Monthly Archives: September 2006

Things that are wrong with the world (#234)

Coming home and downloading ‘stuff’ at 480kb/sec when most often in work (well the Medical School at least) things trickle down somewhere around the 70kb/sec mark. The boxen in Computing Science racks manage megs/sec I admit, but I have to offer up some love for Telewest at this point. The connection gets faster, and the costs stay the same.

I wonder if they will deliver cable to the office in time for the Ashes next year.. I’m sure Simon would chip in for Sky Sports goodness..

Vague annoyances – Puzzle and Puzzleboot

I have a lot of interactions with Martin Embley‘s group at work. They do an awful lot of phylogenetics and I’m often called upon to support their analyses.

Today I have been struggling with Tree-Puzzle and Puzzleboot. Tree-Puzzle is a program I’m long familiar with – a menu driven program that is in common use and that I previously packaged up for Bio-Linux. Puzzleboot is a shell script for automating Puzzle searches when you have multiple bootstraps in a single file and is 20 lines or so of shell script that demonstrates why you shouldn’t let biologists near a computer. Due to a complete lack of error checking Puzzleboot will fail to complete (and sit there apparently hung) if two things happen – both of which happened to be true for the data I was working on.

Firstly the analyses are split with a repeating header. The script takes the first line of the input file, makes a note of the header and then greps the file to find out how many headers there are in the file – giving you the number of concatenated data sets. It then finds the length of the file using wc -l. It then uses expr to divide the length of the file by the number of entries. This is then used to split the file into chunks for further analysis.

The data file I had was 2 entries long. Each entry was separated by a blank line. The script reports 2 entries over 65 lines and expr evaluates 65 / 2 to be 32. So the 65 line input file gets split into 2 files of 32 lines each and 1 file of one line, truncating the final entry and bringing things to a grinding halt.

The solution is simple but undocumented – don’t have blank lines between the entries in your input file.

The next bit however is what brings in the sweet, sweet irony. When you run Puzzleboot it looks for a ‘command’ file, a series of one letter operations which under the interface to Puzzle change the analysis options. It then concatenates this onto the end of the files that it has split up in the previous operation. However it doesn’t work. Why? Because unless your command file starts with a blank line, it is not processed properly. Needless to say most people aren’t going to randomly insert a blank line into a file at the start of the file.

One half of the operation botched due to too much whitespace, one half of the operation botched to too little whitespace. Admittedly this didn’t take more than 30 minutes to sort out, but I could have spent that time writing some Perl that at least did some sanity checking before attempting to run the analyses with a saner way of splitting up the files. What amazes me most is that this script is distributed on the Tree-Puzzle site as being in some way ‘useful’. I dread to think how many poor evolutionary biologists have fallen flat on their face trying to use this and sat doing the analysis manually one at a time instead..

Better late than never (aka: What I did on my summer holidays)

If I don’t write something down, I never will. The following text is subject to amendment as I think of things.

I had a great time in Brazil – possibly much better than I thought I was going to have. I’m not the worlds best traveller, I don’t like the anticipation of travel, I don’t like waiting in airports, the whole build up is very stressful for me and if I’m not at the airport 3 hours in advance of the plane taking off, then I’m approaching panic. The trip to Brazil was somewhat unusual for me, I rarely travel long distance with other people – my last 2 trips to Japan, Australia and the USA have all been solo trips. It was nice therefore to actually be travelling with a group of people – Neil, Matt, Phil, Simon and I forming a finely honed travelling unit, despite the realisation that not everyone is suited to my normal mode of ‘get there early, spend a lot of time hanging around’ of travel. This could have caused some problems if we weren’t all over the age of 28 and extremely calm people.. The main problem with the journey there is that we had such a long layover in Paris, about 11 hours, followed by a through the night flight to Rio. This was made somewhat more pleasant by the fact we left Charles de Gaulle airport, and went into the centre of Paris, taking in some of the locality around Notre Dame and an open air lunch and a few alcoholic refreshments in the glorious sunshine. (Glorious sunshine? Does anyone remember that?). We left Paris in reasonable spirits, having flexed our rusty GCSE French vocabulary ready to begin the bulk of the journey in earnest – about 14 hours after we had started!

