Detecting TB

Tuberculosis infection is a major challenge in today’s world, as has been recognised by the WHO.  The current Gold Standard test requires taking a sputum sample, which is grown for several weeks, to identify the presence of the infectious vector Mycobacterium tuberculosis.  There are a number of efforts underway (for instance, in our department in a collaboration with University of Pretoria, and from the OU as a spinout of the Beagle II space exploration mission) to improve detection methods and speed up the process with improved accuracy.  Hopefully these will come to market soon, to prevent things like the latest scam that is running in South Africa, where TB-infected people are selling their sputum to non-infected people so that they can claim disability grants.

We are also helping in this effort – I have a new PhD student in the group, the recipient of a prestigious university 125th anniversary scholarship, who will be studying how key aspects of the Mycobacteria contribute to biological function.  We have also received sponsorship from Amazon on their Cloud system to help us with the work, and I hope to detail our foray into Cloud computing at a later stage.

Clouds and Waves … computing at the interface

So this has been an action-packed week in my science world:

On Monday, I discovered that I could potentially access the Amazon cloud (EC2) with an academic grant. http://aws.amazon.com/education/

This has a lot of potential and will allow us (hopefully, if the grant is successful) to do computing along the lines of more famous projects such as SETI@home and Folding@home. Although we will not be discovering either aliens or cures for cancer, we do hope to make some contribution to the scourge which is tuberculosis, a disease that kills millions of people each year, and is only set to get worse as the incidence of co-infection with HIV and multidrug resistant strains increases.  At any rate AWS shows great potential so we’re keeping our fingers crossed.

The other cool thing this week was receiving my Google Wave developer preview account.  Google wave is a tool set to revolutionise internet communications through new ways of utilising existing protocols.  Whilst it may not be for everyone (many people don’t like google’s email interface for example, and emphasis on searching, and this is similar), one place it should certainly take hold is in collaborative editing processes.  Hopefully we will be able to adapt the interface to electronic lab recording interfaces (for which it does seem naturally suited), and collaborative paper preparation and publishing (for which it is also ideal). I only bemoan the fact that the public preview is only due on September 30th, far too late really to integrate it into my second year undergraduate course.  And with the current instabilities of the developer preview (she says, to the sound of crashing waves …) it is going to be touch and go whether it would be safe enough for assessed materials.  So perhaps this can be a plan for next year, when people are then used to the new interface.

The next step is of course to get a robot up and running to start to integrate chemistry with the wave.  Already the ability to plot graphs (code), integrate chemical information from chemspider, and incorporate citations from services such as citeulike are available (see some of the things that happened at sci-foo).  Chemical converters are already under development … perhaps a periodic table is next (which will insert specific elemental details on request).

I am hoping to perhaps look at a way to grab files from finished computational chemistry runs (eg gaussian, gamess, nwchem etc) and convert at least some of the output into small graphics.  This seems like it may be possible using a mixture of the openbabel webservice (for translation) and molecule information retrieval services like the Royal Society of Chemistry‘s chemspider or NIH/PubMed’s PubChem.  Anyway, I need to learn python first, so watch this space.

Clouds and Waves