Good source code documentation tools can greatly enhance developer productivity at almost no cost. By eliminating the need to dig through source code files for documentation, tools like Java’s Javadoc are invaluable for quickly seeing the big picture of a new piece of software. They are also handy as a quick reminder for more familiar APIs.

The previous tutorial in this series showed some techniques for improving the appearance and usability of a simple cheminformatics Web application. That application, Depict, rendered color images of 2-D molecular structures when given a SMILES string. Still, something is missing. Wouldn’t it be better if the application responded to individual keystrokes in the input field, rather than waiting for the user to hit the return key?

The previous article in this series highlighted Molbank as a tool for studying the convergence of Open Access, Open Data, and Open Source in chemistry. This article will outline some of the technical and legal aspects of downloading and using Molbank content.

Molbank, published by Molecuar Diversity Preservation International, is one of the oldest of a handful of Open Access journals in chemistry. Although its longevity is a remarkable accomplishment in itself, there is much more to Molbank than meets eye. Just below the surface is a feature so revolutionary, yet simple, that chemistry publishers years from now will wonder why they didn’t implement it sooner.

Gushee goes on to discuss the decline of ACS journal subscription rates and the simultaneous increase in total pages printed and journals published. One wonders to what extent these trends continued over the last 36 years and how this phenomenon may driving the current escalation in journal costs.

What happens to an article in an Open Access journal that shuts down? Recently, this question was raised on the Blue Obelisk mailing list about an article published in the Internet Journal of Chemistry (IJC). Because the lights now appear to be out for good at IJC, are its articles lost forever? The good news is that by retaining copyright, authors of Open Access articles have the right to copy or reprocess their work in any form they see fit.

A recent article outlined the steps for building a Rails Web application that renders SMILES strings as 2-D molecular images. Although this application, Depict, performed its stated purpose, it was neither much to look at nor as easy to use as it could be. In this tutorial, we’ll give Depict a face-lift and make it more user-friendly.

A molecular fingerprint represents a molecule as series of bits. There are many situations in which this reduced form of molecular representation is useful. For example, fingerprints are frequently used as a fast prescreen for database substructure searches. They can also be used for “fuzzy” comparisons involving molecular similarity, a nice complement to binary queries such as substructure search. Fingerprints have their limitations.

A recent article highlighted the Web as a new cheminformatics platform. Advocacy is one thing, but a working, open, demo built with modern technologies is far more compelling. In the following tutorial we’ll build a first-generation cheminformatics Web application using the Ruby on Rails framework and 100% Open Source components. We’ll just cover the essentials here - look for future articles to discuss the underlying technology in more detail.

A lot has changed since Paul Graham wrote these words about the future of software. To name a few of the biggies: Flickr; Digg; YouTube; MySpace; GMail; Last.fm; Blogger; Writely; Facebook; DabbleDB; Kiko; LibraryThing; and BaseCamp. The list of new and useful Web application just goes on and on, with entries added daily. None of them require major software installation or configuration on the part of the user.

The Sorting Algorithm Demo compares four commonly-used sorting algorithms in a unique way: by showing them in action. Watch as each of these four algorithms performs exactly the same task in very different ways and with varying efficiencies. How could tools like The Sorting Algorithm Demo be designed for cheminformatics?