will try to solve issues in identifying, evaluating and leveraging existing software through re-use.  "It's about following the value chain so the impact of software can be made more apparent,"said Alberto. SciencePad is currently preparing for the operational phase. iSGTW reported on their last workshop on 'Persistent IDs for software workshop' in January. Their next workshop will be on software registries and metadata later this month.  

It’s not only middleware that has that problem with gaining wider recognition and keeping track of its impact. Software is no longer easy to define, says Neil Hong. Neil is the Director for the Software Sustainability Institute (SSI) in the UK. What is required is a simple way of  recognising and monitoring use of a piece of research software.  Neil pointed out that a simple presentation can have a DOI, ORCHID and fig-share, it is more complicated for software because of four considerable problems of "Boundary, Granularity, Versioning and Authorship". 

There were several take-home messages from Neil's talk including the SSI five star of research software. Check out Neil's recent blog for more information. Neil also mentioned the SSI Journal of Open Research Software, which is helping with reusability for software.  SSI also has a top tips page for scientific software. Neil recommended the extensive work of ImpactStory which is developing a framework for measuring impact in non traditional ways by directly monitoring software citations. One day forking a github repository would be as recognised as formally publishing a paper.

Morris Reidel, who chaired the session emphasised the importance of "e-science application enabling".  Information is dense in specific communities, but luckily there is now more coordinated effort to find out what’s happening in the other infrastructure currently.  Towards the end of the session we heard from a community which is trying hard to facilitate software discovery in their domain. The biomedical field is complex covering genomes to systems to everything in between. Julie McMurry from BioMedBridges (a joint effort of ten biomedical sciences research infrastructures on the ESFRI roadmap) introduced a project she is working on building a software/ tools registry. They are collating together information on all types of biomedical software  including web services (REST-style), web UI, desktop GUI, grid enabled tools, command –line tools etc. The software can be filtered attributes and use cases. 

Slides from this session can be found on the EGI website, here. 

Brook Schofield interview

Project Development Officer of TERENA (Trans-European Reseach and Education Networking Association), and he accepted to talk with us about Eduroam:

Pay for use: the road ahead?

Kostas Glinos made it clear in the opening plenary of the community forum: the EC will no longer accept the status quo when it comes to future funding of e-infrastructure projects. The wonderful scientific discoveries and impressive technological developments resulting from the array of projects that make use of distributed computing must now also be backed up by greater sustainability after projects end, better coordination of resources, optimised governance and, potentially, new models for funding.

Pay-for-use is a model familiar to many in the world of cloud computing; one of the reasons that cloud has taken off in industry while grid has struggled is that businesses understand the idea of paying for a service –  paying for what they use. The marketplace in cloud is subsequently enormously diverse, a benefit due in part to the free marketplace that can quickly adapt to changing customer requirements. Competition means that commercial cloud providers now sometimes provide free cloud services to individuals with the offer of upgrading to a ‘pro’ package – more suited to a heavy user, or a business – for a recurring  fee. So could the pay for use model work to bring similar benefits to grid computing?

Scientific research is not a business: there is the need to be cautious and completely shifting to pay-for-use may not be so popular with the e-science community that is used, in Europe, to central funding for e-infrastructures and individual project funding. On the other hand, some parts of the community are already using commercial cloud providers to do everything from supercomputing, to storing large datasets. Already used to the greater agility, dynamism and adaptability of such services, they could be ready for a pay for use grid.

Warburton toll gate, south-west Manchester.
Pay the price: get to use the road.
(CC-BY-SA David Dixon)

“Until e-infrastructure providers try these models, how would we know what works,” said Sy Holsinger, Strategy and Policy Officer at EGI. After a paper from 2012 was endorsed by the EGI Council, the time was right to turn the ‘thought experiment’ into a real-world test. Exploring potential brokering models, EGI have tested ‘matchmaker’ and ‘one stop shop’ models, in addition to the ‘independent advisor’ model currently used. Matchmaker sees the federator (EGI) allocate resources from resource providers that match customer requirements, with the resource provider paying the federator for establishing the the contractual agreement and the customer paying the resource provider; One stop shop sees the federator doing everything including collecting payment from the customer, then paying the resource provider. For pay for use, both of these models work better, with lower overheads, than the independent advisor model currently used by EGI, where interactions are more decentralised (incurring more overheads); the federator listing services offered by resource providers and being funded by a membership. So pay for use may mean a shift in the role that EGI – and other infrastructure providers – adopt.

Problems and challenges ahead? There are some. Some academic research centres cannot, by law or contract, resell services to third parties. There is the question of taxation. Many member countries have VAT, which could have implications for the purpose of invoicing.

