My G-boxes became E-boxes

February 3rd, 2011

In which I am made aware of the old saying “Never say never”, but I’m still quite tempted to say “I’ve moved away from Plants”.

Since last I wrote, many things have happened. OK, not many. Some things, but they are pretty major. I have finished my PhD, yay! Still awaiting the viva, but I’d like to see it as progress. I also got a job, which marked the end of my time as an Arabidopsist* and I am now a Drosophilogist*. The biggest change is that I’ve said goodbye to Warwick, my “home” for the last 7 and a half years.

And what a journey I have had. When I started at Warwick back in 2003 studying Biochemistry I don’t know where I thought I’d end up, but I don’t think I ever imagined that I would end up doing bioinformatic analysis of plant gene regulation. I’ve travelled thousands of miles (around 3500 west, and 6000 east) to tell people about what I’ve spent 3 and a smidge years of my life doing, and hopefully I’ve made some useful contributions along the way. It’s all summed up here.

*I think you will find that these are valid scientific terms.

In which I miss the mix tape.

September 10th, 2010

As much as I love the simplicity of digital music, I sometimes stop to think about what we’ve lost with the advent of music at the touch of a button. I’m no vinyl purist, i’m not saddened by the complexity lost by transforming a wave into 0s and 1s. Just as video killed the radio star (though i’m not sure it did), mp3s killed the mix tape.

My own love of mix tapes started as a purely personal thing, i’d listen to the radio (Atlantic 252!) with a tape on pause waiting to record as soon as the song I liked came on. I remember cringing if the dj ruined the end of the song with some inane prattle, the debate over whether it would be better to record a bit of blank sound over this so the song had an abrupt ending, or whether to inwardly curse the guy every time you listend to that tape in future. When I go a little older, the mix tape was a way to share new music with friends, and most importantly a secret way of saying “I love you, please notice me”. Hours spent picking exactly the right tracks that you knew the person would like, that almost projected the hidden feelings, but didn’t go right out there and say it.

Towards the end of secondary school, mp3s were getting bigger, though mp3 players were still expensive, a lot of people had discmans, so the mix cd was borne. This was almost more fun, there was far more room to decorate the case, and you could print in track names rather than try and read the scrawl of a track name squeezed into a space that was never meant to be written in by humans. Two years later everyone owned an mp3 player and DRM was ruining our lives.

Nowadays you can send someone songs on spotify, social networking makes it easy for us to update our friends with what we’re listening to, but it’s not really the same is it. I think it was “Nick and Norah’s Infinite Playlist” where the mix CD recieves a little exposure, but was anyone still making those things in 2008?

RIP Mix tape…

Thursday’s new experience

August 12th, 2010

Installing the UCSC Genome Browser

At first glance, this looks pretty much idiot-proof, unlike a lot of tools there is a detailed instruction guide, so I thought it would be dead simple.

Hurdle 1, echo $MACHTYPE tells me i386-apple-darwin0.9 The instructions assure me that MACHTYPE will be simple and non-hyphenated. Thinking i’m clever, I type $ export MACHTYPE=i386 then run make libs, and it throws a wobbly about the hyphens in i386-apple-darwin0.9. So off to being more sensible, and editing MACHTYPE in ./profile.

Mistake 1, assuming that MYSQLLIBS and MYSQLINC are set…fix that. Mistake 2, assume you have installed mysql in a standard place, and then fix that.

Mild confusion 1, unzipping jksrc.zip does not give ./kent. Ignore this.
make libs works…the next step cd hg
make compile
does not…google time!
First problem here was:

ld: warning in /usr/local/mysql-5.1.49-osx10.5-x86_64/lib/libmysqlclient.a, file is not of required architecture
So I decided to try another version of mysql which gets past that, then I ran into the same problem as this guy. I went for editing common.mk to SSL=0, as it seemed the quickest (though I am not sure about suggestion 2, as I downloaded the files today and it was set to SSL=1).

