Thirty years may have passed, but the situation described by Garfield rings eerily familiar today. What could not have been anticipated is the degree to which the playing field for information producers is being flattened. Today’s scientist-reviewer employs many of the same tools, accesses the same distribution channels, and eventually will compete for the same readers as established journals, databases, and other services.

The creation of Linux is, in part, the stuff of legend. But ESR does make an interesting observation on one role that Open Source software can play in building complex systems. Rather than viewing Open Source software as a permanent fixture of a larger system, why not view it as temporary scaffolding to be replaced, in part or in full, after the system has been fully implemented and all of its requirements are known?

Existing molecular languages are limited in their ability to represent such commonplace features as multi-center bonding and axial chirality. The practical outcome of these limitations can be seen in PubChem’s four separate entries for ferrocene and the inability to fully represent many molecules now in common use by organic chemists.

A recent Depth-First article highlighted the difficulty that existing molecular languages have in communicating the generalized, multi-atom bonding present in metallocenes such a ferrocene. For software and Web services that do not interact with the outside world, the Ferrocene Problem may not be a big deal. But for the growing number that do, the Ferrocene Problem is but the tip of a very large iceberg.

A very useful feature of many 2-D structure editors is a “clean” function that tidies up bond lengths and angles. Java Molecular Editor (JME) is a lightweight 2-D editor that lacks this functionality. In this article, I’ll describe a small Web application called “Cleanup” that adds a “clean” function to JME through Ajax and server-side programming, rather than directly extending JME itself.

InChI is an open molecular identifier system. Although InChIs obviate the need for a central registration authority, they are complex enough that they must be generated by computer. Currently, a few desktop molecular editors can generate InChI identifiers. But wouldn’t it be more convenient if this capability existed in a simple Web application that could be used from any computer - anywhere?

Yet another appearance of Open Source software in the literature comes by way of a paper from Melville, Riley, and Hirst. This work takes advantage of the alphabet-like nature of SMILES strings and widely-available compression algorithms to perform molecular similarity analyses.

Four different Compound Identifiers. Three different canonical SMILES. Three different InChIs. This is how Ferrocene is represented in PubChem. Even more strangely, none of bonding arrangements accurately reflect the ways most chemists would think about it. It’s not a Good Thing to list the same compound under four different entries in the same molecular database. In the best case it’s inconvenient.

Molbank is an Open Access collection of single-compound articles on synthetic chemistry. Previous articles on Depth-First have highlighted Molbank’s practice of including machine-readable molecular representations of its content, and its very liberal policy on mirroring and robots. In this article, we’ll take advantage of both of these features to build something that was left out of Molbank: a graphical table of contents.

BioRails is an Open Source Biological Information Management System (BIMS) based on Ruby on Rails. The BioRails team expects the first release to be available sometime in December 2006. From the BioRails FAQ: BioRails has a great deal of potential, and it will be interesting to see the system up close when it is released.

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.