Cloudgene is an open-source platform to improve the usability of MapReduce programs by providing a graphical user interface for the execution, the import and export of data and the reproducibility of workflows on in-house and rented clusters, i.e. in the cloud. The aim of Cloudgene is to build a standardized graphical execution environment for currently available and future MapReduce programs, which can all be integrated by using its plug-in interface.