Recently there have been two papers asking whether cheminformatics or virtual screening in general, have really helped drug discovery, in terms of lead discovery. The first paper from Muchmore et al focuses on the utility of various cheminformatics tools in drug discovery. Their report is retrospective in nature where they note that while much research […]
Simple XML Parsing with Clojure
A while back I had started playing with Clojure. It’s always been a spare-time hobby and not having had much spare time I haven’t really gotten as far ahead with it as I’d have liked. I’m still not sure why I like Clojure, but it is fun to code in. My interest was revitalized when […]
When is a Bad Plate Bad?
When running a high-throughput screen, one usually deals with hundreds or even thousands of plates. Due to the vagaries of experiments, some plates will not be ervy good. That is, the data will be of poor quality due to a variety of reasons. Usually we can evaluate various statistical quality metrics to asses which plates […]
A Custom Palette for Heatmaps
Heatmaps are a common way to visualize matrices and R provides a variety of methods to generate these diagrams. One of the key features of a heatmap is the color scheme employed. By default the image method uses heat.colors which ranges from red (lowest values) to white (highest values). Other palettes include rainbow and topographical. […]
Oracle Notes
Some handy settings when running a query from the command line via sqlplus set echo off set heading on set linesize 1024 set pagesize 0 set tab on set trims on set wrap off — might want to set column formats here — e.g.: column foo format A10 spool stats — dump results to stats.lst […]