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The very thing you’d like most to do as a developer is the thing your users can’t stand.

How does open source software happen? Although many factors come into play, the majority of answers seem to revolve around a simple theme: developers building solutions to fill their own needs. Yet only a fraction of these solutions end up becoming open source software. And only a fraction of those end up being used by a wider audience. What’s the key ingredient? There’s still a lot to learn from studying individual cases.

SMILES is one of the most widely-used line notations in cheminformatics. Yet until very recently, there has been no concerted attempt to develop open SMILES encoding standards. OpenSMILES aims to change that. By providing a forum in which concerns from the SMILES user community can be voiced, peer-reviewed, and addressed, OpenSMILES introduces a new way for the SMILES language to become better.

Recently, I needed to create a subset of the PubChem database in Structure Data File (SD File) format. Although it’s far from obvious how to do this, the capability does exist. In this article, I’ll give a step-by-step procedure for creating custom datasets in SD File format from arbitrary PubChem structure queries.

Reading SD files is a bread-and-butter cheminformatics operation. At a minimum, a cheminformatics toolkit needs to parse the individual entries of an SD file, and provide access to the embedded molfile and data hash for each. Recent articles have introduced Rubidium, a Ruby cheminformatics scripting environment. The Rubidium team now announces the release of Rubidium-0.1.1, which, among other features, introduces the ability to parse SD files.

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Few would argue against small companies using open source software - indeed many owe their very existence to it. But what real, tangible good can come from a small company releasing open source software? Signal to Noise, the company blog of 37signals, offers a worthwhile perspective on this issue.

If you’ve ever needed to build a Website hosting mostly static content, you’ve probably tried out a few Content Management Systems. The problem is not finding them - there must be hundreds. The problem is finding one that successfully walks the fine line between being minimal (so that you can do things your way) and powerful (so that it can grow with your needs). Radiant CMS is one of those systems.

Cheminformatics has seen the introduction of a diverse array of new open source software over the last few years. Using it all to its fullest potential is not always easy; differing languages, dependencies, interfaces, and varying levels of documentation make the job especially difficult. Rubidium is a new open source project aimed at changing that. Rubidium is a full-featured cheminformatics scripting environment for Ruby.