Interact with the NGS

I recently updated the NGS presence on Facebook to a new interactive page.  Instead of the old-style group page, the NGS now has a new page under the UK NGI banner which reflects our role as the lead in the UK National Grid Initiative along with GridPP.

By “liking” our page you can receive news updates from the NGS all in one place as well as news updates from the Software Sustainability Institute (SSI) and GridPP.  Please feel free to invite your friends and colleagues to "like" our page and to share articles with your friends list - help spread the word about e-infrastructure! 

NGS at SC'11 - round up

The UK presence was fairly significant this year at SC'11 with attendance by David Wallom, NGS Technical Director and a significant number of the leaders of research computing centres from around UK universities. This included NGS member sites @ Bristol, Leeds, Oxford, Southampton and EPCC.

In this blog post, David gives us a round up of NGS activities at this major computing event.

Having got off of the very long flight from Heathrow
to Seattle we settled onto the metro to get us  downtown. After passable sleep the following morning we headed over to the SC’11 venue – the Washington Convention Centre to collect our badges and then visit the workshop on HPC in Smart Grid, where there was UK interest from the EC FP7 HiPerDNO project being presented by Dr Stef Salvini, OeRC. Following a very productive day where we learnt the state of the art in US Smart grids, how they intend to utilize knowledge developed through the national e-infrastructure for research. We then met up with the EGI team who had an exhibition stand at the conference.

The Monday workshop, Many-Task computing on Grids and Clouds 2011,  started off with an interesting keynote from David Abramson (Monash) a long term friend of the NGS through support for their Nimrod tool which is popular with several of our biosciences users. After this there was a panel session which went slightly off topic to talk about exascale more than Many task but it still attracted several questions around the need for exascale, when we are still struggling to get a significant user base onto smaller HPC systems. Overall a good workshop though having the panel first did mean that a number of people didn’t hang around for the rest of the papers. This workshop was operating in a very competitive market with other sessions on cloud and data management which also attracted significant crowds.

The first full day of the conference allowed for the first good look around the exhibition floor alongside several interesting birds of a feather sessions There was also the  first of a number of conversations with different groups and vendors, including Microsoft, Mathworks and Adaptive Computing.  To give an idea of scale this picture is down one of the main aisles in one of the 5 rooms that were all about this size!!



Pretty impressive stands by a number of people
but the coolest was the multi projection globe on the NOAA stand.

We of course also announced
our activity with Globus Online which created a lot of interest and ended with us having a number of interesting conversations with NSF regarding future collaboration between our national e-infrastructures.





During the meeting the EGI booth was continually visited by a reasonably large number of people, we had the Real Time Monitor showing as normal (having seen a lot of 3D screens this needs to be done in 3d now for next year!). They did though give away a pretty large number of t-shirts as did a lot of stands, so I ended up as the moving poster board around down town  Seattle from 6:30-7am every morning on my morning run!

Dinosaurs, DNA and nuclear power

Just a normal month or so in the life of the NGS really but what do all 3 have in common?

They were all research areas investigated using NGS resources.

The research of William Sellers, Phil Manning and Karl Bates on dinosaur locomotion was featured as a “success story” on the EGI website.  They talked about how they used Grid computing to understand better how dinosaurs moved around and what roles they played in their ancient world.  As there are no similar animals around today to compare to dinosaurs such as a T. Rex, the solution is to create a detailed computer simulation of the animal’s skeleton and muscles.

Not only was their research picked up by EGI but it also featured in iSGTW – fantastic publicity for the researchers and for the NGS!

I’ve been busy putting together some user case studies over the last few weeks and I’m pleased to say that there are now a few more up on the website showcasing the large spread of research areas that the NGS facilitates.

First up is Charlie Laughton from the University of Nottingham who has been using the NGS for quite some time now.  He used the NGS to investigate the flexibility and folding properties of DNA as understanding how the tightly packed DNA in human cells can still be read can, in turn, help to understand how cells switch genes on and off.   At present there is no clear understanding of how this works.  Being able to influence this in new ways may ultimately help to find new drugs to treat diseases such as cancer, develop new biofuels, and crops that can resist climate change.

Charlie said “…without the compute power and high-throughput provided by the NGS, we would not have been able to deliver our part of the project in a timely manner. At a more personal level, it led to one of the most highly cited publications I have ever had.”

John Allen from the University of Edinburgh explained how they use NGS resources to power the GridQTL portal which is used worldwide to study gene expression in a wide range of organisms.

The team’s use of the NGS has greatly increased the productivity of their users (currently around 400) in the QTL community. One example of this is a GridQTL user at the University of Missouri Columbia.  They ran a series of studies on carcass, post-natal growth and reproductive traits in commercial Angus cattle and found a speed up of from 20 people-weeks, using their old single server system, to 3 people-weeks to capture and analyse the data with GridQTL. 

