Archive for the ‘Bioinformatics’ Category

A short note on data dynamics

4, Dec 2010

I’ve just checked that at least 400 proteins in Uniprot had their sequence updated since beginning of this year. It could be more, but I work on a subset of human proteins that consists of ca. 1500 proteins, so probably I see only portion of changes. So, instead of wrapping up the paper, I’m redoing analysis [...]

Two metagenomics samples: are they different?

9, Sep 2010

Some other day I was asked to compare taxonomic distribution of two metagenomics samples and answer the question whether they are significantly different. With my deep dislike of using statistical methods without understanding the data, the first thing I’ve tried was to SEE if they are different. What I did was a clustering, but (again) [...]

Biases, biases everywhere

1, Jul 2010

When I skim through list of cognitive biases , I wonder why papers like Over-optimism in bioinformatics: an illustration (hat tip: Neil) do not appear more often. Here’s the abstract: MOTIVATION: In statistical bioinformatics research, different optimization mechanisms potentially lead to “over-optimism” in published papers. So far, however, a systematic critical study concerning the various [...]

Project sketches – spatial dynamic forest metagenome

8, Jun 2010

Project sketches – ideas that have never made it into grant application (for many reasons, but mostly because I’m not an expert on the topic, so they wouldn’t be funded anyway). The idea for this project was quite simple: to build spatial and dynamic map of forest metagenome. I wanted to collect many samples from [...]

In science (tools) we trust

29, Dec 2009

Image via Wikipedia Software generates errors and misuse of software generates even more errors. Here’re few examples of use and misuse of the common, non-scientific software and services. I think I have mentioned this elsewhere: scientists don’t care about search engines, neither can use them. My friend was quite lucky when naming a newly found [...]


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