The Web may be the most effective information-delivery platform ever created. Unfortunately, a variety of barriers, both technical and cultural, restrict the use of the Web for chemistry. In the last few years, three powerful forces for change have emerged: Open Source; Open Access; and Open Data. Most of what’s written on these subjects takes a theoretical angle that makes it difficult to visualize real benefits.

Models of structure and bonding play a critical role in guiding chemical research. These models also define the scope and limitations of any cheminformatics system. Within the last several years, the gap between the structure and bonding models used by chemical information systems and by the chemists who use them has been widening. On this front, chemistry is moving much faster than cheminformatics.

October 12, 2011: An updated version of this post is available at Sixty-Four Free Chemistry Databases. Chemical information is in the early stages of a revolution. Long dominated by a handful of established players, the field has rather suddenly opened up to a variety of innovative newcomers. The Internet now offers a diverse array of free online chemistry databases, twelve of which were summarized in a recent article.

Science happens when the experiments and conclusions of your fellow scientists can be freely questioned and independently verified. For example, readers of the cited paper may have questions about the assumptions in the TMACC method, or how to implement it. Questions may be raised about the suitability of the data set used and how others would perform.

Previous articles have highlighted FlexMol’s ability to represent nearly all forms of molecular chirality, including many that are alien to popular cheminformatics tools. FlexMol provides just a few basic elements and rules for their combination, resulting in a system that is both extensible and systematic.

Good software designed with chemists in mind is still quite rare, and when that software is Open Source it’s even rarer still. Two very popular titles are Jmol and PyMol. A third, Bioclipse, is gaining in popularity. So it was with great interest that I came upon a company called AKos Consulting &

“Web 2.0” has gotten a lot of people thinking about exciting new forms of collaboration made possible through the Internet. Services like Digg, YouTube, Flickr, and Wikipedia, and especially the way they harness the selfish impulses of individuals for the common good, are seen by many as just the start of even better things to come.

Recent articles have discussed FlexMol as a new language capable of representing many of today’s most difficult molecules: metallocenes; axially-chiral biaryls; and other forms of axial chirality. FlexMol can also encode more common molecular features such as E/Z alkene geometrical isomerism.

Recently I stumbled upon a new service called The Scientific Debate by way of a comment on Derek Low’s blog In the Pipeline. It’s actually a very clever idea: think Digg for biology papers. Business seems to be slow right now, but the site is less than one month old. Would something like this work in Chemistry?

Searching the primary literature on the Internet leaves a lot to be desired. For example, nothing puts the brakes on a search faster than finding a reference to a key paper, but being unable to download it due to the access policies of the hosting journal. Enter ChemRefer. The site works very simply: type in a keyword and get a list of papers matching it somewhere in the article.

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.