I have described my experiences of using Emacs for writing ontologies previously (n.d.a) I was not entirely happy with omn-mode, even after recent changes (n.d.b) so I have taken the opportunity to update it a little more. This article most describes some implementation changes.

Recently, I and my PhD student, Jennifer Warrender have become interested in the representation of karyotypes. There are descriptions of chromosome complement of an individual. In essence, they are a birds-eye view of the genome. Normally, they are described using a karyotype string, so my karyotype would be 46,XY (probably!) which is normal male. When describing abnormalities, these can get very complex; take, for example, 46,XX,der(9),t(9;11)(p22;q23)t(11;12)(p13;q22)c,der(11)t(9;11)t(11;12)c,der(12)t(11;12)c[20] which describes a patient with multiple translocations.

After a reasonably long hiatus, I have started to work on the Process Knowledgeblog again. Particularly with the creation of kblog-metadata (n.d.a) the need for more documentation was pressing, and the process kblog seems the obvious place to put it; putting full documentation in the plugin “readme” file is a little painful and hard to debug.

Recently, I was surprised to be told that we could not have colour figures in our paper (n.d.a) even though it was online only. Our assumption is that this is an enormous legacy issue; the publisher in question, OUP, still produces a tree-based version of the journal, Bioinformatics. The distinction between colour and monochrome is important here.

I recently published about my experiences of using Emacs for Ontology building (n.d.) A fairly niche subject area, but I was did get a couple of responses asking for my code; curiously, it appears that although I started to write this 6 or 7 years ago, even before this working draft was produced, I forgot to ever release it publically. The code is now available on my website.