After testing out my new style and tranformation templates for a few months, I finally had enough confidence to switch across all of the archives to use the new stylesheets, so if you go through the archives now, you'll see a bit of consistent styling (instead of it randomly jumping back to the old style).
Incidentally, I'm still waiting for my DSL to work. I don't think there's a single telecommunications company in the world which isn't Evil at the moment.
I had to wait for this bit of software to come out of beta before I let it get close to my email, but MailTags 1.0 has been released. It's a Mail.app bundle which allows you to attach Spotlight comments to your mail messages. I've been making use of Spotlight to manage my research bits and pieces by basically tagging each piece of information that lands on to my computer - via email, pdfs, documents or even bookmarks. Then, when I want to search for that information again, I just do a Google-like search via Spotlight for the information I want. The missing piece in the whole scheme was the mechanism by which I could tag my mail messages. MailTags solves that quite nicely. You can assign priorities, due dates and projects to mail messages, as well as freeform comments. So now, when I do a search for "Florence conference", I get all the relevant material that I've collected together for this particular project. It's quite nifty, as all I do now is just leave various documents in generic bucket folders, and let spotlight do the fine-grained searching for me.
It has been a tough morning for me this morning. I've been hit with a number of challenges to my resolve to devote my life to science. The first came via PhD Comics (that's a bad sign already), where I found some information telling me that the pot of gold at the end of hot coals (mixed metaphors at their best), is actually a lot smaller than other metaphorical pots of gold. I don't even get a leprechaun. Or a pony.
The second hit to my resolve came via the news of further happenings in Indonesia. You see, it seems like it's a really good time to be a lawyer in Indonesia. Especially if you're representing young Australians who just happen to have a few illegal substances on their person. I would personally model my practice on that of Hotman Paris Hutapea. The guy is a celebrity lawyer, big on bling, and probably not adverse to using the Chewbacca defense. You may have heard of him recently defending Schapelle Corby - and a fine job he did of it too! Schapelle is only one in a long line of Australians who have been caught in Indonesia partying hard. There's the Bali 9, some bloke in Sumatra, and Michelle Leslie. It's hard work keeping track of all these Australians doing their country proud, but thankfully Google recently added a news search feed feature - so you can just subscribe to the Australian Full Body Cavity Search feed XML, and keep track of all your favourite Australians facing the death penalty.
On another note - the Beastie Boys (God bless em), have started releasing some vocal-only tracks from their last album. You can grab them from the remixers section on their website. With any luck, my DSL should be alive by this evening, and then I can have a crack at grabbing some fresh new samples, and seeing what rubbish I can produce.
There's a post on Boing Boing pointing out Alan Waddell, who is attempting to walk all the streets of Sydney, taking pictures as he goes along. Is he going out to the safe and secure streets of Cabramatta, or taking long strolls in Macquarie Fields? I hope so.
Having been born in London, I've always had a soft spot for the city of London. I don't really know why - it's dirty, overcrowded, and the inhabitants can sometimes be really annoying. Yet, when I walk around London, I feel completely at ease - it's like a second (or third) home for me there. Since this past weekend was looking quite boring, I had decided to make the trip across the channel (and large swathes of France) since there were a few parties (read weddings) going on there.
The only small problem with my plan to head up to London was that I was missing formal-wear. I had a pair of black trousers, and some reasonable-looking shirts, but I wasn't planning on going to any formal occasions during at least my first year here. One major component which I was missing was a pair of black shoes - turning up in runners would probably overshadow the lack of a fantastic suit. Luckily for me, I was being sent a care-package from Australia, and my pair of black shoes were chucked in there. Now, the package was meant to be sent as an express delivery international package, at most about a day or two travel time (which I could follow using the useful package tracking widget for the dashboard). It did manage to traverse the world in about that time - but (and this is typical of German bureaucracy) it was stopped in customs while they rang me up to make sure that I was a student, secretly hoping they could charge me for customs tax or something. I fax across my details first thing the next morning, in the pathetic hope that I will be able to get my package by the end of the week. Of course, the package was stuck in customs for 5 days, arriving far too late for the wedding. It's pretty clear that the interaction between DHL and the German customs could do with some improvement. Are there any better systems that they could use for package management? I look forward to the community's response.
