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Monday, January 31, 2011

In Silico Toxicology

Today my copy of In Silico Toxicology: Principles and Applications (Issues in Toxicology) arrived at the local Library. Library with a capital L: we requested the book 1.5 weeks ago, got confirmation it got ordered last week Monday, and just picked it up. Well done!

The book covers in 24 chapters the prediction of toxicological properties of small molecules, and extensively discusses aspects of QSAR studies. As such, various Blue Obelisk tools are described, including the CDK (page 184 and 413), Bioclipse (page 414), JOELib (page 185), OpenBabel (page 414), Oscar (page 415), as well as other Open Source tools, including AMBIT (page 315 ff), InChI (page 72), Toxtree (page 313 and 417), and others. (Nina, should I classify AMBIT and ToxTree as Blue Obelisk projects, now that you are a Blue Obelisk Award winner?)

Much of these are actually listed in Chapter 17, Open Source Tools for Read-Across and Category Formation, by Nina et al., but also worth mentioning is the prominent placement of Open Source tools in Chapter 6 by Uko Maran et al., Molecular Descriptors from Two-Dimensional Chemical Structure, where the REACH documentation focuses on proprietary tools.

Obviously, these are not the bits I am eager to read. Instead, I'm very much looking forward to reading the chapters on data quality (Ch. 4), model validation (Ch. 11), application domain (Ch. 12), linking chemical structures to adverse reactions (Ch. 14), and toxicokinetics (Ch. 21). The book sums up to some 669 pages, so it will keep me busy for the next few hours ;)