An older article I did on Wiswesser Line Notation (WLN) seems to have interested a few people over the years. For the unfamiliar, WLN was a line notation system that at one point was the way to name organic compounds. Among its most remarkable attributes was how easy it was to learn - supporters claimed that high school graduates with minimal chemistry knowledge could be taught WLN in a matter of days.

One of the useful (and unnerving) things about running a blog is that you’re forced to face what you don’t know (usually very publicly). I’ve been looking for the simplest way to maintain an up-to-date local copy of PubChem. I previously posted an article describing one way to mirror PubChem through the use of rsync and curlftpfs. Although this method works, it turns out that there’s an even simpler way to do this with wget.

PubChem’s massive size presents special challenges when working with this chemical dataset. Synchronization in particular requires special care. Although it’s very easy to use a tool such as wget to perform a complete, one-time download PubChem’s archive files, this approach scales poorly if our goal is to maintain a copy that’s always up-to-date.

Nature News is running a story on Matthew Todd and his initiative to develop a more practical treatment for Schistosomiasis by thinking different: Call me an optimist, but the problems with getting something like this to work will have less to do with a scarcity of volunteer-minded chemists and more to do with finding them around the world and connecting them to each other. Chempedia Lab is a service that might have a role to play.

If you’ve ever worked with the PubChem dataset, you may have found yourself wanting to create a custom subset that filters out certain records. This article, the fourth in a continuing series, shows a very simple way to create a custom PubChem dataset using PubCouch. The Problem I really like PubChem. It’s the world’s largest collection of freely-downloadable chemical structures and an excellent use of taxpayer dollars.

If you’ve been following along with the development of PubCouch, the CouchDB interface for PubChem, you’ve probably noticed that only a fraction of the code relates to CouchDB itself. What’s the rest of it doing?

Although I find CouchDB’s slogan “Relax” comforting, after having worked with Couch both on OS X and Linux, I can say with confidence that the only time to relax is after CouchDB is installed and tested. The process of getting to that point is about as relaxing as root canal.

The choice of a database can have far-reaching consequences on an application’s design and capabilities. I’ve recently become interested in CouchDB and other so-called NoSQL databases as an alternative to traditional approaches. This article, the first in a series, explores how CouchDB can be applied to real-world cheminformatics problems using the PubChem dataset. Get Involved An open source project called PubCouch has been set up on GitHub.

The pymol.org site is reporting that Schrödinger will now provide maintenance, support, and sales for PyMOL: There are many ways to ‘sell’ open source software. Delano Scientific used a freemium model; the basic PyMOL package was free, but premium services, such as support and “incentive builds”, could be purchased separately. Delano took this one step further by licensing the basic package as open source.

Molecular fingerprints play an important role in cheminformatics. MX, the high-performance cheminformatics toolkit written in Java, comes complete with the ability to generate molecular fingerprints. This article, the first of a new series discussing MX through compilable snippets of Java code, shows how to interactively test fingerprints in MX through a simple command-line utility.

[Flash Content Scrubbed] I came across this intriguing presentation, apparently by Jonathan Alvarsson, while doing some research on Mychem. Although the context is not described in detail, the fundamental problems should be familiar to anyone who has built a chemical database. For those who may not know, Mychem is is an open source cheminformatics extension for MySQL based on Open Babel.