Finally we have nuclear power!  Paul Martin from the University of Huddersfield has been using the NGS to investigate the suitability of Thoria asan alternative form of nuclear fuel.  Paul’s research is particularly timely as there is increased interest in the use of thorium dioxide for nuclear power rods not least because of its comparatively high abundance in the earth’s crust and low cost.  It is for this reason that, although the main fuel for nuclear power reactors is currently urania-based, thoria-based fuel is attracting much attention as an alternative high performance nuclear fuel.

All of our case studies can be found on the NGS website and we now have a collection of 26 covering a wide range of research areas.  If you are interested in using the NGS case studies to promote grid resources then please let us know.

A tangled web we weave

In the September 2011 edition of NGS News, we published an article by our Technical Director David Wallom which highlighted the networks of champions that exist within the NGS.  To compliment this I also received and published an article on our website from Simon Hettrick from the Software Sustainability Institute about their network of champions which they have thankfully called Agents.  Too many champions spoil the broth and all that...

It got me thinking about how these networks all fit together like a spiders web as some people are members of more than one champions network and some institutions have more than one person involved.  A tangled web indeed!

This has probably come to the forefront of my mind as, due to some staff changes at the NGS, I'll be a lot more involved in the organisation of the Campus and Community Champions here at the NGS.

So what are these Champions and who are they?

The Campus Champions as suggested by the name, promote the NGS and the services we provide on their university campus or in their institution.  They tend to be people involved in research computing or ITS but we also have researchers involved.  All NGS member sites are expected to nominate a Campus Champion but we welcome Campus Champions from any UK university or institution.  Your site doesn't have to be a member to have a Campus Champion!  If you are interested in promoting the NGS at your institution or university (with help and support from the NGS) then please get in touch!

The Community Champions are funded by the EPSRC funded SeIUCCR project and are researchers who actively use e-infrastructure in their research.  They promote to their research community, peers and colleagues from all institutions and universities.  We are looking for more Community Champions from all and every research area so if you are interested in promoting your research and your use of the NGS then please get in touch!

There will be some slight changes to our Champions networks and hopefully you will see a lot more activity from these already active groups.  I want to highlight their activities more and demonstrate their contribution to the NGS and e-infrastructure as a whole.  I'd also like to link them more closely with the SSI Agents.

Lots of plans are afoot so watch this space!

A smattering of updates

Over conference season there was what can only be described as a smattering of small announcements that you may have missed during your travels.  The blog seems like an ideal place to gather these together!

NGS News
The latest edition of our quarterly newsletter was released in time for conference season.  Available to download from our website, September’s edition contains articles on -

• A round up of news from Europe including the release of the first Unified Middleware Distribution
• An introduction to the new Certificate Wizard
• Championing e-Research and e-infrastructure - the Campus and Community Champions
• NGS user case study - Using the NGS to model the climate impact of aircraft emissions
• ...and more!

Tell us what you think!
Also on the website we have a new poll on the home page.  This time we are asking people how easy it is to find the information they are looking for on the NGS website.  So no matter if you are a frequent or occasional visitor to the NGS website, let us know by voting in our poll.  It can be found on the right hand side of the homepage.

 
Busy users
There is a new NGS user case study on the website.  Maria Holstensson from the Institute of Cancer Research explains how she is using the NGS to optimise cancer treatment for children suffering neuroblastoma.

Children with neuroblastoma who are being treated with targeted radionuclide therapy can have their treatment monitored with gamma camera images. These images are used to calculate the amount of drug taken up by the tumour and to estimate the radiation dose. However the image quality can be poor due to scattering and interference. Maria Holstensson from the Institute of Cancer Research is looking at tackling these problems.

Maria said "We have had absolutely fantastic help from the NGS and as a result of using the Grid we have been able to run multiple parallel simulations that we would not have been able to run otherwise".

 
How many?!
We’re pleased to announce that we now have over 1000 subscribers our fortnightly NGS news bulletin.  We have subscribers from all over the UK and much further afield with 21 countries represented amongst our subscribers. 
The news bulletin is delivered to your inbox every second Friday (with some exceptions during conference and holiday season!) and contains news from the NGS, updates from our member sites, details of forthcoming relevant conferences, calls for papers for relevant journals and much more.  You can subscribe to the mailing list from the JISCmail site.

Lounging in Lyon and yawning in York

Oh I wish! 

The September conference season was hectic as always for the NGS team with the EGI Technical Forum (Lyon) and the UK e-Science All Hands Meeting (York) back to back.  There was definitely no time for lounging in the Lyon sunshine although we may have yawned on the train home from York as the conference travel came to an end.

The EGI meeting in Lyon was a great success as always with over 600 attendees.  The meeting is an excellent opportunity for the NGS, in it’s role as the UK National Grid Initiative (NGI), to meet up with other NGI’s from all over Europe.  As well as looking after and organising the UK NGI exhibition stand in conjunction with GridPP, I was also involved in a session in my role as NGS Liaison Officer.

The NGS has held successful roadshow events for several years and these have caught the eye of EGI who are looking at doing something similar through the NGI’s.  I was asked to take part in the EGI / NGI roadshow session and present on my experiences of organising and holding roadshows and measuring the feedback and impact of these events.

