Taverna and Cloud on the NGS website

Incase you missed it (and we wouldn’t want that now!), a quick heads up of some new articles on the NGS website.

First up is an article on running Taverna workflows on the NGS. Mike Jones (NGS) and Donal Fellow (RCS) from the University of Manchester have been tackling this issue and are making rapid progress. The success of this project could result in an increase in NGS usage by the large Taverna user community.

The second article is an update on the NGS cloud prototype which has been running since last summer when we asked for users willing to try this new service. We were inundated with volunteers and this article by David Fergusson (NGS, NeSC) looks at the user communities taking advantage of this prototype service.

Arts and Humanities and ICT

Following on from my previous blog post about the JISC- Future of Research? conference, the next parallel session I attended was “Evolution and Revolution in ICT and Arts and Humanities research”.

The first presenter was Simon Tanner from King’s College London who spoke about some JISC digitised collections. No slides from this one I’m afraid as he showed us pretty pictures instead!

The next speaker was from Mimas who spoke about “long tails and efficiencies of scale”. The slides for this one are available and of particular relevance to myself and the NGS, was the observation that services have to show –

• User demand
• Benefits
• Impact and value
• Sustainability

This is something that the NGS has been undertaking recently and will continue to do so as we come up for refunding next year. You may have seen a small flurry of stats etc on the website and we have been undertaking more stats gathering behind the scenes from the proliferation of data available from usage stats and user applications. From this we are building up a picture of user demand, impact and value etc.

We hope that our users will help us by contributing to our forthcoming annual user survey and our follow up roadshow survey. If you have attended any NGS roadshows we would be grateful if you could complete the short survey which will take about a minute to complete! This will help us shape future roadshow events and also analyse the benefits that users get from attending these events.

The final speaker was John Coleman from the University of Oxford who presented on “Large Scale Computational Research in Arts and Humanities”. He started with an interesting fact that in 2008 YouTube was the second most popular search engine with people looking for speech / audio instead of text. He is currently working on a JISC funded project to “mine a year of speech” which aims to annotate a years worth of data in the form of a corpus. To do this he is currently using about 20 computers set up as a cluster in a local lab. However he is now looking at placing the data in several other universities which he says is “like grid computing”. John also highlighted a report available on "ICT Tools for searching, annotation and analysis of audiovisual material" which may be of interest to people.

The JISC Future of Research? conference had some very interesting parallel sessions and I hope it continues next year!

Hello from AHM

A selection of NGS staff are all now settled into conference mode at the UK e-Science All Hands Meeting in a wet Cardiff.

The stand was put up last night and our first demo was held this morning. A big thanks to Jonathan Churchill whose demo of the UI/WMS managed to pull in a substantial crowd despite a quiet start to the event as people continue arrive during the morning.

Jonathan will be doing a follow up demo this lunchtime on the "gLite WMS Enabled NGS Applications Portal" so pop by our stand with your lunch if you are in Cardiff!

The conference proper kicks off this afternoon with the first themes and workshops. I'll be going to the "Sharing, collaboration and interfaces for e-Research" which looks as though it will have some interesting presentations about user tools.

A flurry of activity

There has been a batch of new speakers recently announced for the NGS Innovation Forum '10 and further information about their presentations are now on the website. The latest presentations are NGS tool demos which will consist of walk-throughs of NGS tools using real research examples so delegates can leave the event with the knowledge of new tools to use in their research.

NGS tool demos
1. Transcriptome Analysis using the NGS User Interface /Workload Management System (UI/WMS) – Jonathan Churchill, NGS, STFC RAL
The UI/WMS is a tool which allows users to easily submit jobs to the whole of the NGS relying on the WMS to chose which NGS resources to use for their jobs. Use of the UI/WMS will be demonstrated with a user case study in which analysis time of mRNA was decreased from a month to less than 12 hours.

2. Accessing the NGS using the Application Hosting Environment (AHE) – Stefan Zasada, UCL
An overview of how access to the NGS can be simplified using the Application Hosting Environment, a lightweight application portal system.

3. Using the HERMES data management tool – David Wallom, NGS, University of Oxford
Here we will show how easy it is to install and connect into various NGS resources to move data between them, your home institution and your desktop.

