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March 19, 2012
Dealing with the Data
So how do we deal with the piles of data? A reader sent along this question, and it's worth thinking about. Drug research - even the preclinical kind - generates an awful lot of information. The other day, it was pointed out that one of our projects, if you expanded everything out, would be displayed on a spreadsheet with compounds running down the left, and over two hundred columns stretching across the page. Not all of those are populated for every compound, by any means, especially the newer ones. But compounds that stay in the screening collection tend to accumulate a lot of data with time, and there are hundreds of thousands (or millions) of compounds in a good-sized screening collection. How do we keep track of it all?
Most larger companies have some sort of proprietary software for the job (or jobs). The idea is that you can enter a structure (or substructure) of a compound and find out the project it was made for, every assay that's been run on it, all its spectral data and physical properties (experimental and calculated), every batch that's been made or bought (and from whom and from where, with notebook and catalog references), and the bar code of every vial or bottle of it that's running around the labs. You obviously don't want all of those every time, so you need to be able to define your queries over a wide range, setting a few common ones as defaults and customizing them for individual projects while they're running.
Displaying all this data isn't trivial, either. The good old fashioned spreadsheet is perfectly useful, but you're going to need the ability to plot and chart in all sorts of ways to actually see what's going on in a big project. How does human microsomal stability relate to the logP of the right-hand side chain in the pyrimidinyl-series compounds with molecular weight under 425? And how do those numbers compare to the dog microsomes? And how do either of those compare to the blood levels in the whole animal, keeping in mind that you've been using two different dosing vehicles along the way? To visualize these kinds of questions - perfectly reasonable ones, let me tell you - you'll need all the help you can get.
You run into the problem of any large, multifunctional program, though: if it can do everything, it may not do any one thing very well. Or there may be a way to do whatever you want, if only you can memorize the magic spell that will make it happen. If it's one of those programs that you have to use constantly or run the risk of totally forgetting how it goes, there will be trouble.
So what's been the experience out there? In-house home-built software? Adaptations of commercial packages? How does a smaller company afford to do what it needs to do? Comments welcome. . .
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