JavaEE for breakfast: start off on the right foot developing biological Web applications.

Abstract

Bioinformaticians may be intimidated by the apparent complexity of programming languages such as Java and stick to efficient but less suited languages for building rich applications and web sites. Nevertheless, with Java Enterprise Edition (EE), the part of programming is drastically reduced and many tools and frameworks allow for building professional applications rapidly. Indeed in order to access local or remote data, to extend existing software or build user friendly, and good looking, web interfaces, most of the pieces are already provided. The developer can assemble and finalise the applications with his/her own business classes, focusing on the biological concepts. Here we present an overview of some useful and easy to use tools and frameworks based on Java programming, and provide as an example a simple web interface to browse annotations associated with cancer samples provided by the Cancer Genome Atlas (TCGA).