The previous article in this series outlined some reasons to consider JRuby for cheminformatics. Now I’ll show how easy it is to get started by describing how to parse SMILES strings with the help of the Chemistry Development Kit (CDK). What About Ruby CDK? A number of Depth-First articles have discussed Ruby CDK.

JRuby is an implementation of the Ruby programming language on the Java Virtual Machine. Until about six months ago, JRuby was merely a technical curiosity; few seemed interested in using it for ‘serious’ development work. This perception has changed over the last six months, as JRuby’s progress has accelerated. Here, in no particular order, are five reasons to consider using JRuby for your current or next project.

Greg Williams has done some great graphics using Wikipedia articles as source material.

Whatever your views on Wikipedia, it’s clear that the volunteer online encyclopedia has left it’s mark on society. But the most important things about Wikipedia have less to do with its contents and more to do with the people contributing and using the service. To understand how and why people collaborate on the Web, you have to understand Wikipedia.

Scripting languages and cheminformatics can be a highly-effective combination. With their relaxed syntax, compilation-free execution, and interactive testing environments, scripting languages offer fast development iteration cycles. And scripting languages’ support for manipulating libraries written in other languages can be key in today’s heterogeneous cheminformatics software environment.

Pssssst. Want to know a secret? Some of the best inventions are completely obvious. That is, given a half dozen years or so. At the time they’re conceived, however, most good, obvious ideas just seem dumb, dangerous, or uninteresting. They have to - otherwise they’d have been developed already. Case in point: the blog permalink.

A recent Depth-First article discussed the advantages of minimal Web APIs in Cheminformatics. Recently, Antony Williams unveiled some simplified ChemSpider URL schemes, mainly from the perspective of enabling Google indexing. However, it’s possible to take this scheme much, much further. Here I present a proposal for radically simplifying (and unifying) the development of cheminformatics Web APIs and the software that interacts with them.

Ein Fehler ist aufgetreten. Sieh dir dieses Video auf www.youtube.com an oder aktiviere JavaScript, falls es in deinem Browser deaktiviert sein sollte. It’s a fine line between crazy enough and just crazy. The dilemma is that you never know which category you’re in before you start.

Designing good user interfaces is difficult work. One of the hardest things about it is what you’re forced to give up: abandoning your hard-won mental map and adopting that of the user; stripping half the product’s features - and then stripping half of what’s left; and fending off featuritis with a big club as the product matures. Everyone knows these things are important, but for some reason we repeat the same mistakes over and over.

The IUPAC International Chemical Indentifier (InChI) provides an open system for converting molecular representations into strings of text. Because text processing is one of the things computers do very well, InChI serves as an important link between chemistry and computer science. Unfortunately, the InChI documentation is rather scattered. To help remedy this problem, I have selected some links to Depth-First articles discussing InChI.