Friday, 12 December 2008

Final day at e-Science 2008

This morning I attended two sessions - one on bioinformatics and the other on cheminformatics which were handily in rooms across from each other. (Everything I wanted to go to today clashed with everything else - all the strongly user focused sessions seemed to be today!).

I found the Bioinformatics session particularly interesting with Simon Lin, Director of Bioinformatics Consulting (Robert H. Lurie Comprehensive Cancer Center & Biomedical, Northwestern University). He is using Amazon cloud computing (which is turning out to be affordable) rather than traditional computing clusters which he also has access to. Part of the reason for this is that it is easier to wipe images on cloud systems unlike university resources. Also there is no queue on cloud resources unlike many university systems. Lin is using Amazon to demonstrate proof of concept as it is the first commercially available cloud computing system. However he is currently investigating running an internal cloud using Eucalyptus, something which was discussed earlier in the week at this conference.

An interesting question was asked at the end as to the difference between cloud and grid. Lin pointed out that they were highly related but there are some important differences such as grid being the joining of distributed clusters using an extra layer whereas cloud used virtual images.

Lins talk was followed by Jake Chen from Indiana University – Purdue University (IUPUI) who spoke about "Bio-computing and Knowledge Discovery of Molecular Networks". He described a method to find potential drugs to treat Alzheimers disease by searching the Pubmed abstract database for specific proteins. His group has found many novel compounds that have been used for treating other diseases but have not yet been applied to Alzheimers.

This afternoons key note was given by Ed Seidel, Director, Office of Cyberinfrastructure who spoke about where cyberinfrastructure (CI) is going over the next 2 years. It's not written in stone yet but plans are beginning to be formed. Seidel is aggressively trying to increase the budget for CI and it seems to be working. He also talked about the lack of suitably trained computational scientists coming out of universities. No one seems to be teaching the skills required to deal with the infrastructure that is now in place. The lack of funding for software was also discussed with funding very much focused on the actual machines as a machine in the Top 500 is better understood than a piece of software by the people who matter in the Senate. He also spoke of the new machines coming onto TeraGrid over the next few years.

Overall his talk brought home to me that every grid faces the same problems at the moment. We are all really at the beginning of implementing and building a system for researchers (I'm not going to include the particle physicists in this!) and we're all in the same boat. Food for thought in his presentation and I'd recommend watching it when it comes online at the end of next week.

Thursday, 11 December 2008

Day 4 - nanotechnology and avalanches

A quick round up of some of the presentations I attended today on day 4 of the ieee conference.

Mike Jones from Research Computing Services at the University of Manchester and, of course, the National Grid Service, gave a presentation on nano-CMOS. The nano-CMOS project is using e-science and grid technology to tackle some of the challenges in nano-CMOS transistor design in the semi-conductor industry.

Mikes presentation looked at storing the vast amounts of data with the options being databases with an OGSA-dAI interface, SRB or AFS. In this presentation Mike spoke of the comparison between SRB and AFS. AFS came out as the top choice due to being compatible with grids especially the NGS, control of the main data lies with the stakeholder, it is robust and provides easy access. The NGS actually has AFS available which is unusual for a grid system so in that respect the NGS is pretty unique.

Following Mikes presentation was Sebastian Michel from Switzerland who spoke about SwissEx. The talk was entitled "Sensor metadata management and its application in collaborative environmental research" and looked at bringing together the vast number of environmental monitoring experiments that take place in Switzerland.

SwissEx is an infrastucture of web based technologies, wireless communications and low cost high density sensors. They are building a portal or wiki for SwissEx to enable people to share data about their projects. SwissEx involves looking at several environmental events such as flooding, earthquakes, river restoration and "mass movements" which I took to be avalanches but I may be wrong! This seems to be a project which heavily involves the scientists ie the actual users which can only be a good thing!

PS incase you are wondering about the photo - it's part of the Christmas decorations here in Indianpolis!

Wednesday, 10 December 2008

e-Humanities at ieee and e-science down under

Today is the first proper day of the ieee conference and I’m currently in the e-Humanities workshop which is being chaired by Tobias Blanke from the Arts and Humanities e-Science Support Centre (AHeSSC) at Kings College London.

There have been some very interesting presentations this afternoon (I’m afraid that I missed the morning session) including 2 on the use of grid computing in linguistical analysis. There was an interesting presentation from TextGrid who is part of the D-Grid initiative in Germany. They are aiming to create a community grid for the collaborative editing, annotation, analysis and publication of specialist texts.

I missed the morning e-Humanities session as I was having a very interesting chat with Ann Borda from VeRSI. VeRSI is a multi-million dollar funded initiative in Australia which aims to provide a coordinated approach to accelerating the uptake of eResearch by Victorian researchers. I should point out that Victorian does not refer to a historical time period but to the state of Victoria in Australia!. The project is a collaboration between the University of Melbourne, Monash University, La Trobe University and the Department of Primary Industries.

