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Saturday, February 02, 2013

Book: "Open source software in life science research"


Recently, Lee Harland and Mark Forster published a book called "Open source software in life science research" (see book cover on the right; ISBN-13:978 1 907568 97 8; available from e.g. Amazon) featuring a chapter on Bioclipse-OpenTox, in which we applied our earlier work published (doi:10.1186/1756-0500-4-487) to the Tres Cantos interesting Antimalarial Set, TCAMS, nowadays available from the ChEMBL Neglected Tropical Disease Database. Big thumbs up to Roman who primarily did that part.

This book is not Open Access, but three chapters are. Ours is one of them: our chapter is available under the Creative Commons 3.0 Share Alike Attribution (CC-BY-SA) license. Currently, the sources are available as a Word and as Libre/OpenOffice document at GitHub, but I think I will convert that to LaTex later so that I can share a nicely formatted PDF version of the chapter. We used the Mendeley plugin for the references, with mixed experiences. All references are therefore available from this Mendeley group.

We plan to keep this chapter updated. That is, when there are significant changes in the OpenTox or Bioclipse platforms, we will update the chapter content to match those chances. Well, that is at least the idea.
Of course, everyone who likes to do that is allowed to do it. So, feel free to clone the chapter.

 Willighagen, E.; Affentranger, R.; Grafström, R.; Hardy, B.; Jeliazkova, N.; Spjuth, O. Interactive Predictive Toxicology with Bioclipse and OpenTox. In Open Source Software in Life Science Research: Practical Solutions to Common Challenges in the Pharmaceutical Industry and Beyond, 1 Ed.; Harland, L.; Forster, M., Eds.; Biohealthcare Publishing Ltd: Oxford, 2012.