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!