From The Realm of Organic Synthesis comes a common feeling of frustration with the way scientific information is distributed, and an increasingly common proposal for a solution: Today we’re witnessing a major re-evaluation of the scientific publication system. At issue is the fundamental inefficiency with the way things work - in terms of time, effort, and especially money.

The GitHub Blog has published a writeup about Bioclipse’s method for importing scripts from GitHub. Although there are obvious security issues with allowing arbitrary code to be run directly from the Web without a sandbox, this approach has some potential. GitHub has many other potential uses for chemistry.

Substructure search is a fundamental cheminformatics operation. MX, the open source cheminformatics toolkit, contains an implementation based on the VF monomorphism algorithm. How fast is it? Let’s compare it to CDK’s UniversalIsomorphismTester. The full report is available here. The full source code can be found on GitHub. This test reads the molecules contained in a 416-record SD file into memory during setup.

Benchmarking can be a useful first step in optimizing the performance of software. Recently a group of developers including myself began creating an open suite of benchmarks for cheminformatics. Currently, two open source cheminformatics toolkits are included: MX and CDK. Ring perception is the foundation of many cheminformatics algorithms, so performance is an important issue. How do MX and CDK compare?

The previous article in this series discussed Japex in the context of creating open cheminformatics benchmarks. If you’re not familiar with it, Japex is a microbenchmarking framework written in Java that does for benchmarking what Ant does for building projects. Among its many interesting features is the ability to generate bar charts for performance comparisions.

A chemical registration system forms the core of most database-driven cheminformatics applications. Yet detailed instructions, in the traditional literature or otherwise, on how to create one from free components are surprisingly rare.

Recently, Egon Willighagen announced a project to develop an open benchmark suite for cheminformatics. Currently Egon, Rajarshi Guha, and myself have each created forks of the project on GitHub. After a brief period of quiet, things have started moving with incorporation of the Japex benchmarking framework. If you’re not familiar with Japex, it does for benchmarking what Ant does for building.

My company is developing a commercial cheminformatics Web application with Ruby on Rails. Due to the nature of the problem domain, this application will require interaction with MX, an essential cheminformatics library written in Java. This article will first explain how and why Merb entered the picture and then explain how to get Merb installed on a clean JRuby-1.1.6 installation.

The latest release of MX now supports exhaustive ring perception. Both a platform-independent jarfile and source distribution can be downloaded. Background The ability to perceive all rings in a chemical structure is essential for a number of important cheminformatics capabilities including Structure Diagram Generation, aromaticity detection, and binary fingerprint generation.