Jemboss is a java-based EMBOSS interface developed by Tim Carver and other EMBOSS developers. It works with a local EMBOSS installation or one installed on a remote server where both local or remote files may be used. Applications may be run interactively or as batch processes. Sensible default values are provided on-the-fly for a given sequence or input parameter. A project manager maintains the details of each run and the input and output files used, allowing experiments to be easily managed and annotated. This in-depth hands-on tutorial covers how to get started, file management, data analysis, saving and retrieving results, customisation, documentation and troubleshooting.