UWI Team Writes Winning Software

Two University of the West Indies departments at Mona have received US$50,000 for licensing a software package to a United States software manufacturer. The money is the first installment in a contract worth US$115,000 over five years for a programme called the JCAMP-DX viewer. It is licensed to MDL Information Systems Inc. of California from the Departments of Chemistry and Mathematics and Computer Science.
JCAMP-DX was developed by Dr Robert Lancashire (Chemistry) and Mr. Chris
Muir and Professor Han Reichgelt (Mathematics and Computer Science) using a grant from the IDB under the UWI/IDB Development Programme. JCAMP-DX stands for Joint Committee of Atomic and Molecular Physical Data Exchange.

The software is expected to be used for teaching and research in chemistry. Chemists use a number of different spectroscopic techniques to determine the chemical structure of unknown compounds. These include, irradiating the samples with ultra-violet, visible, infrared light or radio frequencies and observing changes. But instrument makers have each developed their own proprietary data formats for storing results. So it was often difficult or impossible to convert data from one instrument to the other.

The International Union of Pure and Applied Chemistry was unhappy with this state of affairs. It set up a committee to look into problems of data translation and compatibility. The Union wanted a format it could place in the public domain. The aim was to get an arrangement where everyone would have a mechanism for translating that everyone could read. Because it would not be owned by anyone, it would be free for use in the market.

The UWI team first started writing software to aid in teaching for spectroscopy. One of the things they looked at was how to show and display the spectrum. Through the web network, some people mentioned to MDL that here were some guys in the Caribbean working on a plug -in that might interest the company. Eventually he contacted MDL and asked if the company was interested.

MDL had a programme that could show molecular graphics and the UWI team had a programme that could show spectra. They wanted to combine both, to be able to have a picture of a molecule up on the screen and the spectrum on the screen and have the possibility of being able to click and highlight areas in the spectrum to see which part of the molecule gave rise to which feature in the spectrum.

In December 1996, Chris Muir went to MDL to investigate how easy or difficult it was going to be to merge the two programs. As it happened, both groups were using identical platforms and code and programming languages and the merger turned out to be relatively painless.

Dr. Lancashire had initially put out test versions of the code on the Chemistry Department's web site so those interested could download, test and give feedback. Chemistry scientists and students quickly recognised that it was a robust code. "They could throw a lot at it," said Dr. Lancashire.

The program enables a browser to take data directly from a scientific instrument and display it on a monitor. Being able to take data from two different instruments and compare them is a major breakthrough for scientists who use the Internet.

In the same way that there are plug-ins for showing quick time movies, the software is now a plug-in, and when the browser sees a file on a web site that it recognises as a Jcamp file, it loads the data into the plug-in and views the file in the browser.
"The beauty of the technique," says Dr. Lancashire, "is that it is just like net documents (HTML) where you can click to other documents and have pictures and download them as one file and the document as a separate file and display them."

For years, MDL had a plug-in on the net that allowed users to show molecular structures. Rather than send a static bit map picture on the net, users can put in the coordinates, send them over the net and the plug-in at the other end will recognise the coordinates. The data will then go to the plug-in and the user will see the molecule that he or she can rotate.

Webmaster Extraordinaire

Dr. Robert Lancashire is the primary builder of UWI's Chemistry Department's web site, where the software that is now on the world market was first tested. An extensive site, it features the usual course work and laboratory data. But it distinguishes itself in the large volume of data it has on local materials such as spices, coffee, bauxite and fruits and vegetables.

The Melbourne, Australian native who came to Jamaican to teach in 1979, has put the site together almost singlehandedly. The site has received several awards, including "Chemistry on the Infobahn" American Chemical Society meeting in Sept 1995, ChemWeb pick of the day for 21st Nov 1997 and HMS Beagle pick of the day for 25th Feb 1998.

Dr. Lancashire began working on the software nearly ten years ago when the Chemistry Department bought an infrared spectrometer just after Gilbert as part of replacements for machines that were damaged. Money was tight, so the department had to buy a scaled down ("El Cheapo" Dr. Lancashire calls it) version of the instrument for reading the spectrum that had no data drive or keyboard or any peripheral.

Essentially, Dr. Lancashire and his colleagues had an instrument that could record the spectrum, display it on their screen, but did not have a mechanism for storage. When it was turned off the data was gone. Dr. Lancashire wrote a program to collect the data through the serial connection to a personal computer. Then he wrote a second programme to display the spectrum.

Since then, Dr. Lancashire has begged, built and borrowed the hardware and software he has needed to build his impressive site. During all of that, he found time to create and develop a piece of software that students and chemists will enjoy for the life of the net in millenniums to come.