The flight to Rio was uneventful, although I was cursing the lack of ‘back seat’ screens on the primitive Air France tin can we flew in. I couldn’t be bothered to crane my neck to watch the ceiling mounted screens showing Hollywood movies kindly dubbed into French (please.. just subtitle them!) and this lack of entertainment did teach me a new technique – the ‘falling asleep on aeroplanes’ skills that have sadly eluded me in the past. I slept most of the way to Rio, and on arriving in a grey, drizzly Brazilian airport, a year older than when I departed France, I did wonder why I had bothered waking up. I promptly fell asleep most of the way to Fortaleza from Rio. No bad thing.

So we arrived in Fortaleza in the afternoon. One quick check outside the aiport revealed it to be about 30oC outside and gloriously sunny. Our bags never made it to the airport, but had actually made it on the flight behind us, so we hunkered down in the cafe, ordered some Chinese food and started our long association with a fine Brazilian beer called Antarctica (pronounced An-tar-sh-tee-ka). We also hit the first problem of the holiday – one that was to haunt us repeatedly – the complete inability to find a cash point that would take a Maestro card. Visa? Fine. Pay through the nose for your holiday cash with those lovely cash advance interest rates.. Maestro? Only if you can find the 2 cash machines in town that take it (note for the traveller Banco Brazil and their friendly yellow cash machines are the winners).

Reunited with our bags we took a taxi to the hotel. This introduced us to another recurring motif of the holiday. The taxi drivers are insane. You honestly would believe there were no rules on the roads except ‘stop if the light is red’. Overtaking and undertaking are both performed with speed and fluidity. Hit a red light at a petrol station on the corner? Merely drive full pelt through the forecourt! Over the coming two weeks we had to put up with Phil whining with fear as various drivers tested his mettle. We had a few close scrapes as well. The looming sides of giant trucks caused all our hearts to leap into our mouths at some point.

We checked into the “Quality Hotel” in Fortaleza, which exuded far more quality than its name suggests. Not awarded more than 3 stars it was bright, airy, clean with tiled floors, views of the sea and an atmosphere that was quite convivial to midday drinking out of the heat of the sun.

The holiday quickly settled into the kind of routine I imagine most beach holidays take. Having never been on one before I was worried this was going to bore me to tears, but in fact it turned out to be rather pleasant. The average day went something like this:

1) Get up for breakfast when you feel like it but try to get up some time before 10am.
2) Go for breakfast. Eat a fruit course, followed by a course of meat and eggs, followed by a yogurt and cakes. Wash down with one of the many fruit juices and 2 cups of Brazilian coffee (strong).
3) Pick up towel. Head to beach. Lay on beach for 5 minutes shooing away hawkers.
4) Get in sea. Marvel how warm it is. Marvel how clear it is. Marvel how few people are in it. Swim for a bit. Get out.
5) Lay on beach until dry/completely sick of hawkers/get sat on by some lunatic woman (yes this did happen to me).
6) Return to hotel, pick up book. Head to rooftop pool. Go to gym, get hot and sweaty. Leap in slightly cooler pool. Dry off. Wait for someone with less morals than me to open a beer or pour a Cuba Libre. Start drinking!
7) Ignore any pretence of requiring lunch, it’s too hot. Start to burn, retire to room to watch CNN before the main evenings boozing begins.

Lather, rinse, repeat for several days. Oh yes eventually we went for a conference but there’s better places to discuss that. For the conference we did check into a 5 star hotel. The main advantages were it had a decent cocktail waiter. half-decent lounge pianist, a sushi restaurant, a bigger pool, a sauna and bigger gym and if you were fast, coconuts for breakfast! The disadvantages stemmed from having to pay for internet access (Quality Hotel was free), an incredibly noisy lobby owing to a rather enthusiastic water feature, having to pay for the gym, and having dingy (though large) rooms.

