PubChem is an increasingly popular, free-access, online molecular database operated by the National Institutes of Health. Web services are a hot topic, with sites such as Flickr, Google, and eBay offering developers the tools to build rich content through “mashups” of several web APIs. Although there is no formal PubChem API, it’s possible to roll your own.

Rendering 2-D molecular structures is a fundamental part of chemical informatics. It’s used in building end user systems, and more immediately, it can be critical for creating and debugging developer tools. The Chemistry Development Kit (CDK) is a highly-functional chemical informatics library written in Java.

Although JRuby solves many Java/Ruby integration issues, in some cases it’s not the right solution. One situation is when you want your Ruby code to use extensions written in C. The JRuby documentation makes very clear that this will never be supported. Another situation is if your code needs full access to Ruby on Rails, or if your hosting service makes it difficult to configure JRuby on Rails.

Integrating Ruby and Java is fast and easy with Ruby Java Bridge (RJB), which was discussed previously. In this article, I’ll show how RJB can be used to solve a practical chemical informatics problem - the conversion of SMILES strings into InChI identifiers. Prerequisites This tutorial is aimed at Linux users, but you should be able to accomplish the same thing in Windows and Mac OS X, although these systems have not been tested.

Raster images of 2-D molecular structures are everywhere - in books, in journal articles, on photocopies, in notebooks, and most importantly, on the internet (for example, on this page and this one). Although readily interpretable by humans, these renderings are useless to computer indexing systems - unless they can be translated into machine-readable representational schemes such as connection tables.

A previous article discussed the use of the Java chemical informatics library Octet from JRuby. This article will discuss the use of another Java chemical infomatics library, CDK, from JRuby. A small Ruby class will be developed that generates a molfile with completely assigned 2-D coordinates from a SMILES string.

Science moves forward only insofar as observations can be validated and put to use by a third party. Chemical informatics is no different from any other field in this respect. Yet publications of the type Mr. Figueras opposed can still be found in 2006. Why is this? At issue isn’t just software. The ACS has recently spoken out on the necessity of open data sets.

JRuby is a Java implementation of the Ruby language. It lets developers manipulate Java classes and objects using Ruby syntax. Why would anybody want to do this? One reason is to enable Ruby developers to work with ‘legacy’ Java code. Another less obvious reason it that Java classes and objects can manipulated interactively with the JRuby version of Interactive Ruby, or irb.

At the start of the twentieth century, Chemical Abstracts Service was itself an upstart in a field dominated by large players, mainly in Europe. Mr. Urbach cites four factors that changed all of that: The practical importance of chemical information relative to other scientific fields gave it an edge in competing for federal funds.

The increasing trend toward hosting free chemical databases and other services on the web brings with it the need for a free, ergonomic, capable, and fast 2-D structure editor. For years, the options were rather limited. However, this situation has started to change. Four web-enabled editors are discussed here, with an emphasis on the steps needed to deploy them within a webpage and retrieve a text-based molecular representation.

Given the emergence of worldwide all-volunteer documentation efforts like Wikipedia, perhaps now is a good time to reconsider the feasibility of a very different form of all-volunteer chemical abstracting service. The all-volunteer system was used by CAS almost exclusively until 1966. Although these abstractors were called “volunteers”, they did receive a payment for their work - about $0.18/line in 1979.