What does the NGS do for Europe?

Quite a lot actually is the answer!

The NGS will be hosting a second seminar series this summer and the theme of the 3 seminar event focuses on the services that we provide for the European Grid Infrastructure (EGI).  As with last time, the seminar series will be held using EVO allowing people from all over the world to participate in the seminar and to quiz the presenters.  The details for this series are -


20th June - Grid Accounting and APEL
This talk will give an overview of how accounting is done on the grid, and what it is used for.  It will cover the NGS accounting system at a high level.  It will then go into more detail about the implementation of APEL, the accounting system for EGI, including the particular challenges involved and the plans for development.

27th June - GOCDB, the NGS and EGI 
This talk will cover a brief overview of the functionality provided by GOCDB, the official repository for storing and presenting EGI topology and resources information. The seminar will explain how it is used within the NGS, recent developments, useful features on the future roadmap and a chance to ask questions about the system. There will also be a short overview of how GOCDB is used in the context of the EGI project.

4th July -  The Training Marketplace
The Training Marketplace is a one-stop shop for training developed by STFC and the EGI InSPIRE project. Here you will find information about classroom-based training courses and online training materials including a repository containing thousands of resources. You can also search for PhD or MSc courses, or for resources for trainers such as a Training CA. The Training Marketplace equally allows you to advertise and a freely available gadget enables you to customise and embed the Training marketplace in your own website. This seminar will talk you through the Training Marketplace and demonstrate how you can embed a customised version of a training calendar, map or repository in your own website.

If you are interested in attending any of these online seminars then please see the webpage for further details and how to join in online.  There are also Facebook event pages available for each seminar series to help you inform interested colleagues and to invite them along.

Are you a molecular modeller?

Two free training events announced in the space of 2 weeks?  Don't say we're not good to you!

Incase you missed it, last week I announced that we were accepting applications for our "Using e-infrastructure for Research" summer school which will be held in August.  It's completely totally and utterly fully funded so there is absolutely no cost to the participants.  More information can be found on our website.

However the latest event I have to tell you about today is being organised by one of our Community Champions who is funded through the same project as the above summer school - Supporting e-Infrastructure Uptake through Community Champions for Research (SeIUCCR) funded by EPSRC.

Dr Pamela Greenwell, who is based at the University of Westminster, has organised a 3 day training event entitled "Biobytes", a molecular modelling event for bioscientists.  It's a 3 day event held at Westminster consisting of breakout groups, seminars, demos and practical workshops.

For more information and details on how to register, see the event page on the NGS website.  Don't delay as spaces are limited!

Fully funded e-infrastructure summer school anyone?

Yes it is that time of year again.  I've spent this morning opening registration for the 2012 SeIUCCR e-infrastructure summer school.  Why a whole morning you may ask?

Well by the time you've double and triple checked the registration form, put the web page live, sorted out the Facebook event page, written the advertising blurb, put together the news bulletin containing the announcement and tidied up another 101 loose ends, it takes a while!

The summer school is taking a similar format as last years successful event.  It will run from lunchtime Monday to lunchtime Thursday with a mix of presentations, hands on and consultation sessions.  It will cover cloud, grid and other e-infrastructures to ensure that attendees gain the widest possible knowledge of e-infrastructure in the UK.

The summer school is primarily aimed at UK engineering and physical science PhD students and post docs but researchers from other disciplines can also apply.  The school is fully funded including meals, accommodation and travel - all you have to do is tell us of a problem or issue in your research that could potentially be tackled by the application of e-infrastructure!

For more information and to apply for a place visit the event webpage.

Renewals available now!

Hopefully you'll have already seen the announcement on one of our many communication channels such as our website, Facebook page or Twitter feed but if not then read on.

Many of you will remember the changes we brought in last year in April 2011.  Due to funding restrictions, we had to reduce the CPU allocation of all users to a maximum of 2000 free cpu hours in one year.  You can read the original announcement on our website.  As we are now a year on, all NGS users can apply for another free 2000 cpu hours.

