Jason S. Iacovoni (INSERM U858, Toulouse)

GeneHuggers is the name attributed to a set of development frameworks for bioinformatics. In the beginning, GeneHuggers consisted of a C API to develop command line programs that glued together various text formats so that DNA microarray data could drive database annotation searches and genomic sequence analysis programs. Presently, GeneHuggers represents two distinct projects, one for linux servers and the other for portable Java Swing clients. Server side GeneHuggers has matured into a fully functional set of C++ templates and classes that permit rapid development of command line and cgi applications that manage databases and wrap the execution of various Linux bioinformatic packages.
GeneHuggers is also being extended to include a Java client framework that aids in the development of graphical user interfaces that interact with an apache web server to aid biologists in performing tasks previously limited to the command line or web interfaces. Again, the functional concept of glue is ever present and the GUI enables the client to serially transform data through various stages without switching programs or copy/paste. Through the development of three disparate applications in Java, a set of packages is emerging that contain generic, reusable classes. The long term goal is to create a framework that can be used to build GUI modules that plug into a JDesktopPane GHLauncher application. By releasing GeneHuggers to a community development process at this early stage, it is envisioned that the Launcher and Module components can be designed to be extensible for a wide variety of bioinformatic applications.