Bio-jETI is largely based on the jETI, jABC and PROPHETS software, hence a major part of its documentation is available from the respective project web sites. Links are given below. The example projects that are provided in the Download section are equipped with further, project-specific documentation.
The user manual of the jABC (the user interface of Bio-jETI) provides general information on how to use the software for the development of workflows.
The PROPHETS homepage explains the loose programming approach to (semi-) automatic workflow composition and provides documentation for the PROPHETS plugin.