testing site

Posted: January 23rd, 2009 under Uncategorized.
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Setting up PHP, Apache and MySQL

Mac OS 10.5 is a great place for web developing, as I am discovering. When I got my new MacBook Pro, I found that it had Apache already installed, including several other development tools that are useful to me, such as perl, PHP and subversion. It did not, however, have MySQL.

Through many web searches, and much trial and error, I finally got my system up and running and working how it’s suppose to. Mostly. Read more »

Posted: March 28th, 2008 under coding, computers, web development.
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You know you’re in an emerging field when you see things like this:

…Asia’s oldest bioinformatics organisation set up in 1998. (Bioinformatics research in the Asia Pacific: a 2007 update)

I simply find it worthy of note that I work and study in a field whose ‘old and venerable’ organizations are between 10-20 years old.

Makes you realize how far we’ve come in such a short time.

Posted: February 14th, 2008 under bioinformatics, hmmmmm.
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There’s a new blog out there, called io9, and it’s pure scifi. It covers everything from spoilers of the newest scifi shows/movies to the latest info on from NASA on sunspot activity. The posts are interesting and witty, and full of nostalgia for the great scifi of the past that’s becoming lost among the shiny gloss of Hollywood’s sudden interest.

One of today’s posts feature Eliza Gauger, the designer of the io9 logo - which is very unique, trendy and cool. She talks about a few different things, including how she became converted to the scifi monsters of the world. However, in my opinion, the best part of the entire interview is when she starts talking about what she hopes to never see again in scifi art, one of which is “hot people”.

Look at Aliens. Or any Cameron film from that era. If he had attractive women in his movies, and he did, they weren’t “women” in the way that movies define women: harpies, hags, or idiots. Scifi ditto. Ripley was not wearing any fucking mascara. She was a CHARACTER, she wasn’t a GIRL. Ditto for everyone else. They were people before they were badasses, or killers, or idiots. This is not a luxury in sci fi. It is a necessity. Cookie cutter characters are unbelievable, and in a wider context of unbelievable things happening (aliens, lasers, spaceships, all imaginary), it is vitally important for as much of the rest of the package to be well-developed and believable.

These are the types of people I hope mold and promote scifi away from the glamour and shiny-ness of Hollywood. Scifi movies - and really, any movie that has a modicum of science in it - are already on a downslide credibility-wise, that having perfect people starring as humble scientists doesn’t really endear a lot of people. So, putting Denise Richards in a lab coat and glasses does not make her any more credible as a nuclear scientist, than if you’d cast some less-than-perfect actress. In fact, it might even detract from the movie (I know I rolled my eyes).

However, bad movie science is for another, and longer, post.

Posted: January 9th, 2008 under scifi.
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There are some interesting science images over at National Geographic.

Click on the image to go directly there.

Posted: September 28th, 2007 under interesting stuff, science.
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A co-worker found this while scanning through Wikipedia’s entry on the genetic code…

Needless to say, it’s been changed.

Posted: September 13th, 2007 under amusing.
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It’s interesting to see what happens when someone who has a grasp of the capability of technology today, is also the person who can best make use of it.

When Munroe took over as chief two years ago, his department was drowning in crime and data. Police had a mass of data from 911 calls and crime reports; what they didn’t have was a way to connect the dots and see a pattern of behaviour.

Using some sophisticated software and hardware they started overlaying crime reports with other data, such as weather, traffic, sports events and paydays for large employers. The data was analyzed three times a day and something interesting emerged: Robberies spiked on paydays near cheque cashing storefronts in specific neighbourhoods. Other clusters also became apparent, and pretty soon police were deploying resources in advance and predicting where crime was most likely to occur.

Link - via CBC

Posted: August 10th, 2007 under news.
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One of my recent projects has been to map short sequences of DNA (tags) to specific positions in transcripts (ie. exons, introns, UTRs). Everything was going along nicely, until I was looking through my output data and saw something weird.

I had one sequence map itself to an exon and a 5′UTR - on the same transcript. This caused me some concern (and an afternoon of frustration), because it seemed that according to the Ensembl database, this one position is both an exon and a 5′UTR. I thought I had done something wrong in my code, such as calculating the start and end position of the UTRs wrong or pulling out the wrong starting position for the start of translation.

Seems that wasn’t the problem. What it turned out to be was partially my fault, but also partially the fault of the Ensembl gene annotation.

Read more »

Posted: July 15th, 2007 under bioinformatics, hmmmmm.
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I recently stumbled upon this paper:
Conversion of amino-acid sequence in proteins to classical music: search for auditory patterns
Rie Takahashi & Jeffrey H Miller
Genome Biology 2007, *8*:405

_”The primary goal of this work is to convert genome-encoded protein sequences into musical notes in order to hear auditory protein patterns.”_

This is an interesting - and unique - approach to analyzing protein sequences. They’ve taken many things into consideration, including codon distribution and amino acid frequency. They’ve developped rules for rhythm, range, dynamics and note lengths. Unlike previous efforts which have tried to directly translate an amino acid to a musical note, this approach uses chords and musical rules to generate these compositions.

Read more »

Posted: July 8th, 2007 under bioinformatics, unique.
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Blogs are a great way to get involved in the bioinformatics/computational biology/systems biology world. At the most basic level, it allows you to learn what others are doing, how they’re doing it and what problems they’ve encountered. It can also point you in new directions, by referencing papers, people or sites that are good/bad/instructional and why. Additionally, there’s also the networking aspect of it, where if you’re persistent enough (but not stalker-persistent), you can gain valuable colleagues and resources. Because if you haven’t figured it out yet, in any scientific field, collaborations are gold. (Our lab in particular is involved is at least 6-8 different collaborations at any given time. This means more published papers, which leads to more funding and bigger projects.)

But blogging isn’t just about you getting involved in the field. It’s also about distribution of knowledge, transparency in science and global communications, which all lead to a better you. Having a conversation over a blog post can be a great way to develop your reasoning and researching skills. A lot of people starting out - especially those who haven’t gone through a thesis defence - have a hard time holding a reasonable ‘on topic’ conversation with their colleagues/peers. In most cases, it’s not because of lack of knowledge, but because of an ability to express your ideas in a concise and reasoning manner. A good ‘on topic’ conversation between two people in the same/similar field will be intelligent, well articulated and will make each participant consider new ideas or perspectives. (This type of conversation or debate is not solely isolated to the science field, but that’s what I’ll concentrate on.)

Read more »

Posted: June 25th, 2007 under bioinformatics.
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