There was an interesting discussion after the presentations regarding what the NGI’s would need to host these events and what materials they would find useful.  In some cases more staff and more time would be very helpful but the ability for the EGI to provide these resources are somewhat limited!  I was also asked about practical points such as organising registration and finding the right people in institutions to help host the events.  Hopefully the discussion minutes will be made available at some point.  Some more discussion points were captured on the GridCast blog entry on the session.

The AHM meeting at York attracted 150 people this year and seemed dominated by one word – Cloud!  I lost count of the number of cloud sessions taking place over the 4 days.  The meeting was stimulating and thought provoking judging by the copious amount of notes I took.  However one of the main activities for the NGS was the SeIUCCR organised workshop – Meet the Champions.

The purpose of this workshop was to give attendees an opportunity to meet the researchers that have been promoting and championing research in different e-Science areas and to find out about their work and how they utilise e-infrastructure.  The guest speaker was Scott Lathrop from the XSEDE project where he is the Director for Education, Outreach and Training.  Scott talked about their Campus Champion programme and how they ensure that Campus Champions feel involved and part of the project.  They have many of the same responsibilities as our Campus Champions including raising awareness of XSEDE and even providing training in using the resources. 

Two of our Community Champions also presented at this event outlining the issues in their research areas regarding e-infrastructure, getting started, having the right support at their institution etc.  There was also a very lively discussion panel at the end of the session with many issues raised including how scientific researchers work and the risks involved in devoting time to starting to use new technologies.

It’s great to hear researchers and users speaking about their experiences of actually using this technology, as it sometimes seems, that users get forgotten about in all the discussion about standards and programming.  We need a reminder that at the end of the day this is about building tools and providing a service that people will want to use and find beneficial and that will help further their research.  It’s most definitely not a case of “build it and they shall come”!

I’ll make sure that all the presentations from the AHM workshop are available on the NGS website soon so watch this space!

A long long time ago... or so it seems

Before the mayhem of the September conference season was upon us, the NGS ran a successful summer school at the beginning of the month.  The e-infrastructure summer school was part of the SeIUCCR project.  You can read more about the background to the summer school and project in my blog post from the beginning of August.

We had over 25 students join us down in Coesner's House in Abingdon for 4 days and they came from a wide variety of backgrounds.  We had students who were in their first year or two of their PhD as well as post docs and they came from Edinburgh to Essex and everywhere inbetween.

So how was the summer school?  Was it a success?  Did the students learn and enjoy it?

Well the best people to ask are the students themselves.  All the students were asked to provide us with feedback and some were even willing to write a few more words.

Ed Day from Canterbury Christ Church University attended the summer school and this is what he had to say:

"The recent SeIUCCR Summer School was a very enjoyable and informative experience. As a newcomer to grid research I found the the summer school extemely useful. It contained some important introductory pieces as well as covering many topics in more depth suitable for anyone wishing to use the NGS. Sessions consisted of a good mix of high level overviews and hands-on practicals such as using the P-GRADE portal.

The presenters were very knowledgable and helpful and were eager to inform on all aspects of grid computing. Some sessions involved the speakers talking individually with attendees and I found the staff gave useful advice and were very supportive of my project.

Before the school I thought my particular research area, the forensic investigation of mobile phones, might be a good fit for grid computing, and by the end of the summer school I felt much more able to pursue my research in an informed manner using the NGS. It was useful to know how grid, cloud and high performance computing relate to one another  and over the four days I feel I became much more aware, in a less naive way, of how my research would benefit from the resources the NGS has to offer. In particular I learnt to think about my research differently: how my phone investigation process would be best able to benefit from a grid architecture.

Indeed the school helped support my view that the NGS would be a good resource for ANY project that needs HPC not just vast number crunching modelling applications such as those such by molecular biologists or quantum level physicists (although of course it is good for that too).

I liked the food too!"

And it wasn't just Ed who enjoyed the summer school!

"The summer school has been a fascinating activity. The hands on sessions have familiarized us with HPC/Grid/Cloud, which are useful resourses that I have never had access to or known how to access, whilst the Meeting Champions and Q&A sessions made it possible for us to know how these resourses could facilitate our research. The SeiUCCR summer school provides a great opportunity of learning, communicating and networking. I would like to thank all the people who made this summer school possible"

"The summer school was a relaxed and friendly environment. It provided detailed information about the various resources available to researchers both in terms of computer resources and support. The staff where very approachable and keen to show an interest in the attendees work. Overall it was a great experience I would recommend to anyone who has an interest in grid/cloud/HPC or who's work may benefit from such technologies."


For anyone who was unsuccessful in obtaining a place at the e-infrastructure summer school, the presentations are now available online.  Due to receiving over 120 applications for the summer school and only having a limited number of places, I know many people were keen to see the presentations.

There will be another summer school in 2012 so watch this space for forthcoming announcements next year!