Imdbfs: Bridging The Gap Between In-Memory Database Technology And File-Based Tools For Life Sciences

Many established processing and analysis tools in life sciences are still operating on files, e.g. alignment of genome data. Their integration into optimized workftows requires time-consuming transformation, import and export of data.In the given contribution, we introduce IMDBfs: a shared file system operating on top of an in-memory database system. Our IMDBfs provides transparent access to database resources via traditional file system operations. For the first time, it allows seamless integration of file-based life science tools into processes optimized for latest IMDB technology. As a result, existing tools neither need to be ported nor modified whilst transparent IMDB data access is provided.