Bioinformatics training from the NGS

In conjunction with the Scottish Bioinformatics Forum, the NGS is running a one day training event at NeSC in Edinburgh in March and the event is open to all.

The course will cover accessing the facilities of the NGS to run high through put applications across multiple nodes for bioinformatics. Attendees will launch jobs using command line and GUI interfaces and use some of the pre-installed bioinformatics applications available from the NGS nodes. Also included will be a short introduction to the practicalities of translating bioinformatics formats between XML formats.

If you would like to attend this event then please see the event page on the NeSC website. Remember you don't have to be a SBF member to attend or indeed Scottish!

Roaming around the EBI

Earlier this week, I was down in Cambridge at the European Bioinformatics Institute for the NMR Software Workshop.

I was there to issue certificates to users as a "Roaming RA" operator. The NGS runs the UK e-Science Certificate Authority, which issues certificates not only to the people who want to make use of NGS services and resources, but for any UK academics involved in Grid computing. The certificates are accepted and recognised across the world and can be used to enable authentication of people across different Universities - even in different continents.

Usually, certificates are authorised for someone by an operator in their own institution but this is not always available.... which is where I come in. There are a number of Roaming RA operators with the ability to issue certificates at events where there is no local provision for issuing certificates. Quite often this will be at one of the many NGS roadshows or events we attend.

If you have an event where you think people would like a convenient opportunity to get a certificate for use on the NGS or elsewhere, get in touch with us at support@grid-support.ac.uk.

The Grid in Action

The team from the JISC-funded eIUS project have recently released a new video showing the grid in action.

This video features a group of researchers in Bioinformatics at the University of Manchester who, in collaboration with the myGrid Consortium, use the Taverna Workbench and the myExperiment virtual research environment to assist with the analysis and sharing of data relating to sleeping sickness (Trypanosomiasis) in African cattle.

This is the second video released by eIUS with the first video focusing on the use of grid in field archaeology.

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.

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.