They are funding some very interesting projects including neuroimaging, mouse brain map, dataset mining and much more. Details of all their projects can be found here.

Tuesday, 9 December 2008

Day 2 in Indianapolis

Yesterday afternoon I attended the workshop on “Project Management and User Engagement” which was organised by several people from the Oxford e-Research Centre and David Abramson from Monash University in Australia. Dimitrina Spencer from oerc was our host yesterday and chaired a very interesting workshop consisting of 9 presentations.

The presentations covered many different themes and aspects of working with disparate groups, how to manage virtual organisations, how researchers find and decide upon potential collaborators, how researchers collaborate remotely and how to develop global networks. I gave a presentation on how the NGS is organised and managed and the challenges that brings to our organisation. It was a really interesting workshop and gave some human perspective on what can sometimes be a very technology focused area. It provided the missing human element!

All the presentations from the entire conference are being streamed live over the internet and have been recorded so the presentations from yesterday will be online soon. If you aren’t able to make ieee but are interested in seeing what you missed then visit this website for a list of speakers and presentations. The conference is on until Friday so there are a lot more presentations to come!

Monday, 8 December 2008

NGS in Indianapolis

I'm currently at the ieee e-Science 2008 conference in Indianapolis. The actual conference proper doesn't start until Wednesday with Monday and Tuesday being taken up with tutorials and workshops.

I'm here at the conference venue a little bit early to get some work done ahead of my presentation in the workshop on "Project Management and User Engagement". My aim for today, as well as giving my presentation, is to see daylight at some point as it was dark when I left the hotel this morning and the workshop room has no windows!

I've been here since Saturday evening and my impressions of Indianapolis are mainly that it's cold! It didn't get above freezing yesterday and I'm very glad I brought a case full of thick winter clothing!

Wednesday, 19 November 2008

Were you caught on camera?

A selection of photos from the NGS Innovation Forum '08 are now available on the NGS Flickr and NGS Facebook groups. Feel free to tag, annotate, comment etc on photos!

Most of the presentations from the event are now available from the NGS website so if you'd like to have a look to see what you missed, to grab that website address you missed on the day or to refresh your memory now is your chance. The outstanding presentations will hopefully be added soon.

The NGS fortnightly news email bulletin has recently had an overhaul and now comes to you in lovely colourful html format. The fortnightly email contains news of software updates on the NGS, updates to NGS services, job adverts, conference announcements, training events and much more. If you'd like to be kept informed then please join our mailing list.

Tuesday, 11 November 2008

After the storm

I'd like to say thank you to everyone who came along to the National Grid Service Innovation Forum '08 last week. We played host to over 120 people over 2 days at the Museum of Science and Industry (MoSI) in Manchester where delegates heard over 20 presentations ranging from services currently available to NGS users to upcoming services and the future direction of the NGS.

Thank you to everyone who has so far completed a feedback form and I'm pleased to say that the feedback so far has been extremely positive. If you still have a feedback form that you would like to submit then please contact me. The feedback has strongly indicated that we should hold a similar event at least once a year so watch this space!

It's also nice to see that reports about the event are popping up in other blogs such as this one from the ESRC National Centre for e-Social Science (NCeSS).

The slides from the presentations will be up on the NGS website very soon and nearly all the presentations were videoed by colleagues from the Lancaster University Centre for e-Science so if you couldn't attend in person, you can see what you missed!

In other news there have been further software updates at the NGS so if you are a user of any of the following please take note!

EMBOSS 6.0.1
The latest release of EMBOSS (6.0.1) will be available on the NGS node at RAL ( next week. EMBOSS (The European Molecular Biology Open Software Suite) is an analysis package specially developed for the needs of the molecular biology user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. EMBOSS also integrates a range of currently available packages and tools, for sequence analysis, into a seamless whole. Further information on running EMBOSS on NGS resources can be found here.

Scali-MPI 5.6.4
The latest version of the commercial PlatformMPI (previously known as ‘ScaliMPI Connect’) MPI libraries are available on the NGS node at RAL ( All MPI software at RAL is linked to this latest version and is the default when compiling using mpicc,mpif77,mpif90,mpic++ . It provides a number of bug fixes and, for some user codes which call ‘free()’ repeatedly, it provides a significant speedup. RAL have benchmarked these libraries up to 10% faster than equivalent open source libraries such as MPICH.

Tuesday, 4 November 2008

Live from the NGS Innovation Forum '08

Posting live from a very packed NGS Innovation Forum at the Museum of Science and Industry in Manchester. We have a total of 127 delegates here over the next 2 days from all over the UK.

