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.

Wouldn’t it be great to be able to cross-compile your Java cheminformatics source code to plain old JavaScript files to be used in your Web applications without plugins? JavaScript is the most widely-deployed runtime environment in existence; on today’s Web it’s one of the few things you can count on being there. Java is one of the most advanced programming languages in existence, with a mountain of developer tools and libraries.

An interesting discussion is taking place on the LinkedIn Electronic Laboratory Notebook (ELN) Forum regarding the maturity of the ELN market. Andrew Lemon of The Edge Software Consultancy starts off: Here’s the response I posted: Interesting discussion. The importance of the “Who’s winning?” question might have something to do with how you view ELN software.

From Nature News comes this announcement: It’s unclear how this new initiative will work in practice. The only thing the RNA Biology site has to say on the subject is to offer a link back to the Nature News article. This is a trend to watch very closely. A journal article is dead the moment it’s published, but a Wikipedia article is a living, breathing document that can adapt as information and interpretations change.

Ring perception in chemical structures is essential for a number higher-level cheminformatics operations such as Structure Diagram Generation and aromaticity perception. Several ring perception algorithms have been developed over the last few decades, but many return only a subset of rings. Others are difficult to implement or perform badly.

MDL Structure Data Files (SD Files) are the de facto standard for the exchange of chemical structures and associated data. As a result, methods for efficiently reading and writing these files play an important part in any cheminformatics toolkit. The latest release of MX, the open source cheminformatics toolkit, adds support for reading and writing SD Files. Both source and platform-independent binary distributions are available.

Recently, Duan Lian raised the very interesting possibility of using the Google Web Toolkit to cross-compile Java to JavaScript rather than bytecode. I suggested that MX, the lightweight cheminformatics toolkit, might be a good target due its small size, modular design, and lack of external dependencies.

InChI, useful as it may be, has some important limitations. One of the biggest relates to portability. The InChI source code is written in C, meaning that developers in other languages need to jump through hoops of varying degrees of difficulty to get InChI to work with their development platform of choice.

A few months ago I wrote about some ways that JavaScript could be used for cheminformatics. Although at the time I was considering mainly cheminformatics tools build from scratch with JavaScript, there is another possibility. Today, Duan Lian posted this intriguing comment: If you’ve never heard of Google Web Toolkit, it’s a compiler for Java that instead of generating bytecode generates Javascript.

Calculating molecular mass is an important capability in cheminformatics. Performing the calculation itself is trivial, but determining what the masses will be used can be tricky. Ideally, each measurement in a system of atomic masses and isotopic distributions would be traceable to the primary literature.