Lennart's weblog » Science

Paper on using org-mode for reproducible research

LCK — Thu, 02 Feb 2012 19:15:46 +0000

I’m an avid user of Emacs and have been using org-mode for a couple of years now to write notes, keep a ToDo list and a few other things.

A couple of days ago I came across an article in the Journal of Statistical Software that describes how to use org-mode for reproducible research. It’s a great read and the source code of the complete article can be downloaded as well!

RefTeX, how could I have missed this?

LCK — Sun, 21 Aug 2011 20:34:49 +0000

I’ve been using Emacs and LaTeX for more than ten years now and still I keep learning. For example, last Friday I came across Stephen Eglen’s ESS (Emacs Speaks Statistics) tutorial. In his slides he mentioned RefTeX. I had heard of it before, but for some reason I thought it was either a set of LaTeX styles or an AUCTeX replacement and consequently, I never looked into it.

This time, however, I made the small effort of looking up RefTeX’s website and lo and behold, it’s neither of the two things I thought it was. Instead, it is an extension to LaTeX that makes inserting citation, references, index entries and labels a breeze. Even if you don’t (want to) use all its capabilities, the following keystrokes are worth the effort:

`C-c =`	Show table of contents of the document (also a great way to walk through your document)
`C-c (`	Insert a label at point
`C-c )`	Insert a reference to some label
`C-c [`	Search in your bibliography (either BibTeX or `thebibliography` environment) to insert citations

To start using RefTeX in a document you are already editing simple run

M-x reftex-mode

Insert the following in .emacs file if you want to load RefTeX on startup

;; Enable RefTeX
(add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
(add-hook 'latex-mode-hook 'turn-on-reftex)   ; with Emacs latex mode

A new job in genetic epidemiology

LCK — Wed, 26 May 2010 14:14:17 +0000

Last week I started my new job as a researcher in the field of genetic epidemiology at a university hospital in the Netherlands. Working for a UNIX consultancy firm for some time was a lot of fun, but being back in science is even more fun!

My job will keep me occupied with system administration of the servers used for genetic computations, improving several genetics packages for the programming language R, including getting them adapted to multi-CPU environments, and, maybe later, even try to get those calculations done on graphics cards (GPGPU computing/CUDA). And, of course, I need to get up to speed with genetics and epidemiology, and the math involved, as quickly as possible . So, no physics involved here, but who knows where this will bring me. And so far it’s been a lot of fun!