Currently Dave Fergusson from NeSC is speaking about the training opportunities available from NeSC and the NGS which range from helping new users get started to helping more advanced users make the most of the wide range of services available from the NGS.

Other talks today have included a keynote presentation from Dan Katz about TeraGrid and Michael Wilson speaking about EGI and how the NGS is involved in Europe.

For those of you who can't make the event all the presentations are being videoed and will be available online. Watch this space!

Friday, 24 October 2008

And it's closed

Registration for the National Grid Service Innovation Forum has now closed and I'm pleased to announce that we have 118 people attending over the two days. We are really pleased with the numbers that have registered and it's shaping up to be a great event. If you aren't able to attend, don't worry as colleagues from the Centre for e-Science at the University of Lancaster will be filming the presentations at the event so you can catch all the presentations at your leisure!

The latest fortnightly news bulletin from the NGS was released today and contained information about new software additions on the NGS including Gaussian 3, PC-GAMESS / Firefly 7.1.C and the expansion of the bioinformatics database provision. If you would like to receive a short fortnightly update by email from the NGS, you can subscribe here.

Wednesday, 8 October 2008

NGS Innovation Forum '08 - places are going fast!

It's been a busy couple of weeks here at the NGS. Many of us attended the EGEE conference in Istanbul where, as well as the conference, we were also involved in EGI and other project meetings. Thankfully most of us had arranged to stay on couple of days so we could actually see something of Istanbul rather than the inside of the conference centre!

The presentations from the workshop I organised on Dissemination and Outreach can now be found online and I'd like to take the opportunity to thank my speakers Sy Holsinger from Trust-IT Services and Vicky Huang from AGSC. During EGEE '08 I also got what I call "podded" as I was filmed for a podcast during which I talked about the NGS. I haven't actually been brave enough to watch it yet but if anyone is interested it can be found here.

On return from the conference it was straight back into preparations for the NGS Innovation Forum which is quickly approaching. If you have no idea what I'm talking about then all the information can be found on our website. The agenda is almost finalised and we have a fantastic line up of speakers talking about the latest developments for users at the NGS, use case scenarios for NGS resources and where the NGS is heading in the future. Registrations are coming in thick and fast so if you are thinking about coming along, register soon!

Monday, 15 September 2008

And breathe...well not quite (and some big news!)

Has everyone recovered from last week at AHM 2008? I don't think I have and I know that many people don't have time to. I'm back in the office this week to get ready for the EGEE '08 conference next week in Istanbul. Thankfully my workshop,which I've mentioned previously, is all set as far as I can tell. Just the complicated logistics now of getting the promotional literature sent over for the UK and Ireland Federation stand on which the NGS will be displaying. Oh and writing my presentation....

The other BIG news is that registration has opened for the NGS Innovation Forum '08. It's a 2 day event which will be held in the Manchester Museum of Science and Industry (MoSI) on the 4th - 5th November. The event is free to attend (yes FREE) and we are pleased to announce that Daniel Katz who has recently been appointed TeraGrid GIG (Grid Infrastructure Group) Director of Science, will be speaking at the event.

There will also be presentations by NGS users on how the NGS has become a powerful research tool for them, presentations on novel technologies available through the NGS and of course NGS staff will be on hand to speak to users.

The second day will be run in conjunction with Campus Grid SIG and will focus on the benefits of joining the NGS as well as technical requirements.

Although the event is free to attend, registration is required at the NGS website. There is also a Facebook event page. Everyone who is interested in the NGS is encouraged to attend as well as current, past and potential users. Please feel free to spread the word at your institution about the event!

Wednesday, 10 September 2008

Live from AHM 2008

Everyone else is blogging about the LHC so I thought I would do something completely different! I'm currently in the Infrastructure Provision for Grids, Infrastructure for Users workshop organised by myself and Andrew Richards. This is only due to the world not coming to an end as thought by many people.

We've had some really good talks including one on the Genius project which uses NGS resources. The project was also featured in New Scientist this week. Kudos to the New Scientist for getting our name right unlike The Economist!

The NGS stand has had a steady stream of visitors but of course we'd like to see more of you! We still have lots of demos today and one tomorrow as well. You can also pick up a grid certificate at the stand.

Tonight is the conference dinner which I know a lot of people are looking forward to at Dynamic Earth.

Tuesday, 2 September 2008

Busy time at the NGS

It's been rather busy here at the NGS for the last month or so hence the lack of posts. Well I should say that I've been busy so I haven't been posting!

