A tool for reproducible research: From data analysis (in R) to a typeset laboratory notebook (as .pdf) using the text editor Emacs with the 'mp' package

Software Much scientific research makes use of commonly available 'office' software. While numerous more fully-featured open-source alternatives exist, the integration of diverse tools and platforms which their use often entails can be challenging. The mp package for Emacs aims to bring together a number of these elements with the goal of simplifying the process of converting an .R file, as used for data analysis, to a nicely formatted .pdf which includes the complete description of the methods and interpretation. We discuss the rationale for development of the package and illustrate its applications and options with a series of experiments from our laboratory. Experimental work We demonstrate the inhibitory effects of the ketone body \emph{beta}-hydroxybutyrate (BHB) on the growth and motility of a cancer cell line. BHB is produced endogenously; levels may be increased in certain medial conditions e.g. diabetic ketoacidosis. They may also be raised voluntarily e.g. by adopting the ketogenic diet.  BHB is known to inhibit the growth of other neoplastic cell lines. However the finding that it can do so in a cell line selected for their propensity to metastasize to the brain is novel. Given the challenges in treating patients with melanoma metastatic to brain, this work strengthens the rationale for investigating the ketogenic diet as a potential adjunct to treatment in such cases.