Bioboxes Demo at UC Davis

Michael Barton, JGI sequencing QA/QC group



Suggests reading Malcom McLean (The Box), who implemented idea for standardized cargo containers. All you have to do is load standard container from factory, fit onto truck, cargo ships, and trains. Then unload. Created containerized globalization. Similar concept to standardized containers for software, biobox:

Biobox f:fastq-> assembly

Categorize Docker containers by their inputs and outputs, reads -> assembler -> output assembly, pass data

Problem is really social, need suggestions for improvements from community. Most agree that standards benefit everyone involved. We’re members of the community. Example that we all have a collection of adapters for peripheral hardware, e.g. display and printers, keyboards, etc. At some point, it’s good to have standard adapters, e.g. USB (not going to mention Mac thunder port)

Pass parameters to biobox, e.g. insert size

Develop a machine to make machines (tools to make tools), simliar to software tools – standardized way to develop

Testing! Examples of tests to see whether they pass: Invalid format, missing vresion numer, invalid version number, issing arguments, unknown additional field, create contigs file, given valid input files, metadata mounted

pip install --user biobox_cli

biobox run

short_read_assembler \ bioboxes/velvet \ --input reads.fq.gz \ --output contigs.fa

Tutorial, run through neat examples:

How to make a biobox? See workshop hackpad:

Demo repository:


About Lisa Cohen

PhD student at UC Davis.
This entry was posted in Bioinformatics, workshops. Bookmark the permalink.

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