A couple of weeks later what do I really remember about Brazil? People are very friendly there, and they seem genuinely so, rather than the enforced friendship of North America. The hawkers turned from a major pain in the arse, to a minor annoyance once we learned how to dismiss them in Portuguese. Living in perpetual warmth where it never drops lower than 25oC is in fact wonderful! Looking down from the rooftop of the hotels along the strip along the beach at night was a pretty sight. The sky was clear and a whole new hemisphere of stars were there to look at. Beach life is the best – the baraccas (beach bars) served good food, good coconuts and cold beer, and that’s all you need to have a good time. The whole place reminded me of Miami. At least the recreation of it in GTA:Vice City. It didn’t require much walking though to get the sense that Brazil has a massive gap between the rich and the poor. The country appears not to be poor – the development along the beach was as familiar and luxurious as any western resort, but behind the line of towers, people are still living in shacks. Sitting at night watching the bats flitting in and out of the palm trees was pleasant, watching big lizards shimmying up the walls. At night the beachfront comes alive – lycra clad Brazilians march up and down – walking, running, chatting – I’ve never seen exercise on this scale. Massive communal workouts were conducted from blaring speakers. Volleyball, played with either hands, or football style was always on the go.

We were lucky enough to be there in the middle of a build up to an election – the Brazilian idea of an election campaign is basically to hire a car, strap some 12″ speakers on top and run up and down the strip playing random pieces of music with a picture of the candidate on the side. Great! Unless your campaign theme is the Crazy Fricking Frog. We were most impressed by Cid Gomez who had the swankiest campaign vehicle – a bright yellow open top bus complete with smiling Brazilian youngsters waving enthusiastically at passers by.

One of the most amazing things though, the one thing that will stick in my mind is Capoeira. Capoeira is half way between a martial art and a dance form. Every day the conference kicked off with a dance demonstration, on the second day it was Capoeira. Words cannot describe how I felt seeing this for the first time, although I’m not afraid to say that it brought tears to my eyes (I’m a softy I know). The basic premise seems to be that two ‘combatants’ engage each other in combat with an eye on the complex beats set up by the musicians. It’s a very flowing, athletic, acrobatic martial art – none of the quick punches or kicks of any karate variant and none of the contact of judo. More like a speeded up combat yoga which incorporates, whirls, twists, kicks, cartwheels and headstands. On our last evening we happened across another Capoeira group outside our hotel. Standing on stone benches looking down at a small area encircled by Capoerists from about 7 to 27 as they dance, fought and chanted was captivating. What I cannot forget is the beatific smiles on their faces as they danced, with none of the posed rigor mortis smiling of ballroom. These were people in love with what they were doing and it showed, and it touched me very deeply. If I ever see a Capoeira performance in the North East I will go.

Then we came back… Thrust into European airspace with an 11 hour layover in Sao Paolo (a city we weren’t going to visit on account of all the shooting that happens there). Just 2 days after the ‘TERROR IN THE AIR’ plot was uncovered (sorry getting a bit FOX News there). It was in fact fine, I was a bit cheesed off at the French customers for confiscating my prescription medication (not that it was prescribed to me but who cares), whilst not confiscating Phils (which were imported from the USA where it can be sold over the counter), but at least we weren’t getting our duty free confiscated like some people! I was very happy to be coming back via France though, and not the USA. Flying back into Newcastle and not Heathrow was also a relief. Getting back and finding it was 12oC outside at midday was less than amusing. A full 18oC difference from where we had left not 20 hours before. Actually I’m not sure that was the worst bit of the journey back. The worst bit was flying from Fortaleza to Sao Paolo (4 hours) and then getting on a flight out of Sao Paolo, waking up four hours later on the flight to see that we were right over bloody Fortaleza again. I could have cried. At least we had seat back TV screens on that flight, even though mine was broken. Needless to say, I just went back to sleep.

Yes, I loved it in Brazil, I had a great time, saw some great things, let my stress levels sink to zero. Am I sounding sentimental? I think I wish I was still there.