It must be wedding season again, since there were two weddings on the weekend, one in the northern suburbs of London (my old stomping grounds), and another in the supposedly rural part of England, just outside of Stansted airport. What was most interesting about the weddings was to have a look at the Indian "scene" in its homeland - London. I'm always interested in sub-cultures that you find all over the world (such as the stencil-art/graffiti culture that is somewhat popular at the moment, or the [New|Dark]-wave/Depeche mode music scene). Some of these sub-cultures are more than just hobbies for some people, and form large parts of their identity. They also use the Internet to meet up and communicate, so it's quite easy to go for a bit of cultural tourism by clicking on a few links and browsing some forums. It was with this tourism in mind that I checked out how the Indians all interacted with each other in London. Now, I've never really spent a lot of time amongst Indian groups of people (beyond family), which was largely due to my interests often being mutually exclusive to those other people. For example, I don't really enjoy the pure pulp Bollywood films, or the music that comes out of them, but I absolutely love dismantling them. I also dislike the R&B music that is so loved by many (Hip-hop is not R&B or gangsta-rap before anyone says anything), and I can't really identify with the majority of the youth culture. So with that in mind, I was expecting to see much more of the same in England, taking solace in knowing that the food would be absolutely fantastic. I was completely wrong about the Indian culture in London. Instead of being essentially India in England - it was more like a subset of the population at large, where everyone happens to be related to each other. You'll find people with diverse interests, and even little sub-groups within the larger group itself. I think it's something to do with the age and size of the Indian population in England that allows for this kind of thing to happen. No doubt, if I go to New York again, and look at the Indian groups there, I would find a similar thing. The best thing about the Indian culture is the food of course, and it was pretty good - the first time in about a month and a half that I've had properly cooked Indian food, and I engorged myself on the food such that I would not have to eat for a week.
We had driven up from London to the wedding just outside of Stansted, and somehow the responsibility of finding our way there landed on my shoulders at a critical juncture. I screwed it up, and we ended up finding ourselves in the middle of a village called Braintree. I'd love to know how they got the name of Braintree (Wikipedia knows), because as far as I could see, there wasn't a massive tree with brains hanging off it. You'd assume it would be zombie central, as the zombies would think they've hit the jackpot with a town that has a name like that. I could see a mummy zombie chastising a child zombie that brains don't grow on trees. Like my train of thought, we were thoroughly lost, but we ploughed on deeper into the town hoping that somehow we'll end up on the other side. Once we found ourselves on a small back-road, we finally stopped, and pulled out the ludicrously vague map, hoping to figure out where to go. Luckily for us there was a person walking past, and in a moment of divine inspiration, I decided to stop him and ask for directions.
Me:
Drawing on my years of English school education to produce an almost perfectly delivered sentence
Excuse me! Hello! Do you know the way to the A120?
Polite-looking quintessentially English man (with a beard):
Thinks for a secondYes.
He stops, and then smiles, clearly pleased that he's helped me in the survey I am conducting.
Me:
Er.. Would you please tell me how to get to the A120?
Polite-looking quintessentially English man (with a beard):
Launches into a thorough description of where to go, involving several turns past several roundabouts and a great deal of witchcraft.
Did you get that?
Me (and my Uncle by now):
Staring blanklyHow do you get here?
Stabs finger into the map roughly where we want to go
Polite-looking quintessentially English man (with a beard):Oh, that's easy. Go left at the second roundabout, and head straight down the road.
And I thought I had trouble talking to the Germans. I wonder if Matt has these same problems in Cambridge, as I know Londoners are not like that at all.
