An SQL based Filesystem for Bioinformatics

In many applications of bioinformatics, the data are kept in extremely small files, but since the datasets are very large the number of files becomes huge. This approach means that the filesystem becomes extremely stressed and slow. The proposal is to move the data to a SQL database, which is fairly easy, but since the tools that the community use are based on the filesystem approach, the solution must have a FUSE filesystem that interfaces with the database to provide a compatible interface.

Tags: scientific-programming:HPC

Activities: Analysis, design and implementation

Contact: Brian Vinter, vinter@nbi.ku.dk

Area: Project Bachelor Masters