If you are looking for some proof of concept computing, a "sand pit" area for your PhD students or to test concepts before purcahsing more hours etc then this is an ideal opportunity.

If you have any queries at all then don't hesitate to contact the NGS helpdesk.

Radio silence

It's gone a bit quiet over here at the NGS blog lately mainly because I was completely caught up in writing a bid which took over my life for a few weeks.  As it was all I did for a couple of weeks I didn't have much to blog about.  Hopefully the bid will be successful and we'll have some exciting news for you in the near future!

Apart from that I have been working with colleagues at SSI in preparation for their Collaborations Workshop which will take place on the 21st - 22nd of March.  There has been a great response with maximum attendance and a great range of people attending.  One of the purposes of the workshop is to get researchers and software engineers working networking to find where they can help each other out. There aren't many conferences out there where the aim is to get everyone talking to each other all day instead of just a few people doing the talking!

In completely different news I just posted an article to the NGS website from EGI.  The EGI are showcasing their users research much the same as the NGS user case studies do (wonder where they got the idea from...?).  They are doing their case studies in the form of video interviews and the first one focuses on the research of Henry Hocking of the CONCO project who used the grid to analyse naturally occurring molecules in venoms used by marine snails to immobilise their prey.  You never would have guessed that one!

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! 

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.

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!

What do you do on the NGS?

It's been a busy month or so even though it's the holidays as this is the ideal time for me to contact many of the NGS users who promised to write user case studies for me regarding their research.

We have a wide range of reseachers who use the NGS as part of their every day research and it's important for the NGS to highlight that our resources aren't just used by the "typical suspects" such as physicists.

Over the last few weeks I've added another 2 user case studies to the NGS website -

• Modelling the effect of the peptide sequence on the binding affinity to carbon nanotubes from Susana De Tomasio, University of Warwick
• Systematic modeling of ionic liquids from Edward Ballard, University of Wales Bangor

Both these case studies demonstrate how the use of NGS resources is helping to speed up research enabling results to be produced and published faster than previously.

Edwards supervisor, Dr Anna Croft praised the NGS, "The NGS has been an excellent resource for many of our research projects. In particular, I have been able to use it with undergraduate researchers and give them a taste of what it is like to work on large computing infrastructures - an experience that has helped some of them secure PhD funding, both here and overseas, to continue in the computational area. When we had teething problems, the support staff were always friendly, helpful and got things working. Because of this support and the flexibility in requesting computing time, the NGS is one of our first ports of call for projects requiring a larger computing resource."

Thank you Anna!

E-infrastructure summer school - registration open now!

A brief hiatus here on the NGS blog as several of us are / have been on holiday. Back to normal service now hopefully!

A lot of my time since I returned from holiday has been devoted not to the NGS but to another project I am currently working on. Catchily named SeIUCCR (pronounced "sucker"), the project was funded by the EPSRC "Crossing the Chasm" call which called for networks and "advocates" to promote the wider uptake of UK e-infrastructures by researchers in engineering and the physical sciences.

Part of the SeIUCCR project is an e-infrastructure summer school which is due to take place in Abdingdon near Oxford in September. The residential summer school will offer an introduction to e-infrastructure including Clouds and Grids to UK PhD students and postdocs over 4 days. The summer school is fully funded including travel expenses and applications are open now.

If you (or anyone you know) would like to apply then be quick as applications will close at 9am on Monday 15th of August. Details of the summer school can be found on the SeIUCCR website and a detailed agenda is available from the registration site.

How has it affected you?

As you are aware the NGS has gone under some changes since the beginning of the year. The most obvious to our users was the cap on cpu hours that was introduced on the 1st of April with every user being given 2000 free cpu hours per year. If a user requires more than 2000 cpu hours this can be arranged through the NGS on a "pay per use basis".

So 3 months in since the changes were introduced and we want to hear your views. We are asking all registered NGS users to complete a very short survey to feedback their views and experiences on using our services since the 1st of April. It doesn't matter if you haven't used the NGS since before the 1st of April you are still our target for this survey!