Post-wedding, I returned from London, flying into Frankfurt Hahn, and began the long journey back to Heidelberg. It's not easy doing a weekend trip to the UK, but I've somewhat proven that you can do it. On arriving back to my apartment, I found a little note from DHL telling me that a package had arrived for me. Expecting my 10 kg care-package behemoth, I grabbed my backpack and walked off to the post office. Imagine my surprise when the package actually turned out to be the tiny DSL-splitter which was noticeably missing from the rest of my DSL package that I had obtained on Friday. I set up the DSL, hoping to get back into the broadband world, somehow managing to set it up pretty well, even though I didn't understand the router configuration in German. It doesn't actually work - since I don't think the router/modem is synchronising with the DSL signal. Does anyone know how to test a DSL line? Or do I have to brave the FreeNet customer service to try and get this working?
Update Damn, maybe I should have gone down to Zürich for the weekend - Streetparade was on again, and Ben went along. Looks like it would have been quite a party.
It is not a particularly rational decision to travel half-way across the world to bash your head against the wall to do a PhD, especially when there are perfectly capable universities nearby with walls you can bash your head against. Once you get here though, you do try your best to justify your decision - cheap beer, good research, saving the world, student lifestyle and an excuse to learn another language are a few quick and dirty justifications I've been telling myself. The best reason I've found for why I'm slap-bang in the middle of Europe, is so that I can make the most of travelling around. Accordingly, on the weekend I went on a bit of a road-trip around southern Germany and Bavaria.
Stephan, a friend from the lab, is a bit of a veteran traveller and has been all over the world, although somehow he's missed out completely on Australasia. It was on one of his trips, where he was cycling around India, that he ran into an older Japanese man, who he nicknamed "Shogun". He later went on a trip to Tokyo to visit him, and now he's reciprocated, coming down to Germany with his wife. So I found myself in a car whose inhabitants were two Japanese people whose grasp of English extended only to a handful of verbs (although there was a translation machine to help out), a German guy who can speak English pretty well, and an Australian-English-Indian guy who can speak English much good, but his German is atrocious. The car stereo was naturally playing a mix of the Amelie soundtrack, Pink Floyd and Kraftwerk (more on that later) as we drove along. The whole experience was slightly surreal and international, as we spoke to each other in broken English, trying to get various points across. The Japanese couple were very typically Japanese, making the "Waaah" astonishment sound that it seems like Japanese and Taiwanese seem to share. If they had a mobile phone, I'd expect them to answer it "Wai?". The best reactions from them came when they ordered their typical Bavarian foods in the restaurants, and a plate full of more meat than they'd eat in a year arrives. Lots of "Waaah"'s there. I think the whole interaction between Stephan and his guests would make an absolutely hilarious film - I just need to find a screenwriter to make sure this movie is made. It would be a cross between a road-trip movie, and "Lost in Translation", with a token observer who just sits there chuckling at the cultural differences. The tag-line for the movie would be "I can't believe you guys teamed up for a war!".
We almost managed to cover four countries in one day, but only managed to do Germany, Switzerland and Austria (pronounced Australia if you're from Japan). France was about 20 minutes away (at Strasbourg) but we couldn't be bothered to make the side-trip. We travelled south past Donaueschingen, which is the spring or source of the river Danube apparently, although all I saw was a kid throwing gravel into a bubbly pool. We travelled south to Switzerland from there, popping into the town of Constance, although I'm a bit disappointed we didn't make the short detour to Zürich. I'm starting to think that I should get a car, since it's pretty easy to get to Zürich and Paris from Heidelberg, maybe a few hours in each direction. The driving certainly affords you a lot of freedom to go and stop in little towns and find cheap places to stay.
From Switzerland, we moved on to Austria briefly, checking out the lakes and the increasingly mountainous terrain as we got closer to the Alps. We stopped off close to the Austrian and German border for the night, staying in a cosy B and B. The next day entailed a visit to Krazy Ludwigs Krazy Kastle. It's basically a relatively modern castle (about 150-odd years) that was built in the Romantic period of architecture (or something like that), and basically is a stylistic inspiration for the Disney castles. Like anything Disney, the place was full of tourists, and I spent my time trying to break out of the guided tour of the castle so that I could explore it myself. I didn't have much luck.