The economic situation in Europe means that, looking ahead, the status quo is not an option. Hopefully, by testing some new ways of working, infrastructure projects can explore how their own sustainability might be achieved, while making the range of computing services available to researchers more diverse and more agile: better resources, and better science. The status quo it is not.

eI4Africa and iMENTORS join forces

eI4Africa and iMENTORS:

Two EU co-funded projects join forces for e-Infrastructures

Brussels, 10/04/2013– A memorandum of understanding (MoU), a document describing a bilateral agreement, was signed between eI4Africa and iMENTORS on 4 April indicating an intended common line of action. The two projects have a common interest in a close cooperation in order to achieve their respective objectives and promote the adoption of consolidated standards in the e-Infrastructure with the ultimate aim of boosting RTDI (Research, Technology Development and Innovation) in Africa.

e-Infrastructures– electronic research infrastructures – are collections of ICT based resources and services used by the worldwide research and education community to conduct collaborative projects and generate, exchange and preserve knowledge.

iMENTORS www.imentors.eu launched in April 2012 by Stockholm University and Gov2u is a web-based platform serving as a knowledge repository for sharing and aggregating data on e-infrastructure projects throughout sub-Saharan Africa. The objectives of the project are to: 

• • Create a virtual observatory, acting as one-stop-shop data warehouse providing up-to-date information on all e-infrastructure related development programmes and initiatives of the past 5 years in Sub-Saharan Africa to increase the effectiveness and coherence of international cooperation in the field of research infrastructures.
• • Build a community of practice for support to policy development and programme implementation by creating a social hub facilitating interaction and knowledge sharing, to improve collaboration among different stakeholder groups, and offer them opportunity to create synergies and plan future projects. 

The objectives of the eI4Africa project www.ei4africa.eu are to:

• • Define and implement a structured multi-channel outreach strategy to support the development of African national and regional research and education networks (NRENs/RENs), build cooperation between Euro-African NRENs, RENs and user communities. Raise awareness at policy level on the benefits and value of research and education networks. Promote and strengthen Euro-African collaborative research on e-Infrastructures and their applications.
• • Produce a state-of-the-art study of e-Infrastructure application uptake in Africa to identify who are early adopters of e-Infrastructures (providers) and which user communities are early beneficiaries (consumers) of e-Infrastructures;
• • Select existing flagship demonstrations from other continents and illustrate their relevance to the African context in order to stimulate policy dialogue on e-Infrastructures.
• • Stimulate targeted policy and regulatory discussions, including (but not limited to) cross-border connectivity and affordable access to infrastructures by organising awareness raising flagship African e-Infrastructures application demonstrations.

Activities which will be undertaken in common by the two projects are listed in the MoU. The Project Coordinators, or people in charge of the two projects nominated by them, will maintain regular contact to discuss any managerial matters related to the cooperation described in the MoU. 

Did you say EGI Champion?

Mark Santcroos develops science gateways, workflows and applications for the life sciences. Among others, he is an EGI Champion, and he accepted to answer a few questions:

Good perspectives for the ‘beyond’ EMI

At the University of Manchester, the EGI Community Forum 2013 together with the 3rd EMI Technical Conference (8-12 April) is providing a great opportunity to reflect upon the use of the European Grid Infrastructure (EGI) across all research disciplines.

The afternoon of the first day Alberto Di Meglio, the EMI project leader, opened the afternoon sessions with a vision and strategy for the future ‘beyond EMI’. EMI is coming to an end in April 2013. During its three year duration, EMI has consolidated middleware and established a number of innovative initiatives around collaborative software developments and sustainability.

The future is indeed really promising. There were a number of long-term collaborations presentations given, including: SciencePAD (Platforms, Applications, Data) for Software information management, discovery, support for data-driven applications, open access and collaborations, and Middleware Development and Innovation Alliance (MeDIA), for technical collaborations on middleware for distributed computing and data services. Finally, Dcore Solutions, a company that uses open source and community developed software in other software solutions for eventual commercial exploitation.

SciencePAD is an initiative to capture, store and preserve information about software used in scientific research. It manages information such as publications, data analysis, authors and users, organizations, fundings, etc. in order to create a market place for software developers and users to satisfy the reciprocal needs.     

MeDIA is an open, lightweight collaboration to facilitate the development and evolution of middleware solutions. A launch event for this initiative will take place in Rome on the 22^nd of April.

