Archive for the ‘Uni’ Category

My G-boxes became E-boxes

Thursday, 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.

Thursday’s new experience

Thursday, 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).

Adventure with a Python

Tuesday, 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…

Thursday, 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.

Its been an even longer time…

Tuesday, June 19th, 2007

I always start these things with much enthusiasm that peters out in about 5 minutes. On the off chance anyone is interested, lets have an update on what has changed.

  1. We are homeowners. We bought our first house (a 3 bedroom terrace in a less desierable part of town) back in January.
  2. I went back to Uni (October 2006) to do an MSc in Systems Biology. This should lead to a PhD starting October ’07.
  3. Hamsters have changed round a bit. We still have Archie and Reggie (Theo passed away in May). Robos we have Psyche, baby Redrum, and “the girls”, Alysia, Zosima, Little ‘un and Pearl. We acquired a breeding pair of winter whites (who despite a lot of effort on the male’s part have yet to produce babies), Hank and Peggy.

They say nothing ever changes but the shoes, which clearly is not true. I have 2 new pairs of shoes since the last post.

An end to lab fun?

Monday, May 15th, 2006

I realised today I only have a fortnight left on my lab project. At first, the actual subject seemed pretty boring, but now i’ve really got into it. Having struggled so far with one half of my mutants (three times they’ve died, I only have one surviving to produce protein). Now there are the opportunities of extra substrates, possible inhibitors and…crystallisation!

 I love crystallisation, my first experience (beyond copper sulphate and a bit of string) was back in January in our “Structural Molecular Biology” lab. We took a tray with 24 wells, and using a range of pH and bits and bobs, found out which was the best to crystallise. Of course, we only looked at what actually crystallised, not the structure etc. I don’t understand the whole turning scattered electron images back into a real 3D structure, but it’s amazing.

I’m starting to realise maybe I am getting too into this whole science thing.

In other news, I was chatting to Adrian (one of the doctors in the lab) at lunch time, and saw Sarah from the other side of the hall. Rather than “hello” she shrieked “What is wrong with your eye?”…turns out its gross and bloodshot (and has been all day) but no one thought to point it out. Sometimes people are too polite. Trouble is, I didn’t spot it until it was brought to my attention, now my eye stings and feels a little strange.

Pets and other animals.

Wednesday, May 10th, 2006

I found out today that someone I know has a “pet” squirrel. It was bought to him as a baby and he refused to have it put down (they’re illegal to keep, or return to the wild – greys only). As one who adores squirrels, I was, of course, extra excited, although I must admit a little disappointed that they don’t turn in to tame little lovable pets, but seem to still have plenty of wild instincts. Still, its cool. In return, I shared that I own several hamsters.

While walking down the hill back to the bus stop, I saw several baby rabbits again. No baby ducks yet, I hear there are some at Gibbet but i’ve yet to see any in the fluff. 

Alchemy

Tuesday, May 2nd, 2006

I spent most of today purifying a protein using IMAC, its a modern form of black magic, such as that practised by the wizards of old who searched for the best enzymes to keep their white-wizard underpants white as white can be. Basically, you have a protein tagged with histidine residues, poor it through sepharose containing nickel ions, and then elute (with something to chelate the ions, or something which binds competitively, at increasingly higher concentrations). This isolates your his tagged protein from all the others (which either don’t bind, or bind less strongly and wash off sooner). Still, I prefer to ignore all that chemistry behind how it works, and focus on the more important fact: Its Magic. Its that sort of thing that makes me love biochemistry.

 Also drove up to Birmingham to sell the robo’s old habitrail, so that’s Theo and Archie’s new cage paid for!

 Also its the new series of Lost starting tonight, I rarely get excited about TV but I enjoyed the last series so much (sometimes its fun to be a sheep). I really hope they can keep the idea going, as frankly towards the end of the last series the plot did seem to get a little bizarre, but maybe the writer is just weird.

Drosophila and Asda

Tuesday, March 14th, 2006

Today I started revising Drosophila development, fairly slow going. There are only so many pictures of mutant larvae a girl can look at.
Had a bit of a surf round to see if I could find a cool birthday present for Jill…I want to get a chocolate fountain, but I bet she already has one. It’ll go well with their ice cream maker though.

Went to Asda as its the only supermarket that sells chicken and turkey sausages…well, Big Tesco does but that’s a longer trip. So we wandered round picking up stuff we needed, and stuff we didn’t. It appears Mike’s new idea to stop me buying fun stuff is to make me pay for it myself. First of all, they only had one checkout open and a queue of around 12 customers. Then, they decided to open another, woo-hoo. Put all the sensible shopping through first, with Mike, and after he paid we were asked the postcode. Then as he was putting receipt etc away, she didn’t start to put my shopping through, so we said “we’re together, and she did”. I decided to buy a bottle of Tropical Sourz, because it tastes so damn good. The woman said “Are you over 21”, so I replied “Yes”. She then sat there for a bit, so I decided to get ID out, she then looked at it and appeared to take great difficulty in working out if I was indeed over 21. So I pointed out if I wasn’t, i’d have just got Mike to buy it. I know its their job, but really, have a brain. Or is that why you’re working in Asda…(Is that too controversial?).
Then, to top my evening off, they overcharge me by 99p. Practically £1! So I went to the shelf, whipped off the price tag (I bet they hate it when shoppers do that) and took myself to the “we’re always happy to help desk”. The girl there re-funded me and gave me a £2 Asda voucher, so all was well in the end.

Another thing I feel the need to complain about is that I can’t find an eyeliner for less than £1.99. Perhaps I should just go and buy a 4B pencil…

Revision is boring.

Monday, March 13th, 2006

Today I didn’t leave the house. Tragic isn’t it. I did manage to revise 6 development lectures though, would’ve been more but apparantly my progress report for my final year project wasn’t good enough. Basically, I knew that, but it doesn’t get marked and so many people have been told not to bother I didn’t feel the need to put much effort in. So I re-wrote half of it, then read the reference paper and realised everything i’d researched in other places and added was already in there. Oh well. I’ll right another 1/4 page tomorrow and it’ll be at the maxiumum 2 pages.

I think i’ve already forgotton the stuff I revised, one thing I do remember is that in Staufen- mutants, there are no pole cells, and oskar is found everywhere, not localised to the posterior of the embryo, shock horror!

In hamsters, things are still going well between the three robos. I cleaned one of their three sections of cage, and they don’t seem to be fighting. I also put some fresh bedding in a little house for them, and I hope they move into there. The other bedroom is getting a little “ripe”, but it’ll be worth it if this intro continues to go well.

Finished the bag of “Stacy’s pita chips” arguably the nicest crisp-type snack i’ve had in a while. Perhaps tomorrow I should go to Sainsbury’s and see if there are any left on the reduced shelf.