I’ve been working on a new project at work for a couple of months now, it’s another of those informatics projects that I seem to be doing more of nowadays. Obviously much time was spent coming up with the acronym – Biomedical Research Infrastructure Software Service kit. It is based up at the Glenfield Hospital with the Cardiovascular Biomedical Research Unit.

The main idea behind the project is to plug together a bunch of software packages and stick them on the cloud. We will then let other researchers come along and have an instance of our software stack at the click of button (well a few key stokes really). The obvious benefit being that it will take a few minutes to set up, as opposed to the few years it has taken to get the software to where it is now, and it will be centrally maintained – so no specialist IT skills will be needed.

We are currently going down the route of putting it on a VMWare backed cloud infrastructure, so my main responsibility (on account of being a linux geek) is to get it all into the cloud. Then we need to be able to monitor and manage it, so that’s in my domain also.

As you’d expect, we have a website and blog that we update on an irregular basis.

For the last six months or so I have been working on a project called HALOGEN, this was a venture to bring together various different geospatial data sets into one unified database. By doing this we can start to ask cross data-set queries – something that you certainly couldn’t do when one source is in an Excel file at one university and the other in an Access database at another!

One of the advantages of this approach is that we can then stick a web front end on the database and let the general public look at the data. It is this bit that we launched yesterday. If you head on over to halogen.le.ac.uk and do a query then you should be able to find the derivation of your favourite English place name, or where your ancestors lived during 1881, or even what and where treasure has been found!

Becca and I have bought a couple of antique maps of places we have lived over the years, but we have never got around to getting them properly framed. Well we finally did, and they look awesome!

This is a 1764 hand coloured engraving of Leicestershire by Thomas Kitchen.

This is a 1806 hand coloured copper engraving of of the Environs of London by R. Phillips of New Bridge Street.

This is a c1880 ordnance survey map of Buckinghamshire by G. W. Bacon. Those sharp witted amongst you will know that we used to live in Milton Keynes, which wasn’t invented (in its current form) until 1967, but Milton Keynes village is just about visible if you know where to look.

We got them framed by out local map shop. Just need to get a nice one of Norfolk and Sri Lanka and we will be done.

I am finishing up on a project at work called HALOGEN, it’s a cool geospatial platform that I’ve been developing to help researchers store and use their data more efficiently. At its core, HALOGEN has a MySQL database that stores several different geospatial data sets. Each data set is generally made up of several tables and has a coordinate for each data point. Now most of the geo-folk at work like to use ArcGIS to do their analysis and since we have it (v9.3) installed system-wide I thought I would plug it into our database. Simple.

As it happens the two don’t like to play nicely at all.

To get the ball rolling I installed the MySQL ODBC so they could communicate. That worked pretty well with ArcGIS being able to see the database and the tables in it. However, trying to do anything with the data was close to impossible. Taking the most simple data set that consisted of one table I could not get it to plot as a map. The problem was the way ArcGIS was interpreting the data types from MySQL; each and every one was being interpreted as a text field. This meant that it couldn’t use the coordinates to plot the data. I would have thought that the ODBC would have given ArcGIS something it could understand, but I guess not. The work around I used for this was to change the data types at the database level to INTs (they were stored as MEDIUMINTs on account of being BNG coordinates). I know this is overkill, and a poor use of storage etc, but as a first attempt at a fix it worked.

Then I moved on to the more complex data sets made up of several tables with rather complex JOINs needed to properly describe the data. This posed a new problem, since I couldn’t work out how to JOIN the data ArcGIS side to a satisfactory level. So the solution I implemented here was to create a VIEW in the database that fully denormalized the data set. This gave ArcGIS all the data it needed in one table (well, not a real table, but you get the idea).

If we take a step back and look at the two ‘fixes’ so far, you can see that they can be easily combined in to one ‘fix’. By recasting the different integers in the original data in the VIEW, I can keep the data types I want in the source data and make ArcGIS think it is seeing what it wants.

And then steps in the final of the little annoyances that got in my way. ArcGIS likes to have an index on the source data. When you create a VIEW there is no index information cascaded through, so again ArcGIS just croaks and you can’t do anything with the data. The rather ugly hack I made to fix this (and if anyone has a better idea I will be glad to hear it) was to create a new table that has the same data types as those presented by the VIEW and do an

INSERT INTO new_table SELECT * FROM the_view

That leaves me with a fully denormalised real table with data types that ArcGIS can understand. Albeit at the price of having a lot of duplicate data hanging around.

Ultimately, if I can’t find a better solution, I will probably have a trigger of some description that copies the data into the new real table when the source data is edited. This would give the researchers real-time access to the most up-to-date data as it is updated by others. Let’s face it, it’s a million times better than the many different Excel spreadsheets that were floating around campus!

This weekend we went to the whisky show in London, and it was goooood. It was an all-in day ticket that gave us all the free samples we could drink from all the stands, as well as a few nice extras. As part of our tickets we got to have some ‘dream drams’, these are some very nice (read as rare/expensive) tipples to tickle our taste-buds. We wanted to go for the Bowmore 1964 White, but alas it was all gone when we got to the stand. Gutted. Still, the Auchentoshan 1957 went some way to counter my disappointment.

