InChI is both a molecular identifier and a molecular language. As the use of InChIs spreads, there will be an increasing need to convert InChIs to molecular structures. In this article, I’ll introduce a software package called “Ninja” that can serve as a foundation for writing InChI parsers in a variety of toolkits and programming languages. About Ninja Ninja is a low-level Java toolkit for parsing InChIs.

Recently, Heck cyclizations of axially chiral N -arylacrylanilids were reported by Lapierre, Geib, and Curran. Faithfully communicating this kind of chirality in machine-readable form is virtually impossible using today’s most popular technologies. A previous article showed how a new XML-based molecular language, FlexMol, could fully represent the axial chirality of BINOL.

A recent article introduced FlexMol as a molecular language with the unique capability of encoding axial chirality. A previous article showed how E/Z geometrical isomerism is encoded with FlexMol. Using the popular chiral reagent and ligand 1,1’-bi-2-naphthol (BINOL) as an example, this tutorial will illustrate in detail how axial chirality is encoded in FlexMol. Configuration or Conformation?

Axial chirality results, not from a tetrahedral chiral center, but from a chiral axis. This form of chirality most frequently occurs in biaryls and allenes. The importance of axial chirality to organic chemistry was recognized in 2001, when Ryoji Noyori was co-awarded the Nobel Prize in Chemistry, in part for his work with highly selective catalysts derived from the axially-chiral BINAP ligand.

The number of free chemistry databases on the Web just keeps growing. A recent Depth-First article discussed twelve of them. It turns out that Chembiogrid from Indiana University maintains a list of forty free chemistry databases, most of which are alive and well. As this trend continues, the need for database standards will become painfully obvious.

The appearance of chemical blogspace is just one indication that the amount of new content created by scientists but appearing outside of scientific journals is set to increase in coming years. This new content will likely take the form of written work, images, movies, and digital audio. With this situation comes a new problem for authors - managing all of their new content.

Why did PubChem, the granddaddy of all open chemistry databases, choose a closed, proprietary toolkit for its software infrastructure? A recent Depth-First article highlighted twelve free chemistry databases. Of those for which information is available, many have chosen the same path as PubChem. Why is this? A huge opportunity is being wasted every time this happens.

A recent article introduced FlexMol, a molecular language designed to encode the multi-atom bonding arrangements present in molecules being increasingly made and used by today’s chemists. But FlexMol was designed with much more than bonding in mind. Of all of the difficult areas in molecular representation, perhaps none are more daunting than stereochemistry.

Few subjects cause as much confusion and as many heated debates as Open Source licensing. The Open Source Initiative has approved over 50 licenses compatible with their ten-point definition of “Open Source”. Whenever that many solutions to a problem exist, it’s a sure sign that one size does not fit all. In this article, I’ll introduce some of the key concepts in Open Source licensing.

Yet another appearance of Open Source software in the primary cheminformatics literature comes by way of a paper from Mazzatorta, Tran, Shilter, and Grigorov of the Nestlé Research Center. This work employs two Open Source libraries: lazar, a tool for the prediction of toxic properties of chemical structures; and Open Babel, a widely-used, low-level library for cheminformatics.

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.