2009-10-06

Beware of bioinformatics

The advent of computing in our world has made research endeavours easier. The whole field of bioinformatics is built on the mindset that once you have data, regardless of its quality, you can go on and publish the data-analysis recipe and associated observations. Why do computational biologists feel they have to tell everyone that their sequence contains specific sub-sequences? Even more alarming, unless you are publishing in a good journal -- like Nature -- a bioinformatic paper is very unlikely to undergo extensive copy-editing, and thus, will presumably be super-boring to read, unless you are an outstanding writer. Suppose that a person prepares bread with his own novel recipe (yeah, right -- a novel bread recipe). He mixes the ingredients rightly, then he put the mix in the oven, sets it up, waits, and gets his result. This result is void of any scientific value, just as most of the creepy crap published in the bioinformatics sphere is void of discoveries. One could tell that this lack of discoveries is brought by the methodological aspects of bioinformatics -- that bioinformatics in essence is about how you discover things, not about discovering them. Let me consider the persistent problem of short-read alignment, which is pervasive in resequencing adventures. Considering that a genome sequence is very lengthy, and that those small chunks of data obtained are very short, but long enough to allow unique placement when they occur in unique genome segments, then even a child could design a novel algorithm. People are smashing themselves in walls to publish their own programs that align reads onto genomes. Whoa, reads!, genomes!, my nature, this is complex science. Not it's not. Overall, the open access movement has sparked many publishing start-ups, whose commercial activities lay in the process of making available online manuscripts that they receive, along with about a thousand boxes. Sure this is a winning business model, given that 'genomics' and 'computation' are power words.

Below, I attached a carefully-prepared list of peer-reviewed journals in bioinformatics. Go check them out!


Algorithms in molecular biology
Bioinformatics
Briefings in Bioinformatics
BMC Bioinformatics
BMC Genomics
Computational Biology and Chemistry
Journal of Bioinformatics and Computational Biology
Journal of Computational Biology
PLoS Computational Biology
The Open Bioinformatics Journal

(a more detailed list is available here)

Edits: 2010-06-22 (typos)

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