The USS Quad Damage

First thing - nathan your diet is horrid, you really should eat breakfast if nothing else, it'll help if you get some of your biological systems in order.

As for what's keeping me busy - here's what I wrote to a friend about my research - "

It turns out that I will need to work on my old topic for a while longer, at least for another three weeks. I submitted an abstract to a conference in Korea which was accepted, now I have less than three weeks to submit the paper I'll present at the conference. The paper is on my web application which predicts the disulfide bonds in proteins, these constrain the shape of the protein and this information assists us in determining the protein's function. The main problem I have is that it isn't written yet, I'll get to it soon.. =)

Once I get that done I will be working on protein annotation. When the genes of an organism gets sequenced, we need to work out what proteins they produce, what those proteins do and to record and share that information. A lot of work has been done to improve the process as it is extremely tedious, but there are some large gaps that haven't been addressed properly, mainly in linking together the systems created by different groups. Some people have tried to resolve this by making their own larger system which combines the work of others. This is however limited and others have called for a more open system, so rather than trying to make one system that will do everything, allow others to add their own bits in like how the internet in general works. I read quite an interesting paper on it two years ago, but not has been done on it yet.

I'm hoping to change that, at least for protein annotation, by specifying how the systems will communicate, by creating a new end user application that can draw together the capabilities of relevant systems and working with other groups to make my work the standard. One problem I will face is many of the people working in my field, who are making the new systems, don't have a computing background. Their primary concern is to make a tool to demonstrate a concept, or to address their own needs, so taking the time to make it easy to use their own hasn't been a high priority. What happens is others end up writing the same code to pull the pieces together. That's my vision in a two paragraph anyway, what will probably happen is I'll get one or two groups to work with me, but it'll be some time before the whole field moves in that direction, does my explanation make sense to you? I'm not sure how much you know about biology and web services."


I've also been busy with other things outside of uni, I spent a week in Brisbane for biofutures, a biotech camp, where I was looking after year 11/12 kids. Some of them were quite photogenic, I ended up with 900 photos in the week, not too bad, most of them are good enough to put online. It's scary to see how young they all look now, for people who are so close to starting uni to seem so juvenile.

I had a chat with the other mentors one night where the girls were asking if guys really do have no idea if a girl is interested in them, one of them explained how there was only one guy who knew she liked him, and she soon found he wasn't worth it, he wanted to see if he got any better offers for the formal, and how they normally relied on mutual friends to get the message across. They think they're being extremely obvious, I think the guys were being obvious too. The BBC comedy coupling was quite funny as well.

I spent a little while tonight trying to learn more about what happened when a geek friend of mine tried to approach the cute/smart chick I mentioned some time ago, they have known each other for a few years now. I'm closer to the chick, but she was more of a challenge to get anything out of. In the end she accepted my offer of giving suggestions to the guy, but he shrugged it off and said he's just being himself and he's not going to change for a girl's sake. I tried to explain that you can be who you are and act in a way that will 1. give you a much better shot and 2. stop them running away from you. But I didn't have any luck with that, he just laughed it off. I always thought learning how not to appear to be a stalker or complete weirdo to be a useful thing to learn, particularly if you are one. I'm sure there are girls who would suit them perfectly, I just feel sorry for the girls they meet before they find them.

I'm also going to lectures at the art gallery, been busy with a society at uni and other groups. I will need to catch up with you though. It's getting quite late, so I'll finish off by quoting most of the remainder of the email I wrote earlier:

"I got back from Brisbane on Monday, there wasn't that much to see there, but it was nice to go around the city. I enjoyed visiting south bank and the markets there on the weekend (they're on fri-sun), picking up a few gifts. Queen street mall reminded me a lot of Pitt St mall in Sydney. What I enjoyed most about Brisbane though was how much more affordable it is to live in than Sydney. I was staying some others involved with the biotech camp, biofutures, their townhouse was right next to the train station, so I would l leave the house and be in the city within 15 minutes, including buying the ticket and getting out the other station. Their place has four bedrooms it was large enough to comfortably accommodate three guests, all that for about 300 a week.

I love Sydney, though that tempered by my frustrations with transport. I'm sitting on a bench outside a supermarket at the moment because I missed the 7:22 bus by a few minutes and the next one is 8:22. I have to move somewhere more reasonable, a normal person would just get a car, but I see that as just a waste of time and money, it'll give me some flexibility, but at too high a cost. I normally can use the time I spend in transit constructively and I can't write emails when I'm driving.

Beside the markets in Brisbane, I also went to the art gallery, which was nice, it was a lot quieter than the one in Sydney and there was a piece I quite enjoyed there. It was a large pool of water, say 7 by 20 meters where hollow metal spheres about 15 cm across floated. The water was flowing so the spheres moved around slowly, I sat there for a while being soothed by its gentle motion. The rest of the gallery was fairly standard.

A friend of mine took me to a cafe in the valley, we stayed there chatting for a while, although the place has a bad reputation, it seemed quite mild compared with the shady areas I'm used to. I didn't get to see much of nature in Brisbane, but then I shouldn't be too different to what I've seen.

Most of the time I spent in Brisbane was for biofutures, taking care of the year 11/12 kids, it was shocking to see how young they now appear. Some of them were quite photogenic and happy to be in front of my camera, while others completely refused to be in a photo if there weren't ten others people dragging them into it. It was a tiring week, I learnt that I don't know how to control 16 year old boys, but it was a good week."