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!

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.

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!

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.

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.