4. The NGS from the CCP4 desktop – Matteo Turilli, NGS, University of Oxford
The NGS R&D theme have been working to build access to the NGS into the desktop tools that researchers use on a day-to-day basis, in this presentation we look at the example of CCP4: Software for Macromolecular X-Ray Crystallography.

We also have a presentation from the Director of the NGS -
The future of the NGS – Neil Geddes, NGS Director, STFC RAL
This presentation will look at the focus of activities for the NGS for the coming 2-3 years and possible longer term opportunities.

Remember that registration for the event is now open and that the call for poster abstracts closes on the 10th of September!

Registration for NGS Innovation Forum open now!

The registration for the NGS Innovation Forum is now open - details of how to register can be found on the event page on the NGS website.

We are pleased to announce another speaker for the event. Neil Geddes, director of the NGS, will be speaking about the future of the NGS so if you are a long term NGS user who wants to know the future direction of the NGS or a new user who is planning to use the NGS for the long term, then make sure you attend!

A reminder that we are still looking for NGS users to submit poster abstracts demonstrating how they use our resources in their research. The deadline for abstracts is the 10th of September so it's approaching soon! There are many benefits of submitting an abstract and attending the event -

• Walk through demos of new NGS tools
• NGS staff on-hand to answer your questions
• The opportunity to contribute and feedback to the future of the NGS
  
• The poster abstracts will be peer reviewed by the NGS IF'10 programme committee
• Publicity for your research both at the event and through accepted posters being placed on the NGS website
• The chance to win a prize as "best poster" as voted for by IF'10 delegates
  

All that is required is a short 200 word abstract! Of course you are more than welcome to attend the event without submitting an abstract and you can attend for one or both days. We hope you can come along!

Application hosting environment and UI/WMS - preparations continue!

I've just added some details of more presentations at the forthcoming Innovation Forum to the website. We have two demos - one of the UI/WMS which has proved to be a big hit with our users and the Application Hosting Environment (AHE). Full details of the presentations are available on our event page on the website. Delegates will see walk-throughs of how to use these tools on the NGS and the benefits they can bring to your research.

We have also updated the UI/WMS tutorials if you want to give the UI/WMS a go beforehand!

Have you tried our UI-WMS yet?

It sounds painful but over 50 users since November have proved that it doesn't have to be!

The NGS UI-WMS service has accumulated over 50 users since it was released in November last year, a substantial fraction of the active NGS user base. Users are using the service for all kinds of work from computational chemistry through to bioinformatics.

Their work is automatically distributed by the WMS over the entire NGS, rather than just using one or two sites. If you would like to find out more about how this capability can improve your work flow check the case study in the last NGS Newsletter (page 5-11) or the resources and tutorials linked from the UI-WMS page. Most of the popular pre-installed applications already have examples of how to run them via the UI-WMS.

If you have any questions about the UI-WMS and how it can help you and your research, email our helpdesk - support(at)grid-support(dot)ac(dot)uk.

New on the NGS website

There have been some new additions to the NGS website over the last week or so - mainly news stories but hopefully of interest to you all!

Karl Bateman, a NGS user from the University of Manchester, had his research featured as the headline article on iSGTW recently. Karl is researching into how dinosaurs moved, in particular the dinosaur Acrocanthosaurus atokensis which is essentially the same size as a T-Rex. The full article entitled "Answering a truly big question: how did dinosaurs move?" is available on the iSGTW website.

Another article currently featured on the NGS home page refers to the Certificate wizard which has been recently developed by Jens Jensen at the NGS. Basically the article explains how we are making it easier for you to look after your grid certificate!

We also have a new poll on the NGS home page. We'd like to find out who funds the people that visit our website. So if you have a spare second please tick the appropriate box on the front page! You'll find the poll on the home page just below the NGS load monitor. This will give us an indication of who our visitors are funded by.

Catch up with the news

The latest edition of NGS News, the quarterly newsletter from the NGS, is out now.

This Christmas edition has a European flavour as we describe the NGS activities in Europe and our participation in building the European Grid Infrastructure (EGI). There is also an excellent article from Jonathan Churchill from the NGS at RAL and Paul Wilkinson from Exeter University who give an excellent use case study of the new User interface / workload management system (UI/WMS) for pest insect gene coding. Finally we also have articles on why we need certification and the ongoing developments in this field, a user case study from Dr Narcis Fernandez-Fuentes at the University of Leeds on virtual candidate drug trials and much much more.

