Saturday, December 08, 2007

JSpecView Article on Chemistry Central

Robert Lancashire has just published an article in Chemistry Central Journal:

The JSpecView Project: an Open Source Java viewer and converter for JCAMP-DX, and XML spectral data files

Our lab has found this software to be key for communicating organic chemistry results within an Open Notebook Science environment. All NMR raw data and metadata are automatically recorded and users from anywhere can mine the spectra by expanding and integrating at will from a browser interface. This is an enormous improvement over the traditional method of storing and publishing spectra as images that cannot be expanded.

The article describes other useful applications, such as the integration of JSpecView with Jmol, to show the assignment of specific peaks.

The other reason I really like this article is that Robert has used some UsefulChem blog posts as primary references. This is an important way for the scientific blogosphere to get incorporated and accepted by the mainstream.


Abstract

The JSpecView Open Source project began with the intention of providing both a teaching and research tool for the display of JCAMP-DX spectra. The development of the Java source code commenced under license in 2001 and was released as Open Source in March 2006. The scope was then broadened to take advantage of the XML initiative in Chemistry and routines to read and write AnIML and CMLspect documents were added. JSpecView has the ability to display the full range of JCAMP-DX formats and protocols and to display multiple spectra simultaneously. As an aid for the interpretation of spectra it was found useful to offer routines such that if any part of the spectral display is clicked, that region can be highlighted and the (x,y) coordinates returned. This is conveniently handled using calls from JavaScript and the feedback results can be used to initiate links to other applets like Jmol, to generate a peak table, or even to load audio clips providing helpful hints. Whilst the current user base is still small, there are a number of sites that already feature the applet. A tutorial video showing how to examine NMR spectra using JSpecView has appeared on YouTube and was formatted for replay on iPods and it has been incorporated into a chemistry search engine.


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