If you want to do the kind of cheminformatics that involves manipulating atoms, bonds, and molecules, object-oriented programming works well as a development paradigm. Although perhaps not readily apparent, JavaScript offers everything needed to create object-oriented models just as intricate at those written in languages like C++ and Java. This article discusses one approach that makes use of the Prototype Framework.

[Flash Content Scrubbed] Previous articles have discussed the use of Adobe Flash for cheminformatics. Tetsuya Hoshi has created a 3D structure viewer (embedded above) called Chemul that can be used with the Flash Player and which is written in ActionScript 3.0. Although the documentation is written in Japanese, it appears that Chemul supports multiple display options, as evidenced here.

Previous articles have discussed ways to display chemical structures in a variety of vector graphics formats, including Scalable Vector Graphics (SVG), Vector Markup Language (VML), and Shockwave Flash (SWF, or “Flash”). There is one other vector graphics format still in common use that has so far not been discussed: Encapsulated PostScript (EPS). EPS is a vector graphics format developed by Adobe Systems specifically for desktop publishing.

Indiana University will host a workshop titled “eScience for Cheminformatics and Drug Discovery 2008.” Among the topics to be covered is “grand challenges in cheminformatics.” From Wikipedia, a “grand challenge” is “a fundamental problem in science or engineering, with broad applications, whose solution would be enabled by the application of high performance computing resources that could become available in the near future.” The term has also

I just received the Chemical Information Bulletin for the Fall ACS, a meeting I unfortunately won’t be at. There are quite a few talks that sound good. Here’s a list of eight of them: CINF 5. The rise and fall of British Chemical Abstracts. Helen Cooke, GSK.

The previous article in this series introduced WebSpex, a spectroscopic data visualization tool being designed especially for use in a Web browser. Previously, the platform on which the user interface would be built was discussed. This article will discuss the question of where to put the spectroscopy data that WebSpex will display.

The Chemical Abstracts Service (CAS) registry number system was designed to be fault-tolerant. Built into every CAS number is a check-digit that makes it possible to detect mis-typed numbers. Validation is a mathematical and repetitive process well-suited for software. The Ruby program below validates arbitrary CAS numbers: module CAS def validate cas_number return false unless cas_number &&

Vector Markup Language (VML, not to be confused with VRML) is the XML-based vector graphics system that has been present in Internet Explorer for the last eight years. Although not as widely-documented or well-known as its younger cousin, SVG, VML is a capable system with all of the features needed to create dynamic images on the Web client. Nothing beats an example for discussing technologies.