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

Authors

  • Arnaud Ceol Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT)
  • Heiko Muller Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT)

DOI:

https://doi.org/10.14806/ej.19.B.734

Keywords:

biological web application, java EE

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).

Author Biographies

  • Arnaud Ceol, Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT)
    Computational Research
  • Heiko Muller, Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT)
    Computational Research

Downloads

Published

2013-10-14

Issue

Vol. 19: Supplement B

Section

Posters

License

Authors who publish with this journal agree to the following terms:
  1. Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
  2. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
  3. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).