Taming the Python

August 11th, 2010

So, last night with a little help from Dave, I got a little further in the Python adventure. He suggested setting up a Virtual Environment and trying to install the packages there. In the end, I went with numpy 1.2.0, scipy 0.8, matlibplot 1.0 (0.99 seems to have issues on OSX), but hit a brick wall with rpy. The first problem was rpy is old. Very old. The regex used to try and find your R version number only allowed for \d.\d.\d – I am on R 2.11.1, so I fixed the regex and all was well, but I managed to get an awful lot of other warnings/errors. By this time it was 12:20am, and i’d been trying on and off for 12 hours to get this to work.

This morning I took a fresh approach…enter an old windows laptop, no python install, very old R (2.4!). I instaled python 2.5 (from the .msi), numpy 1.1.0 (from .exe), scipy 0.7 (from .exe), matplotlib 0.99 (from .exe), tried importing and scipy claimed it wanted numpy 1.2.0, so installed that (some good version checking there on checking minimum requirements for the script i’m trying to run…). When I tried importing matplotlib it decided it needed win32api, so had a bit of a google and installed PyWin32, which fixed the matplotlib issue. I then installed rpy 1.0.3 (from .exe) which worked!

Had a bit of a faff trying to sort out the paths, it’s been so long since I used windows I had to check where the System Variables thing is, then when I added R and Python they didn’t come up in the path. After some head scratching, I went with path = %PATH%;C:\python26
and then the same for R.

The script is now running…if it works, I might tell you all what it is 😉

Adventure with a Python

August 10th, 2010

No, not the big snakey kind, just my first attempt to get something working in Python. One of the first things I did when I got my laptop back in 2007 was install all the developer tools. The first thing I did was install a shiny new (well, slightly tarnished in the face of Python v3!) copy of 2.7.

This turned out to be mistake number 1. The script I was trying to run requires numpy, scipy, matlibplot and rpy. numpy installs from a binary no probs, I think “ooh this is easy”, I then realise there wasn’t a binary for scipy that worked with 2.7. No problem, i’ll go simpler. Python apparantly has something called easy_install – yay! $ easy_install scipy …all runs through. I ran python, then tried import scipy, oh, it hasn’t found it. Sneaking suspicion sinks in, and I discover Python 2.5 lurking. OK, no problems, just download scipy.gz (not it’s real name ;-)), uncompress, fiddle in the command line, wait a while (the README warns that this can take an hour on a slow computer, and then everything fails. Realise I forgot to “sudo”, wait another 10 mins, fails again. Sulk a bit. Hit google. Apparantly scipy and 2.7 can be a pain.

Give up. Install python 2.6, install numpy, scipy, matlibplot. Feel smug. Decide to update R, as there is a new version (clearly not learning from the Python mistake here).

So i’m still stuck on rpy, it seems to think it has installed, but none of the python family are capable of importing it. Perhaps, after frustrating me for the afternoon, I will head home, try again and it will work first time.

Ho hum…

April 22nd, 2010

Hello again blogosphere. I wonder how many times i’ll say i’m going to start blogging and then fail to continue?

Its been a slow week…Mike is in London for a course, so i’ve been getting the bus to uni. I’ve managed to pick up a cold, which is quite annoying, but no way near as annoying as last night where I stood at the bus stop for an hour while nothing turned up. According to the paper timetable at the stop there should have been three buses, according to the online timetable only two. Either way it was rather frustrating! I decided to work from home today to save myself a bit of annoyance, and I hope things are better tomorrow.

Comment Spam and other things

November 30th, 2007

Every day now i’ve been getting comment spam (although it doesn’t get through as I have set everything to need approval). Always on the quail post…I wonder if quail is a popular term among spam bots, or whether they’re just set up to go for an older post.

