Update June 10, 2009 : The information in this article, while accurate, has been superseded by Applet-Fu, a small JavaScript library that simplifies the use of the applet deploy technique described here. A 2006 survey on java.net posed a simple question to developers: What’s wrong with applets?

Of the many problems to be solved when building software to view and manipulate 2D chemical structures, one of the trickiest is getting all features to scale proportionally. This problem is widespread because it can seldom be predicted at which resolution a chemical structure will be viewed. This article describes some ways in which this problem was addressed in the Web-based chemical structure editor ChemWriter.

Two-dimensional chemical structure diagrams are part of a language with both grammar and aesthetics. Both aspects play a role in determining scientific usability, and both deserve careful consideration when designing cheminformatics systems. This article, the first of a series, will discuss one aspect of 2D chemical structure diagrams that is only sparsely documented and yet instantly recognizable when done wrong: the layout of double bonds.

Derek Lowe’s In the Pipeline hosts an interesting discussion on Electronic Laboratory Notebooks (ELNs). The wasteful process of entombing valuable scientific data often begins with the paper lab notebook, so the subject of ELNs should be of great interest to anyone involved in creating, using, or reprocessing chemical information. Why do paper notebooks continue to persist in chemistry?

Countless chemical structures exist only in a raster image format such as JPG, GIF, BMP, or on a printed page or PDF. While perfectly readable to humans, they are very difficult for machines to read. Given the sheer number of these structures that have been produced over the last few decades, the only hope of excavating them from their current data tombs is with computer recognition of some kind.

ChemWriter is a 2D chemical structure editor for the Web. Because it’s written in Java and uses both the Swing and Java2D APIs, ChemWriter could be plugged into a variety of chemically-enabled user interfaces deployed within a browser, on the desktop, or in other contexts. The availability of this kind of developer tool would open the door to a large new area of interactive cheminformatics applications.