The survey will take a few minutes to compete if that and everyone who is a registered NGS user either past or present will be entered into a prize draw.

That's not my cow

With apologies to Terry Pratchett for the title of this blog post...

You may have spotted an unusual picture on the NGS home page this week. What on earth have cows got to do with the NGS? A very good question...

The answer lies in a recent iSGTW article which once again promotes NGS users research to an international audience.

The article featured the work of the GridQTL team at the University of Edinburgh who provide the GridQTL grid-based platform for running gene analysis. GridQTL is used by researchers all over the world and, unbeknown to many of them, all the computing jobs are submitted to the NGS providing a massive speed up in analysis time.

Team leader Dr Sarah Knott explained “It would be very difficult to run this kind of software without grid computing. We have an uncertain user base and the grid provides the flexibility to sustain an adequate speed of analysis, regardless of online users.”

To see a NGS user case study on GridQTL visit the case study section of the NGS website.

Beep, beep - NGS coming through...

There is a new NGS user case study up on the website and this time it deals with traffic. I'm sure this is a popular topic particularly at 9am on a Monday morning!

NGS user Aengus McCulloch from Newcastle University has been using NGS resources to tackle the explosion in the volume of data relating to real world events such as systems monitoring weather and road traffic etc. Processing the large volumes of data generated by geographical sensors in a short time period is an enormous computational challenge. Guess where the NGS can help out?

Aengus used the real world problem of traffic monitoring and routing as a test case for classifying near real-time processing operations on geographically referenced data using Grid computing architectures. By using the NGS he managed to successfully test his system with up to 250 vehicles.

Aengus said "The NGS has made endless CPU hours available to me through a standards based interface; it has been an invaluable resource for my research".

To read more about his research, see the scalable road traffic case study.

999 – NGS Surgery

Did you know that the NGS runs Surgery meetings every second Wednesday? The meetings are run over Access Grid / Evo and are open to all.

The surgery meetings have previously been mainly for supporting NGS member sites in installing software etc on their resources. However recent surgery meetings have widened their remit to discuss topics of interest to Campus Champions as well as the Sys Admin community within the NGS.

The NGS is always looking for suggestions for presentations / discussions at forthcoming surgery meetings. If you have any ideas or would like to raise a topic then contact the NGS helpdesk and let us know. Just because you suggest a topic doesn’t mean that you have to present so don’t worry!

To give you an idea of the sort of topics that have been discussed previously, have a look at past NGS surgery meetings on the dedicated section of the NGS website. You can find all the presentations here as well.

If you want to keep up to date with all the forthcoming surgery meetings, make sure you check the NGS website regularly or drop an email to the helpdesk and they will add you to the mailing list.

Getting the users story across

As you are no doubt aware, I’m always after interesting pieces of user research to feature in our user case study section of the NGS website. User case studies are ideal introductions to people who have never used the grid before as it can demonstrate what can be done with the resources and what the benefits are.

Whilst the production of user case studies benefits the NGS, they also benefit the researcher featured as quite often the user case studies are picked up by other grid organisations.

This was the case with NGS user Cristiano Sabiu who hit the headlines in iSGTW last month with his user case study on his cosmology research.

Cristiano from the University of Portsmouth used NGS resources to study the distribution of galaxies in the universe by creating 2000 mock universes for comparison to actual galaxy distribution in the Sloan Digital Sky Survey (SDSS). By using the NGS he managed to run 20 full scale simulations which required approximately 100,000 cpu hours over the course of a year.

His research was made into a user case study for the NGS website from where it was picked up by International Science Grid This Week (iSGTW) and appeared as their headline article in April. iSGTW is a weekly online publication that provides international coverage of distributed computing and the research it supports. They feature articles on all aspects of distributed computing technology, such as grids and clouds from all research areas and are always on the look out for interesting stories to cover.