The newsletter can be found on the NGS website.

AHM kicks off

It’s been a hectic day so far at AHM - the first thing I had to do today as soon as I walked in the venue was to find a presentation for someone to use as they were standing in for a NGS user who was ill. Luckily thanks to our shiny new website a suitable presentation was found and they made their slot with minutes to spare. A huge thank you to Shiv and Dave F for stepping in at the last minute with a presentation on using the NGS for in-silico drug screening.

The exhibition area where the NGS has a booth has been particularly busy. We had our first demo this afternoon on the NGS booth and I am pleased to say that it was extremely busy. Photos will follow tomorrow to prove this! The UI/WMS demo was given by Jonathan Churchill and was very popular with people staying way past the demo slot to ask more questions and find out more. More information on the user interface / work management system (UI/WMS) can be found on the NGS website.

This evening brings the poster session and the journey back into Oxford to find and check into our accommodation for the week.

Open call for Hector

EPSRC are piloting a new access class for the HECToR service called 'Direct Access' (Class 1b) where users can request significant amounts (>1,000,000 AUs) of computing resource only for a period of up to six months.

The Direct Access mechanism will provide successful applicants with discretionary access to the HECToR system in order to provide resource to cover activities such as:

* Bridging access between grant applications,
* Resource to trial application developments at scale,
* Provide preliminary results in aid of grant applications via Responsive Mode or to a Call for Proposals;

There is no deadline for submission, however:

* the proposals will be assessed by a Resource Allocation Panel (RAP) which will meet every four months (February 2010, June 2010 and October 2010)
* the deadline for applications being submitted to the Panel will be three weeks before the Panel meeting.

More information can be found on the EPSRC website.

Make the most of the NGS

We are keen to make sure that everyone is aware of the new tool recently developed and released by the NGS.

The NGS UI/WMS service is now in full production allowing NGS users to exploit all sites on the NGS including the partner resources.

Since going into pre-production in October, the UI has been upgraded and extensive stress testing has been undertaken with 1000's of jobs run through the service. The UI now also checks your certificate proxy when logging in and corrects for many common proxy problems hopefully making your life easier!

The documentation has also been extensively updated on the new NGS web site and the NGS wiki. The majority of scientific application documentation pages now have examples of running the applications via the UI-WMS. Some of these are fleshed out in tutorials on the NGS wiki, linked from the main tutorials above), with more tutorials and examples in the pipeline.

If you have any questions or problems using the service, please mail the NGS helpdesk at support(at)grid-support.ac.uk.

New GridSAM tutorial from OMII-UK

Our colleagues at OMII-UK have released a new tutorial which shows how to run a command-line-based client: from generating results locally, through to running the same command line in a controlled manner on GridSAM.

The tutorial is aimed at researchers who would like to learn more about deploying a custom GridSAM application in a grid environment but systems administrators and technical managers may also be interested in the tutorial. It can be found here on the OMII-UK website.

A new way to access the NGS

The NGS member site RAL, is trialling a new system that allows users to login to grid resources using any SSH client. They are currently inviting users to come along and have a play!

In a nutshell, all you need to do is to create a MyProxy credential (easily done, with the MyProxy Upload Tool) and then use virtually any SSH client (such as Putty, WinSCP or Nautilus) to login to ngs.rl.ac.uk with the username and password to your MyProxy credential. It's a very simple way to get connected to a grid resource.

Further details available here are available on the NGS wiki.

New Wizardry at the NGS

We are pleased to annouce that an updated version of the MyProxy Upload Tool has now been released for your comments and feedback. The tool is available from this page of the NGS website.

The general layout has been overhauled and we'd like to have some feedback on this. The main new feature is the capability of generating proxies with VOMS attribute certificates for those that need them.

Please note that this tool is still in development and should be considered a Beta rather than a production release! The tool also depends on Java 1.6 (although we may be able to extend support to 1.5 shortly).

If you have any comments or feedback on the tool then please let us know! Comments should be sent to David Meredith (david.meredith(at)stfc.ac.uk) and Will Rogers (will.rogers(at)stfc.ac.uk).