A very fruitful discussion on this very complex issue ended the afternoon sessions with a call to action for middleware developers to show their interest in the MeDIA initiative. “The continuous evolution of the middleware is essential for the development of the distributed computing software and EMI has created the opportunity for the future collaborations to secure its future” – concluded David Foster, CERN IT deputy department head.

Using the grid to picture the stars

EGI Champion Joeri van Leeuwen is an astronomer who uses grid computing to process images of distant stars and galaxies. We caught up with him at EGICF13 and this is what he said:

The European Grid Infrastructure Community Forum kicks off in Manchester

The European Grid Infrastructure Community Forum kicked off in Manchester this morning. Manchester is famous for many things (architecture, culture, music, science and engineering to name just a few) but arguably is recognised most widely for a certain football team or two. There is a distinct football theme to the artwork for this week’s event, and even Professor Nancy Rothwell, Vice Chancellor of the University of Manchester, recommended in her welcome address that we refrain from discussing it with locals if at all possible.

Peter Coveney, Director of the Centre for Computational Science at University College London presented recent developments in e-Infrastructures that are helping to unlock new science. He outlined the challenges he sees in putting the rapidly growing body of scientific data to use and particularly focused on applications in biomedicine and materials science research. Discussions were around how to fund these activities and Coveney gave some examples of recent UK funding calls.

Kostas Glinos, Head of the e-Infrastructures Unit at the European Commission focused on Horizon2020, which is the European level funding programme set to start in 2014. Glinos noted that the approach to funding will be integrated and service driven. The aim is to provide integrated, de-siloed services and to establish synergies with individual member state’s e-infrastructure development programmes. Horizon2020 will move beyond science to include the science-industry-society triangle, mapping out societal and policy needs and integrating innovation into the process. Key to success is financial sustainability with ‘proper’ positioning on the user pays / provider pays axis, and a governance structure that maximises EU added value. The Commission has several priorities in the e-Infrastructure arena (to stick with the football theme). They are interested in big data, with seamless and open access for researchers. Their strategy for computational infrastructure covers supercomputing and open computing, such as grids and clouds. The funding will also focus on implementing the recommendations of the GÉANT expert group.

As a result, the first projects in Horizon2020 should produce data centric science and engineering, community driven data infrastructures and global coordination for research data. The programme will also aim to fund a series of centres of excellence that will provide training and skills development for HPC. Essentially, the three pillars of their HPC strategy include next generation exascale computing, provision of the best facilities and services for academia and industry, and should achieve excellence in HPC applications. They are also considering Public Private Partnerships to link demand and supply. According to the discussions though, the European Commission should make sure to support researchers to find ways of working with the data. In between gathering, storing and ensuring the long term archiving and labelling of data in an accessible way, researchers actually need to be able to handle the data successfully to produce results in the first place.

Steven Newhouse, Director of EGI, closed the session with a look at the road ahead. “Where have we come from and where are we going?” asked Newhouse. He looked back at the journey from the web to the grid to the discovery of the Higgs particle and asked, where do we go from here? Back in the days of the European Data Grid ten years ago, the grid boasted 4000 cores and 30 sites. In 2013, the infrastructure includes 400,000 cores and 350 resource centres. For EGI, the three areas of innovation that will take the world's largest production grid infrastructure into the future are in community and coordination, operational infrastructure and Virtual research environments. With one year to go before the final whistle blows on the EGI-InSPIRE project, but at least 18 months until Horzon2020 projects start warming up, there are some tough questions to be asked – and answered. The focus has to be on the critical core services - who needs what, and how can we sustain what we currently have? Discussions have been underway in the community for some time, and no doubt will continue intensively this week.

One thing is clear however, developing our human network is vital. You can’t win the game without the right players on the pitch. EGI already fields a network of National Grid Infrastructure Liaisons who focus on supporting the user community from inside the EGI-InSPIRE project. This Community Forum is the first EGI conference that also welcomes EGI’s new champions, a hand-picked team of researchers hailing from communities such as engineering, biomedical science, astronomy and beyond, who are supported financially by EGI to promote grid computing and EGI within their community. Several of them are at the event and you can find them online at http://www.egi.eu/community/egi_champions. If you bump into any of them, please say hello to our latest players and welcome them to the field!

Integration across computational scales

Following the opening welcome from Prof Dame Nancy Rothwell, the President and Vice-Chancellor  of the University of Manchester the first keynote presentation from Prof Peter Coveney updated the EGI community on the UK e-infrastructure situation as well as the need from a number of communities for access to resources from multiple providers at multiple scales, i.e. from EGI, EUDAT and PRACE for example. This is the nirvana to interoperability and should eventually be standardised between different e-infrastructure provided by the public and private sectors.