Conference preparations really are in full swing for next weeks AHM 2008 in Edinburgh. I've been running around organising demos for the NGS exhibition booth (No.13 in Appleton Tower) and we've got some new interesting demos for you to come and see from geodemographic modelling to how the NGS is helping to treat cancer.
We're also involved in several workshops including "Infrastructure Provision for ‘Grids’, Infrastructure for Users" which I'm organising along with Andrew Richards. This workshop has an interesting range of papers so it would be good to see you there!

I've also finalised preparations for the workshop that I'm organising at the EGEE conference in Istanbul at the end of September. Entitled "Beating the drum: your trials, tribulations and tips for successful grid dissemination", this workshop will look at ways and means of telling people about the grid be they academic users or business users.

In other news the new edition of the NGS newsletter, NGS News, is out now. If you won't be at AHM 2008 or EGEE you can download a copy from our website.

See you next week in Edinburgh!

Wednesday, 9 July 2008

NGS and Mimas

I'm currently at the Mimas Open Forum at the University of Manchester.

There have been some very interesting talks about future directions and applications including a good presentation on mobile access. The NGS has been mentioned several times mainly in relation to databases which is encouraging.

A full agenda is available here -

Tuesday, 10 June 2008

New edition of NGS News available now!

The June edition of the NGS newsletter, NGS News, is now available in pdf format from the NGS website.

The latest edition features articles on how the NGS is helping shed light on how life on earth began, the new NGS roadshow events, a user case study on geodemograpic modelling from the MoSeS project (NCeSS funded), an update on the joint OMII-UK and NGS ENGAGE project, the new MySQL database service from th NGS, an update on EGI, an introduction to the new National Visualisation Service and many more of our regular features.

Please feel free to advertise the new edition of the newsletter wherever you think appropriate!

Tuesday, 20 May 2008

Tell us what you think!

A user survey for the NGS has just been launched. We are looking for active and past users of the NGS to tell us what they think about the services that we offer and how they use the service. The survey is quite short and should only take about 5 minutes to complete. There is the opportunity to add in additional information if there is something in particular you would like to bring up that isn't mentioned in the survey.

The survey can be found at

The results will be published in a report during the summer and will contribute to the future direction and goals of the NGS.

Tuesday, 13 May 2008

Fostering e-infrastructure in Edinburgh

Last week I presented at the “Fostering e-Infrastructure: from user-designer relations to community engagement” workshop ( held at the National e-Science Institute in Edinburgh. The event was organised by Alex Voss from NCeSS (

The event focused on the difficulties of engaging non-traditional grid computing communities and the barriers, either real or perceived, that dissuade wider uptake.

I gave a presentation on the current outreach and awareness raising methods used at the NGS as well as discussing anecdotal evidence of barriers or problems. A particularly interesting presentation was given by Elpiniki Fragkouli from AHeSSC ( who is a research associate on the “Enabling Uptake of e-Infrastructure Services” project ( Initial results and findings were presented and it looks as though plenty of people have heard of the NGS so it looks as though the outreach mechanisms are working!

The workshop also contained plenty of time for discussion which was well utilised – my 30 minute talk ended up lasting an hour and 20 minutes! Representatives from NGS, AHeSSC, NCeSS and OMII-UK were all present and the discussions demonstrated that many of us face similar problems. Hopefully the slides from the meeting will be available soon.

A follow up meeting is planned in Manchester at the end of this month.

Wednesday, 30 April 2008

Getting ready for AHM2008

Just submitted an abstract for the AHM due to be held in September this year. Nice to see it's in Edinburgh for a change. Everyone is wondering what effect that will have on the meeting as we won't all be cooped up on a campus stuck on the outskirts of town.

The NGS is running a workshop at AHM entitled "Infrastructure Provision for "Grids", Infrastructure for Users". This will be focused on the users as, lets face it, there's no point in building all this if no one wants to use it! More details on the workshop can be found at

I've also submitted a poster abstract for the NCeSS conference in June which has been accepted. NCeSS is the National Centre for e-Social Science and is based here at the University of Manchester. The conference is now in it's 4th year and more information on that can be found at The poster I am preparing will concentrate on the services the NGS can offer social scientists including our database service and a little bit on the ENGAGE initiative that we are involved in ( along with OMII-UK.

Tuesday, 22 April 2008


Hello from Imperial College London. I've taken the plunge and it looks as though I'm the first to post on the new NGS blog.

I'm currently at the BioSysBio conference ( down in London. The NGS has an exhibition stand here and I've been here since Monday morning. The exhibition stands couldn't be further away from the delegates if they tried which is a shame but I have managed to talk to some interested people including a research group leader who needs more compute resources. Turned out he wasn't even attending the conference but was passing through on his way to buy a coffee!

I have made an interesting press contact who can hopefully help me spread the word about research done on the NGS and our user case studies.

Thankfully this is the last of a whole series of conferences this month and I'm looking forward to getting back to the office for a while.