One of the things that got my gastronomic seal of approval was the food pairings with different whiskies. One of their tasters had gone to Borough market and bought some nice nibbles (cheese, sausage, chutney, chocolate etc) and matched them to various whiskies. It really highlighted some of the different aspects of whiskies that I know well, bringing out an almost new flavour to them.

I tried to scribble down the whiskies I tried on the train on the way home and I got a respectable list, there are at least two or three more that I can’t remember the name of.

• Caol Ila Moch
• Caol Ila 25yo
• Lagavulin Distillers edition 1995
• Port Askaig 30yo
• Amrut intermediate sherry matured
• Glengoyne 40yo
• Auchentoshan 1957 (50yo)
• Jameson Vintage
• Bunnahabhain 25yo
• Bunnahabhain 30yo
• Hakushu Bourbon barrel
• Springbank 18yo
• Bowmore 21yo
• TWE Port Ellen x2
• TWE Springbank
• Whisky society Bruichladdich
• Ardbeg 10yo
• Craggenmore 12yo
• Amrut
• Aberlour 10yo
• Caol Ila 12yo
• Mortlach 32yo Cask strength
• Balvenie 12yo
• Mackmyra first edition

I think I shall definitely be making an annual pilgrimage to this!

I don’t usually talk about emotional stuff on our blog but needed to vent somewhere.  Our friend, Echo, who had been fighting leukaemia sadly passed away on 19th May, she was just 29 years old. We found out whilst on holiday for my birthday which kind of put a damper on things

Olly and I only knew Echo for ~ 2 years, since we moved to Leicester and I started in the chemistry department. Echo was a PhD student in Chemistry but in a different research group to myself. A testament to her strength of character is that she left her home country (China) to come to the UK to pursue her PhD, and was writing up her thesis when she found out she was ill.

Echo was a positive, quirky person, always making everyone laugh and smile.   She would come out with some of the funniest things….. such as asking whether Olly’s pot-belly was real or whether it was a fake belly!!!!!!! Even the last time we spoke we were laughing about how she had taken up knitting as a hobby in the hospital.

Below are some of my favourite pictures of that I have of Echo that capture her cheeky fun loving ways.  Rest in peace. xxx

Gorgeous chemistry girls all dressed up for my 28th bday

Alan disrupts things and makes everyone laugh!

We eventually managed to convince Echo that apple bobbing was a great British tradition.... she had a go at it!

Echo as Chun-Li from streetfighter!

Echo's alcohol tolerance was never much!

Echo and Archie in the office

As you may or may not notice I have rewritten my entire website. Given that the old version was written when I was just learning HTML4 about six years ago I figured it was time for a bit of an update. It’s also given me a chance to have a play with some of the new HTML5 and CSS3 features as well as move a few things around. Notibly I moved the holidays pages to a blog category – there was starting to be too many.

In terms of the HTML5 stuff, I have employed the new structural tags <header>, <nav>, <footer> for now, with the likes of <section> to follow soon. One of the more noticable things is the use of the new <video> tag, in using this I am slowly converting all my video to Ogg Theora. This does mean that I am not supporting IE in the first instance, I may or may not get around to fixing it someone asks me nicely.

There’s a few other HTML5 bits and pieces around, my favourite may be the new <form> behaviour. They have rewritten it so you can upload many files at once and a lot of the validation of user input is done on-the-fly. I have a nice CMS that I use to manage my photos now with all these implemented

Obviously there is a nice sprinkling of CSS3 styles around which will work in modern browsers – even IE (if you are using IE9 and have compatibility mode turned off that is).

Let me know if you have any problems with the new style (things not displaying properly etc).

It just occurred to me that I have been in my new job for almost a month and not really told anyone what it is about, so here goes.

I am still at Leicester – I got ‘redeployed’ at the last minute as I am awesome and they couldn’t bear the thought of me leaving. I now work in the research computing support team in IT services. Like all my jobs it is split into a couple of different roles, although this time it is more of an equal split. First of all I am working in the HALOGEN project. This aims to bring together a collection of different spatial data-sets and allow correlations to be found between them, hopefully in the guise of a web front end that can do all sorts of pretty plotting etc. In that sense it is very similar to the work I have done in the past with the astronomy data sets.

The second aspect of the job is to help the RCS guys deploy their new LAMP stack to users. This means that I am going to have to deal with people, shudder.

It’s a fairly short term position, but at least it will keep me off the streets for a while.

So my WASP public archive paper has been accepted and is the highlight of this weeks issue of A&A You can see it on the A&A website.

So Becca and I have finally finished our Ph.D.s. We have the certificates, the photos and the scars. All that is left to do now is bask in our own smugness and get some leather bound copies of our thesis made up. If you are really bored you can read my thesis. One day I will upload Becca’s thesis too