One of the difficult issues when working with software is that technology continuously changes. This is even more true in the mobile era. In chemical visualization, we have seen several solutions over the last few decades, and a lot of them are very good. One, in particular, is Jmol, a Java application that is popularly deployed as an applet for molecular visualization and interaction in web sites and web applications. However, current trends are not favoring Java applets. First, no mobile devices support Java applications, and certainly Java applets will not run in mobile browsers. Secondly, we are seeing a increasing trend in hackers exploiting Java applet vulnerabilities. The recent problems on Mac OS X with the Flashback virus is a key example. To combat the virus, a recent Mac OS X update actually disabled all Java applets (which can then be reenabled by the user in Java Preferences, but will also disable them again after a certain amount of time has passed). Combined with poor performance of some applet solutions across desktop platforms, it is clear that developers need to reduce their dependence on Java applets.

The best solution for web based visualization and interaction is HTML5, where performance is very good, loading is instantaneous, and security issues are handled by the browser. The ChemDoodle Web Components library provides many visualization and interactive tools for creating immersive HTML5 based scientific applications. We have been working with Robert Hanson and the Jmol community to integrate the ChemDoodle Web Components into Jmol. Doing so allows Jmol developers to easily deploy their content to mobile users and to those that do not have Java enabled; this is in addition to their current user base. For platforms that support Java, the Jmol applet will be used. If Java is not present or enabled, and WebGL is available, then a 3D ChemDoodle Web Component will be used. If Java and WebGL are unavailable, then a 2D ChemDoodle Web Component will provide an interactive component. Of course, the 2D component is only a temporary solution while WebGL support broadens to include all mobile devices. As development continues, we will further match the entire capabilities of the Jmol application, including a Jmol script interface to the ChemDoodle Web Components. Using this strategy, developers can deploy their content once, and reach users across desktop, web and mobile platforms, supporting the greatest range of current technologies. Robert Hanson and the Jmol community are hard at work rebuilding the Jmol applet Javascript library using the ChemDoodle Web Components and its patterns. It will be the way to deploy the applet moving forward.

Concerning licensing, the Jmol source is under LGPL license, while the ChemDoodle Web Components are distributed under a GPL v3 license with liberal HTML exception. Most academic and open source projects will not have any issues and should feel free to use Jmol/ChemDoodle in those projects. If you feel that the GPL license does not allow you to use Jmol’s mobile features (for instance, proprietary commercial use), feel free to contact us, we are happy to provide you with alternate licensing.

The integration of the ChemDoodle Web Components into Jmol is a great example of how we can create scientific applications that can work with evolving technologies, while retaining compatibility with current user bases. HTML5 tools are becoming very popular, and we have several components in the ChemDoodle Web Components library to suit your products needs, from a chemical sketcher, to spectra rendering, to 3D graphics and interaction across desktop and mobile devices. Update your product today and expand your market into the mobile arena!

Here are a few demo pages: