The Baserate Fallacy, revisited

In which I share some iPython code for an interactive demo to calculate and visualise the probability that a positive test implies a positive result. You can get it here, and preview it here. Then I get entangled in a topic outwith my expertise.

ANI are you okay? Are you okay ANI?

In which I describe Average Nucleotide Identity (ANI), which we can use to pigeonhole bacteria into conceptual boxes labelled as 'species'. And I share more code.

KEGGWatch, part III

In which I finally get around to sharing some code, and give some examples of downloading and modifying KEGG pathway maps.

KEGGWatch, part II

In which I don't quite get around to writing a KGML parser and visualisation module (all very Tristram Shandy, this!), with a view to submitting to Biopython. This post describes some of the rationale and design choices - tune into part III for code and examples of use.

KEGGWatch, part I

In which I attempt to visualise metabolic maps for comparative genomics, and lead up to making a contribution to Biopython.

The Colours, Man! The Colours!

In which I take a short diversion into colour theory, and share some code to automate colour selection for class data.

23 And Me and Me: Part 3

In which I get a nice surprise.

On Reciprocal Best BLAST Hits

In which I narrowly avoid a rant. Reciprocal best BLAST hits can improve the quality of your searching, and are a good way to find candidate orthologues. There's evidence and everything.

23 And Me And Me: Part 2

In which the most difficult part of getting yourself genotyped turns out to be dealing with shopkeepers, and I impress the eight-year-old me.

23 And Me And Me: Part 1

In which I cave in to curiosity, and get myself genotyped.

Dead fish, and multiple-test correction

In which a salmon is resurrected, but not enough to really be significant.  Why finding 20 positive results when your P-value threshold suggests you should only see 10 isn't necessarily anything to be excited about.  And an introduction to Bonferroni and Benjamini-Hochberg multiple test correction.

The Base Rate Fallacy in Effector-Finding

In which an oft-overlooked bit of genome-mining statistics is considered, and your enjoyment of a holiday could depend heavily on other people's hygiene.

What is this 'effector' thing, anyway?

In which I opine about the definition of (plant) pathogen effectors.

New plots for old kinetics

In which basic enzyme kinetics are revisited, systematically incorrect lab statistics are bemoaned, and a little-known elegant 40 year old solution to estimating enzyme kinetic parameters is explored.