Ruby Chemistry Development Kit (RCDK) version 0.2.0 is now available. This version adds built-in support for Structure-CDK, a 2-D rendering framework. Simplifying the use of this library is a convenience layer enabling many common tasks to be accomplished with a single line of Ruby code. Installing RCDK-0.2.0 is simple.

A recent article poses the question of how to balance the rights of owners of open chemical information resources against those of their users, while promoting an innovative environment for third-party developers. Although PubChem was the focus, the discussion could apply to any other chemical information resource.

ProgrammableWeb offers one-stop shopping for all things mashup-related. If you’ve ever wanted to try your hand at Web programming, this site makes an excellent first stop. Be sure to check out the listing of over 1,000 mashup sites indexed by category and API. The move toward open, Web-based chemical information resources is fully underway. The genie has been let out of the bottle, and there’s no putting him back.

Like no other medium, the Internet tests our basic beliefs about the rights of resource owners and resource users. As the Internet increasingly becomes home to scientific publication mechanisms that have no counterpart in the physical world, a larger question looms: what separates fair use of these services from abuse?

Recently, I showed how a simple PubChem API could be built from a few lines of Ruby code. The API we created could retrieve a molfile and a 2-D molecular rendering given a PubChem compound ID (CID). In this tutorial, we’ll see how a SMILES query mechanism can be added to the API, enabling CIDs to be retrieved from any valid SMILES string.

One of my favorite software-related blogs is Signal to Noise. It’s contributors are employees of the web application company 37signals, one of whom is the founder of the Ruby on Rails project. This company is very focused on its customers, and it shows. The information here ranges from software development strategies to product design. A recent article discusses the concept of point and shoot software.

InChI identifiers are unique, ASCII-based molecular identifiers well-suited for chemical informatics on the Web. But they are also much more than that. Encoded in every InChI is all of the information needed to reconstruct a valid, machine-readable molecular representation.

Several online chemical information services, including PubChem, NMRShiftDB, and ZINC, have emerged in a relatively short period of time. As these systems go from being toys for hackers to essential components of scientific workflow, their true potential will be unlocked by developing innovative ways to tie these disparate systems together.

The IUPAC InChI developer toolkit is written in C. It is currently the only Open Source software capable of generating InChI identifiers. Software that needs to write InChIs must use the C toolkit in one form or another. This poses a problem for the large amount of chemical informatics software being written in other languages. In this article, I’ll explain how the Open Source tool SWIG can solve this problem in a semi-automated way.

Previous articles have discussed how the Chemistry Development Kit (CDK) can interface with Ruby using the Ruby Java Bridge (RJB). However, each of these articles included a repetitive setup in which the CDK jarfile needed to be copied and the CLASSPATH variable needed to be set. In writing, as in programming, repeating yourself is a sure sign that something needs to be refactored.

Recently, I wrote a tutorial on embedding 2-D molecular renderings into webpages as Scalable Vector Graphics (SVG). This tutorial also contained a small experiment on the current chemical informatics capabilities of the Web. Here is a scenario from the near future: Joe is writing a review on Cephalosporin C that he wants to publish the modern way - directly to the Web. An entirely new concept in scientific publishing has started to take hold.