Summarizing Collections of Curves

I was browsing live notes from the recent IEEE conference on visualization and came across a paper about functional boxplots. The idea is an extension of the boxplot visualization (shown alongside), to a set of functions. Intuitively, one can think of a functional box plot as specific envelopes for a set of functions. The construction […]

Thoughts on the DREAM Synergy Prediction Challenge

The DREAM consortium has run a number of predictive modeling challenges and the latest one on predicting small molecule synergies has just been published. The dataset that was provided included baseline gene expression of the cell line (OCI-LY3), expression in presence of compound (2 concentrations, 2 time points), dose response data for 14 compounds and […]

Metabolite Similarity & Dirty Compounds

Edit 10/9/14 – Updated statistics for the 1024 bit fingerprints There’s been some discussion about a paper by O’Hagan et al that have proposed a Rule of 0.5 that states that 90% of approved drugs exhibit a Tanimoto similarity > 0.5 to one or more human metabolites. Their analysis is based on metabolites listed in […]

rinchi – An R package to generate InChI’s and InChI Keys

While trying to update rcdk on CRAN it was pointed out to me that usage of the library resulted in modifications to the users home directory. Specifically, this occurred when generating InChI‘s. The CDK makes use of jni-inchi, which in turn depends on JNATI which enables Java code to work with native libraries in a platform […]