Instant JChem - An Integrated Environment for Scientists, Built on NetBeans

August 2007

When Chemaxon, a Budapest-based chemical software development firm, set out to create Instant JChem, an out-of-box application that would let scientists work easily with chemical structures, the NetBeans Platform was an undisputed choice for the development team of Tim Dudgeon and Petr Hamernik.

"We used NetBeans because it is an extensible modular application built on Java," Dudgeon said in a recent interview. "The window management side of things: the way you can put together parts of the application and get all the benefits of the windowing system; the APIs and building wizards with them—these were all very important to us."

While selecting a tool that addressed and satisfied many of the project's parameters was a given, there was also past experience to consider.

Dudgeon, a scientist and developer, and the founder of Informatics Matters, a software solutions and consultancy firm, has used the NetBeans Platform for previous projects for other companies. Hamernik was one of the original creators of NetBeans, and has also worked with Dudgeon on custom applications built on NetBeans.

In defense of what might appear to be a development tool bias, Hamernik, who is now an independent developer, pointed out that the team's choice was not based solely on personal preference but on which platform had the easiest framework to work with.

"Eclipse has its own native widgets, UI and visual components, which were difficult to manipulate," Hamernik asserted. "NetBeans is Java-based and has a straight-forward framework that  was very helpful in creating a Swing-heavy application like Instant JChem."

Instant JChem Schema Editor Instant JChem Form View
(Click on images for larger view.)

Instant JChem belongs to a class of chemistry applications that function much like IDEs for those working in the pharmaceutical and bio-tech industries. But instead of code, these applications handle chemical and biological data.

A desktop software that houses the functionality of other Chemaxon tools, Instant JChem allows chemists and biologists to create, manage and analyze hundreds of thousands of chemical structures in a database-conducive environment. It is also a platform on which other chemistry applications can be built.

"Representing scientific data as searchable data is quite complex and different than when dealing with numeric data," Dudgeon explained. "One problem with some of the powerful tools out there is that you need to have some background to use them, and tools that are simpler to work with lack power. [Scientists] want a powerful yet easy-to-use application that lets them sketch structures and run queries efficiently while insulating them from the complexities of how."

With Instant JChem, users can easily create, connect and share local databases, and also connect to external ones. Structure files can be imported, exported and merged, their data tabulated, sorted and queried. There is support for 2D and 3D structure display, and relational data. Users can build or apply their own chemical business rules; the tool also allows for third-party functionality to be integrated.

In the past, drug research and life science companies often built their own database tools or hired firms like Chemaxon to build them, while the average scientist had to pay thousands of dollars for such software on the market. Instant JChem offers a solution for both groups, a ready-made application that's easy to install and that runs out of the box. The database tool is free for individual and academic use; however, accessing external database engines requires a license key that can be purchased from Chemaxon. Chemistry plugins are also available.

Hamernik and Dudgeon said they worked with the NetBeans Platform 5.5 and later, milestones of 6.0 with minimal problems. They even used what Dudgeon termed a "NetBeans approach" by rolling out milestone releases of Instant JChem. The response to Instant JChem at user group meetings, from scientists, and other companies, they said, have been positive. The team plans to release Instant JChem 2.0 in late August 2007. The release will include improvements to relational data support, multi-user access and a form design similar to NetBeans's GUI builder. There has also been a major rewrite of the architecture.

Chemaxon's marketing director Allan Allardyce expressed excitement about the upcoming release.

"Instant JChem could move the field of cheminformatics," he said. (Cheminformatics deals with the representation and use of chemical structures and related information on computer.)  "It's a very cool and modern-looking tool with search capabilities to draw and perceive chemical structures at the very highest level. It's great for someone who doesn't want to spend money on software to explore chemical information. Yet, it is also a state-of-the-art application for the biotechnology and pharmaceutical industry."

Watch a Screencast of Instant JChem

Additional Demos: Working with Instant JChem

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