Tomorrow is the MHC Christmas Show, which should be good. It was a pretty big show last year, I got to poke my first tiny baby dwarfs and they put on a nice buffet. We’re also buying an extra hen to try and settle the quail fighting, although I put all the birds in the playpen together last night and they didn’t seem too bothered about each other.

Something to do…

October 24th, 2007

Today in the office, Marc asked if anyone had a website…so I said yes. He asked about what could be put on it, so I said pretty much anything. That lead me to realise that i’ve had “proper” hosting for about 7 years now and the only fancy-pants thing i’ve done with it is install wordpress. I decided that i’d have a go at installing media wiki (despite the fact I don’t really have anything to write a wiki about). I’m taking bets on how long it takes me to get fed up with the idea…it’ll either be when I have to tinkle with the database, or if I survive that it’ll be when I realise I have to write content…

On keeping Quail

October 16th, 2007

A fortnight ago, I bought 3 quail “chicks” (they were 3.5 weeks old), Waylon, Rose and Daisy. The idea was that they were two females and a male. They would live indoors in a large rabbit cage over the winter, and move outside when spring sprung. I set about buying all sorts of quaily bits and bobs, a nest box, some hay for nesting in, a water dispenser, grit, leg rings, chick crumb and pellets. On the second day I discovered mistake number one. Quail drink a LOT, and one budgie drinker (approx 250ml) needs refilling twice a day, so I invested in a 1.3L mushroom drinker. One thing I had been warned about was that they would kick bedding into their food, but I thought bowls would be OK. However it did get to be a bit of a pain, so I bought a food hopper at the same time as the drinker.

It became obvious after a week that Daisy was actually Dan when further speckly breast feathers came through (there were a few when we bought “her”). From the little information I managed to scrape from the internet, I knew that i’d need an excess of females as the males are over-amorous. Although the lady I bought the quail from had offered to swap Daisy if she did turn out to be a he, I felt reluctant to part with him. I’d joined a Quail Forum and luckily there was a member near enough for me to buy females from. When we got these two home, I let them run round with the others, and all seemed well. 5 quail in a cage 1m x 50cm take up a lot more room than 3 quail though, and so the mushroom drinker became major mistake number 2. After it falling over twice due to much quail stampeding I realised I was going to have to invest in a rabbit bottle for the birds. The two new quail were used to it, and seem to have done a good job of showing the other quail how to use it.

I miss Manchester

July 2nd, 2007

On Thursday I went up to Manchester for a joint conference with their Systems Biology people. The MIB that they’re based in is a lovely building, far nicer than our one. We never did decide who has the best deal, they get more money, a nicer building but we have offices, a shower and tea, coffee, squash and biscuits on tap.

In the evening, we went to San Carlo for a meal. It was very nice, fairly posh (I had monkfish!) and Mike had a Tartufo for pudding that was set on fire with a shot of sambuca (the waste!).

After that we went to the awesome Baa Bar (although it was a bit late, and we only stayed for two drinks (my shots were the storm, and a springbok). We stayed at the Thistle hotel on Picadilly Gardens, which was reasonably comfortable, although hideously overpriced. I was not impressed with their lack of veggie breakfast (yes, I can eat eggs and hash browns, but i’d like a veggie sausage and the knowledge stuff has been fried in seperate pans than you very much!).

Anyway, Friday evening we went to Sinclairs, and one of the Wetherspoons. People are so much politer than in the midlands, a man bumped into me and actually apologised, and a woman held a door open for me on the way to the loo rather than letting it smash into my face! After that, we went to Cafe Rouge…unfortunately we picked a new one, “just off” Deansgate. Its part of a new development, and is the only place open, and is as far off the main road as you can get. We were starting to have doubts when we walked through all the hoardings, but there it was right at the end with happy little balloons outside. We were the only customers, and paid half the bill in Tesco vouchers my Mum had given Mike the day before, but hey…i’m sure the 15 staff that were on enjoyed serving us…