The NGS user case studies keep on coming though and the most recent one is on quantum mechanics modelling. Stewart Reed from the University of Leeds used NGS resources to develop new methods of performing accurate computer simulations of quantum mechanical tunnelling.

Stewart explained how "the NGS provides excellent computing resources with which to perform these calculations. The computational capacity available from the NGS allows larger systems to be studied more accurately than are possible with standard workstations”.

To read more about his research, see the quantum mechanics modelling case study.

I’ve recently added a new poll to the NGS website home page which asks if our users collaborate internationally and, if so, if this involves the NGS.

The latest question is the 7th poll to appear on the NGS website so I thought that in this blog post I would recap some of the results of previous posts.

The polls have covered a wide range of topics from “do you like our new website?” way back in November 2009 when we launched the new site, to questions regarding funding and access to resources.

Back in March last year we asked people which operating system they used to access the NGS. This has an important bearing on how our tools and applications are developed in the future as we need to ensure that they are usable by NGS users regardless of their operating system. We had 175 responses and the results were -

• Windows – 35%
• Linux – 43%
• Mac – 19%
• Other – 3%

The results were pretty much as expected with Linux users being in the majority. However it was interesting to see that Windows users are catching up and Mac users growing in numbers.

Also many moons ago we asked if our users would like us to offer an academic cloud service. This was a popular poll with 137 replies and the following results –

• Yes -66%
• No - 20%
• Don’t know – 14%

We are pleased to say that the NGS cloud prototype has been very popular and is currently running at capacity as we help and assist NGS users to make the most of this new prototype service.

Of course it’s not just specialised services that we offer, we also offer the day to day stuff that enables people to get started using the NGS. We wanted to see how the users thought we were doing in terms of authorising new applications to use NGS resources. Were we taking too long? Were we meeting expectations? We were pleased to see that nearly half (46%) of applications were approved the same day with 28% approved in the next 1 – 3 days.

We are always looking for new polls for the NGS website so if you have any suggestions then we would love to hear them. You can ask anything about software, hardware, services, usage, user stats etc. All the polls are anonymous.

The sun is out

Given the very sunny Bank holiday weekend we've just had here in the UK, it seems apt to highlight the latest user case study to appear on the NGS website.

The latest case study highlights the research of Marco Califano at the University of Leeds who has been looking into exploiting solar power using the NGS. Marco used NGS resources to try to identify the best materials, sizes and shapes of nanocrystals that could lead to high-efficiency energy conversion in the next-generation solar cells.

Marco explained how "the outcome of my research could help the UK develop alternative, renewable energy technologies that enhance the cleanliness and efficiency of energy production. This, in turn, will contribute to the Government's commitment to meet the greenhouse gas emission targets set in Kyoto".

To read more about his research, see the exploiting solar power case study.

EGI User Forum round up

Last week saw many NGS staff attend the EGI User Forum 2011 which was held in Vilnius, Lithuania. Many NGS staff attending were actively involved in sessions either chairing or presenting as well as helping out on the UK NGI (UK National Grid Initiative) exhibition stand.
Personally my main involvement was ensuring that the UK NGI exhibition stand got there in one piece and that staff from NGS and GridPP were on hand to answer questions from delegates about our organisation. We had a very busy stand – possibly one of the busiest we’ve had at these events which was good to see.

I was also presenting at the EGI Dissemination session which was chaired by Neasan O’Neill, NGI Dissemination Coordinator. Neasan had asked some of the more established NGI’s to discuss the dissemination methods they had found most useful and effective. I presented on the NGS roadshows of which there have been 12. I discussed the content of a typical roadshow, the feedback we receive directly after the event and the follow up I do approximately 3 months after the event.

I also ran through (very quickly!) the other dissemination methods we have including our user case studies, our quarterly newsletter and the innovation forums. There were quite a few questions and some good discussion after the presentations with quite a few leaflets disappearing from the stand as well which meant less to carry home!

The conference was excellent in general with a brilliant venue and fantastic organisation. The next EGI event is the Technical Forum which will take place in Lyon in France on the 19th – 23rd September 2011.