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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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.
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.
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.)
Posted: June 25th, 2007 under bioinformatics.
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