The castle itself has a great big papier-mache cave inside for no discernible reason, and might have been the tip-off that the king of Bavaria was just a little crazy-go-nuts. He looked like a whole heap of fun though, and he dedicated the entire castle to Wagner - so he liked his music. If I were King, I know I would spend my money on making this big-ass castle in the middle of nowhere - I mean what else does royalty do nowadays anyway?
We popped into Munich after the castle, dropped off the guests, and started the long drive back to Heidelberg. To pass the time, I ended up trying to translate various German songs that were living on the resident iPod. Kraftwerk ended up being the easiest to translate, and I managed (with a lot of help) to get through "The Model" and "The Robots". I can't say that I'm too sure the words that I picked up would be the most useful, I don't know how many people really have batteries which are fully charged, and see models drinking only champagne in night-clubs.
I've also been doing the planning for my trip to Florence, and I re-found this great website WikiTravel with a bit of info on various cities. The number of Wikis that are springing up to contain information about various pet projects is amazing, and we're getting really close to finally having that wildly inaccurate tome of information - The Hitchhiker's Guide to the Galaxy - available to us. Sometimes you don't want to know the fully referenced history for a particular country, or what the exact form of government is - but you really want to know how to find a good place to catch a few hours of sleep at Stansted airport.
I've taken to wearing my cap a lot recently, which is related to the fact that I'm trying to grow my hair a bit longer. It's now looking pretty damn crap, but in three months time, I'm hoping I'll have a firm crop of wavy hair to insulate me from the oncoming winter. The cap and headphones on tend to deliver a bit of a hip-hop look to myself, which is only amplified by the music seeping out from my ears. It's a pity that I don't have some rudimentary equipment here with me, since the music I'm listening to has inspired me enough (or I'm bored enough) to have a go at doing the electronic music thing again - maybe using samples from CCmixter. The whole sampling of music thing (exemplified by The Avalanches) is all part of that Remix culture idea that has been floating around for a while, and has only recently got a cute name. I'm not sure why that phrase has really received so much traction in the media (or at least in the corner of the web I frequent). What it seems to really mean is that the stuff which is being remixed is either a) no longer relevant b) crap or c) not to someone's exact tastes, and people think they can (and in fact often do) do a better job at making whatever type of content. Next thing you know, someone is going to claim to be at the vanguard of remix culture by customising their Yahoo homepage. Just to be clear, I've got nothing against the whole idea - in fact I'd say that my PhD is really just an exercise in re-interpreting other peoples work, and adding my own little creative spin on it. On the other hand, the results from re-doing stuff is sometimes just hilarious.
On a bit of an impulsive buy on the weekend (A credit card and the internet make things far too easy), I ordered a copy of The Party, for prompt delivery here (Thanks Cd-Wow!). I've been searching around for the movie for a while now, and only after having a conversation about Peter Sellers, did I actually remember I was looking for it. The reason I wanted the movie was that I apparently look (and act?!) a lot like Peter Sellers character in the movie. I'll watch it and then report back as to the veracity of these claims. English and German language subtitles too! At the local (well local being 20 minutes away by bus) student bar, they're showing movies on Monday nights. This week they're showing "The Village", which is not a great movie, but it might have been worth going just in case they had some brilliant Engrish subtitles. I also somehow managed to end up going to watch the Karaoke there on Friday night - where a number of increasingly drunk Germans got up and sung bad 80s pop, in both English and German. The notable exceptions were two guys who got up and sung songs in Mandarin/Cantonese (I can't pick between the two)! Their voices were drowned out by the actual song though, so only 1 point for execution, and a million for style.
To try and learn a bit more German, I've decided to tackle the language head-on, and look at what makes up the language, and to be brutally honest, I've found it lacking. It's not really enough to have incomprehensible rules regarding grammar, compound words which can stretch across lines, and separable verbs which may or may not decide to break up with its companion. What is really needed is some colour, vivid metaphors and similes which leave indelible images upon the victim you're talking to. I've seen some such phrases as graffiti all over the place (my favourite being "Esst mehr Nazis" - Eat more Nazis). With that in mind, any phrases or made-up words which I miss using, I have decided to translate into German. The latest phrases are "Schießt der Bear im den Wald?!" or "Shießt der Papst im den Wald?!". I've got the words memorised, so I have to work on the delivery now. It doesn't work when you meekly say things like "Excuse me", or order things in a quiet voice, and it certainly doesn't help when those phrases are mumbled out. Consider this my attempt at remixing the German language.
