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CML Today

© Adam Hughes

Over the last few weeks, we've spent some time looking at XML, the Extensible Markup Language, and one of its specific descendants, CML, the Chemical Markup Language. Last week, we saw that the original CML specifications laid out an ambitious set of standards and proposed applications for the new markup language when they were released in the mid-1990's. The obvious next step is to see how things have panned out for this project in the intervening years, and that's exactly what we're going to do this time around.

A visit to the CML web page at http://www.xml-cml.org will quickly reveal that there have been some major advances made on this project. Accessible from this page are several recent technical papers pertaining to CML, CML documentation, the complete CML DTD, and various useful XML links. For the purpose of this discussion, however, its the "CML Software" section that holds the real goodies.

The programs shown on the software page include molecular display packages and a tool for marking PDB files with CML tags, both undoubtedly important utilities. However, one piece of software, looming above the rest, catches your eye as soon as your browser loads the page : JUMBO, the CML browser. Given the prominence of the browser utility in the CML specifications published in 1995, indications are that this software is aptly named.

With the introduction of JUMBO, it is clear that CML is intended to be a technology of the future. The JUMBO CML browser is written purely in Java, which means that it will be available to users of nearly any computer platform imaginable, thanks to the "compile once, run anywhere" nature of Java. What's more, JUMBO was written with generality in mind, and so is able to demonstrate XML documents as well as those composed in CML.

As far as learning about the "meat" of the JUMBO CML browser, the documentation on the web site is pretty scarce. It might be helpful to browse through the "Screenshots from a JUMBO-CML demonstration" to get some idea of the capabilities of this software. At any rate, it appears that the browser is powerful enough to display the various structures from a CML document and render pictures of molecules embedded in the paper of interest. If you're really interested in what JUMBO can do, you can download it and examples from the web site.

Next time around, we'll wrap up our CML discussion with a brief survey of the other advances made in this area in the last few years.

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