What is a biobox?

Software has proliferated in bioinformatics and so have the problems associated with it: missing or unobtainable code, difficult to install dependencies, unreproducible workflows, all with terrible user experiences. We have created bioboxes with the aim to make accessing and using bioinformatics software more simple and more easy.

A biobox is a Docker image where the input files, input parameters, and output files are specified so that every biobox of the same type has the same interface. The Docker platform, which bioboxes uses, makes it much simpler for developers to share their their bioinformatics tools. The bioboxes' standardised interface then makes swapping one tool for another much simpler because they have indentical interfaces.

An example biobox type is a short-read assembler. The interface for these image accepts an input paired-FASTQ file and returns a contig FASTA file. Each developer creating a biobox should make sure the container accepts these inputs and returns the expected outputs. A list of biobox images shows which short read assembler containers are currently available.

We believe a community standard, using software containers, has the opportunity to solve the current software usability problems and increase the standard of scientific software as a whole. A standard for bioinformatics containers will move us towards a more open environment for anyone to innovate, collaborate and share their scientific software. Working in a truly standardized and interoperable ecosystem, will allow bioinformatics algorithmic developments to become useful to everyone.