Food update: I managed to pull off a pretty much perfect implementation of the peanut stir fry last night. It was missing a few more varied vegetables (my broccoli had died in the fridge), and there was probably too much ginger and not enough garlic, but I was pretty damn impressed with the results. I also tried out my budget beer from the Penny Markt, and it is surprisingly drinkable.
Another week, another post. In an attempt to make it at least look like I'm doing some work here, I'm going to talk a bit about programming here. If you are not a geek, you'll can wait around till tomorrow when I will talk about less geeky things (promise). I've got a paper to critically review for a group meeting tomorrow...
In the process of preparing for a presentation I've got to give in Florence, I realised that I should really have something somewhat original or interesting to talk about. I basically figured that I should do a quick little experiment involving performing a theoretical treatment on some theoretically generated sugars. The idea makes sense to me at least. Back at the ranch, it would have just been a simple matter of writing a few tiny scripts to manipulate a well established series of modules and database access modules to generate the data I was after. I don't have any of those little bits and pieces now - so I've got to basically start from scratch. This is a bit of a mixed blessing to most programmers out there - by starting from scratch you can implement a clean design, but you can spend months getting your code back up to the level that you had before. There's also the problem that the API which you used - while it may not be the best one - was the one you were most familiar with, and your design decisions are somewhat subliminally affected by it.
Starting from scratch also gives you the freedom to discard with any legacies that you had to deal with in previous projects. One of the big legacies is programming language. The de-facto standard for bioinformatics is Perl, a swiss-army-knife which makes any problem look like a nail. I've programmed a lot in perl now, and my days of being confused by it's syntax (since I came from a land of Java/C) are long since past. It's a great hackable language, and I'm never surprised at how versatile it is. This is beginning to sound like a love-letter to Perl, and with that set-up for the punch-line, I can't resist the urge to say that I've been cheating on Perl with Ruby.
Beyond the sheen of a new language - what exactly does Ruby have that Perl doesn't? Object oriented programming is the key. I realise people like to claim that Perl is an object oriented language, but whenever I see people say it, there's a cheeky look on their faces - because they know fully well that perl doesn't really do the whole object oriented thing in a rigourous way. For example, class constants aren't inherited, and breaking encapsulation is easy. Ruby doesn't implement a whole object oriented languge - but I think it's a whole lot better at it than perl. It manages to encapsulate data quite well in it's objects, but is lacking in some aspects of its implementation. Things like method overloading (which is a very useful trick to use) are notably absent. That said, it includes a whole bunch of cool tricks like prototyping, and dynamically adding methods to objects at runtime, as well as a module you can use to implement things like method overloading. The language ends up like a strange mix between JavaScript/ECMAscript. This type of functionality is achievable in perl - but not in a very consistent way. You would end up placing overloaded methods in the hash (which inevitably is used to model the object) using argument sniffing to dispatch the methods, and you'd have to find specific hacks to get the constants from a class inherited by all it's child classes. It's just not 100% intuitive.
Ruby is a "better" (or more well designed) language than Perl, I've got no doubt about that. But is it the right language to use? For all of Perl's problems, you can be sure that if you're in the middle of a medium to large-sized project, and there's some limitation in your design that you never even thought about (Yes, I know about software engineering), you can at the very least work around it in perl to get the program done. Can Ruby do that? Is there anything like CPAN for Ruby? Can you write poetry in Ruby? I've also thought about Java, and it's not really appropriate at this stage of development. Given that the point of my PhD is to actually learn things, I'm going to stick with Ruby, but Perl 6 might woo me back over. Regardless (or rather because) of my decision, I still haven't managed to actually collect the data, or run an experiment yet. Not entirely true actually - I've got one running at the moment, generating all possible isoforms of a tree.