St. Patricks day at the OU.

Our new house

As some of you may already know; we have bought a flat. It’s all part of our relocation to Bristol for work (which I shall write about at some point). It does give me a (good?) excuse to revive the blog I wrote about our last place.

It’s a 1960s flat in the Clifton area of Bristol, so it is a short walk to work in the morning. I think it is fair to say that it is a ‘project’, all the usual cosmetic stuff needs doing, the kitchen and bathroom both need doing, the wiring needs some TLC, the garage needs water tightening, and it needs some heating. In fact it might just be easier to knock it down and start from scratch.

You can have a look at some photos of the flat before we moved all our stuff in. Needless to say it looks a lot more crowded now.


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.

HALOGEN goes live!

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!

ArcGIS 9.3 -> MySQL jiggery pokery

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!

HALOGEN/RCS – my new job

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.

Highlight of the week

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.

National Astronomy Meeting 2010

And so another N.A.M. has ended – I am writing this on the long train journey home. Luckily I booked my seat long before Eyjafjallajokull started to stir, and ground all the planes (unlike many that could not make it, or get back). The N.A.M. was at Glasgow University, close to the centre of the city, the university is an ancient one with many pretty old buildings that look like they belong in a work of fiction.

My main reason for coming to the N.A.M. was the launch of the SuperWASP public archive. I have been working on this for around a year now, and on Monday it was officially let loose on the public. This first data release has 14 billion data points and over 3.5 million images now available to be queried and downloaded. The general consensus among the people I spoke to about it was that it will be a very useful resource. The trouble I am having is that it is rather difficult to get people excited about an astronomical data base, and then getting them to tell their friends!

As ever with N.A.M.s there was a wide range of sessions to go to, one that I particularly enjoyed was the software astronomy session. In it the chair introduced the term astroinformaticsto me as a way of describing what it is that I do – a much sexier title than archive scientist me thinks 🙂

As you would expect there were a few people rather irate at the open forum which had representatives from the funding councils. One poor guy told us how he had his three year post-doc ended one year in, with one months notice, due to the current funding issues. Needless to say, this is precisely why more and more of my friends are moving abroad.

Besides the conference I did get to do some other stuff – mainly revolving around drinking of some description. The conference dinner was in the Kelvingrive museum, which was pretty cool. And so it is that I am heading back to Leicester with a bottle of double matured lagavulin in my case, and a head full of new ideas…

Boulder, CO – A Working Holiday Day 6!

After another big home cooked breaky at Allenspark Lodge we went in search for the Allenspark Trailhead. Its quite remote and starts fairly high up. Infact the car park to this trailhead is just a dirt track. On the drive up to the trailhead we passed some very posh looking log cabins with glass fronts! They were nestled in between all the pine trees and looked very pretty.

The trail we took towards Calypso Cascades was a forest trail, which was quite rocky and a little snowy/icy in places. We only saw one other person on our way out there to the waterfall. The trail itself was built after a lightening storm caused forest fires in 1978. So a lot of the trees have been cleared leaving great views of Longs Peak. You can also see places where landslips have occurred.

We ate lunch sitting on a boulder at Calypso Cascades and were pestered by a rather persistent Blue Jay! On the way back to Allenspark Trailhead we saw some the interesting site of a tree growing within a tree (presumably after the forest fire!).

Allenshead Trail Stats:

6.2 mile there and back.
Allenspark trailhead elevation: 8520 ft / 2597 m
Calypso cascade elevation: 9200 ft / 2804 m

After our hike we went back into Estes Park for some souvenir shopping and even found time to sample some ice cream and local beer : )
We are currently staying in the Colorado Cottages and even have a log fire in our room. We had a soak in the hot tub before heading out to dinner (I sooooooo want a hot tub!!!! we should definately have more in the UK!). And finally we have internet and phone reception again so can upload lots of posts and pictures!

Boulder, CO – A working Holiday Day 5!

After a hearty home cooked breakfast supplied by the Allenspark Lodge, Zoe and I ventured out on our first trip to RMNP. We went in through the Beaver Meadows entrance. We started out at Bear Lake ranger station and took the Bear Lake Trailhead. It started out really easy – a concrete path up to Nymph Lake. We stopped here to have lunch amongst the wildlife including a boisterous chipmunk that was trying to get in to Zoe’s backpack, a blue jay and another grey fluffy bird that tried to beg for food. The lake itself was partly frozen over still.

We ventured on and got to Dream Lake which was completely picturesque! Again the lake was partly frozen, and the mountains were in the background. Here we deviated from the path the majority of people were taking. We decided to tackle the snowy and seriously icy trail up to Lake Haiyaha – native American for “Big Rocks”. En route we got some scenic views of Glacier Gorge and Longs Peak. The “Big Rocks” refer to a massive boulder field you have to scrabble over to get to views of the lake.

After a short stop at Haiyaha Lake we began the descent back to Bear Lake – there were some moments where I was ice skating down the trail!!!!

Hiking stats:
Lake Haiyaha Trail – 4.2 miles there and back.
Bear Lake elevation: 9,475 ft / 2888 m
Lake Haiyaha elevation: 10,220 ft / 3115 m
High point of hike: 10,240 ft / 3121 m

After the hike we head into downtown Estes Park to have a look at tourist tat! We found a nice mexican restaurant to eat in – although portion sizes were ridiculous! My fajitas could have fed three people!!!!! We headed back to Allenspark Lodge for a dip in the hot tub after dinner and I was out like a light! I didn’t even hear Zoe get up the next morning to go for her run!

Boulder, CO – A working holiday Day 4!

Today was the last day of the conference, after which we headed to the west of Boulder and up to NCAR (National Centre for Atmospheric Research) which is the sister organisation of NCAS (National Centre of Atmospheric Science – to which Zoe belongs). NCAR is situated perched up on top of a large hill overlooking the entirety of Boulder. In fact from the viewpoint at NCAR we could even see Denver cos of the clear sky.

NCAR has a visitor centre with lots of interactive outreach toys in it [i will upload some pictures soon either here on on the photos page!]. After learning all about properties of the atmosphere we walked the NCAR weather trail which was a gentle stroll with information points telling us about weather and atmospheric conditions of the region.

After our walk we headed north towards Rocky Mountain National Park and stopped off at Allenspark Lodge, Allenspark. It is a breathtakingly beautiful cozy log lodge. Apparnetly it was built approx 75 years ago from reclaimed wood after a nearby forest fire (by American standards it is probably classed as a historical building!!!). The owners are extremely welcoming and make you feel quite at home. The lodge is fairly large, there are three floors, a hot tub, dining room/kitchen with complimentary tea/coffee/hot chocolate, a cozy living room with a fire and a stove and a tv/games room. I have never stayed anywhere so homely before and would highly recommend it to anyone!

We headed out to the Baldpate Inn for dinner. The Baldpate Inn is named after the book ” 7 keys to Baldpate” written by Earl Derr Biggers. It is about some people that each think they hold the key to the mythical Baldpate Inn. The original owners built the building in 1917 and named it after the book, the film was just out too. They planned to give each guest a key as a souvenir of their stay at the Inn. This proved too costly for them, in the end guests started leaving their own keys as a memento! There are tens of thousands of keys in the collection now, including things like the key to Hitler’s writing desk, the key to the gate of Sherwood forest etc. Each key has been donated with a message or letter from the sender.

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