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?

The 2006 documentary Who Killed the Electric Car? should give anyone involved with Open Access reason to ponder. The film tells the story of GM’s electric car experiment (the EV1) in California and its eventual failure. Open Access bears a striking resemblance to the electric car, including the ways parties on both sides frame the discussion, the market dynamics involved, and steps by government to mandate a solution.

How would you enumerate all of the molecules represented by a molecular formula? This question was recently posed to members of the Blue Obelisk mailing list. Formula-based exhaustive structure enumeration may seem on the surface to be just another esoteric problem. Nevertheless, playing with open, interactive software that can perform such enumerations can be a great source of new ideas for applications and unit tests.

A recent question on Yahoo’s chemoinf forum got me thinking about free cheminformatics scripting environments. If you’ve ever wanted to learn an object-oriented scripting language such as Ruby, Python, Perl, or Groovy in the context of cheminformatics, there are many good options to choose from. Few experiences expand a programmer’s horizons more than learning one of these freedom languages.

The Structure Data File (SDF) format is the de facto standard for cheminformatics data exchange. One of the problems that arises when working with SD Files, especially large ones like those distributed by PubChem, is “seeing” the structures they contain. Although commercial software packages are available for doing so, they are generally closed, unreasonably expensive, or overly complex.

This picture is worth at least 1,000 words on the subject of Open Access in chemistry. But since it's Friday, I'll put up the picture today and leave the words for next week.

The state of the art in structure editors for chemical Web services is Java applets. Although closed editors have long dominated this field, Open Source editors are a possibly viable option. Java applets are great from a developer’s perspective. But applets are avoided by some end users and IT support for their underlying need to install a Java plug-in of some kind and long startup times.

The situation described by Granito in 1973 seems eerily familiar today. The names of the players, the technologies, and encoding systems have changed, but the problem of multiple incompatible molecular languages has persisted for over 30 years. This problem will become even more pronounced in the near future as free chemistry databases on the Web continue their rapid proliferation.

October 12, 2011: An updated version of this post is available at Sixty-Four Free Chemistry Databases. Just two years ago, trying to find free online chemistry databases was an exercise in futility. Now, they’re sprouting up all over the Web like wildflowers after a wet Spring. What follows is a far-from-complete roundup of some of the more interesting places to start your chemical search.

Recently eMolecules donated a substantial amount of new code to the Open Babel project. This code, which could help developers of molecular databases write faster query engines, is now free for anyone to use for any purpose. Are eMolecules worried about having parted with something it took them time and money to develop and which could eventually help a competitor?

SMILES and InChI are two commonly-used molecular line notations. Although each has its advantages and limitations, the novelty of InChI and the ubiquity of SMILES makes the SMILES to InChI conversion especially useful. Many of the situations in which the need for this conversion will arise are particularly well-suited for the Ruby programming language. A recent article described how RCDK and Rino could be used to accomplish this conversion.