Two commands¶

One install gives you two commands.

Command	What it does
`mbio`	the toolkit: cloning, primers, barcodes, codon choice, plasmid maps, bench protocols
`synbio`	the methods this lab works by, built from that toolkit

Type mbio for a job with a standard name — Golden Gate, Gibson, restriction and ligation, Gateway, a primer pair, a map. Type synbio for a method this lab named: iGGA, which builds a library, and DMX, which reads one back.

pixi run mbio cloning goldengate plan vector.dna insert.dna --out plan/
pixi run synbio igga plan project.json --out library/
pixi run synbio dmx plan build.json --out readback/

Every command on this site starts with one of the two, so you never have to work out which. From Python the names match:

from mbio.cloning.goldengate import plan_assembly
from synbio.igga import plan_igga
from synbio.dmx import plan_dmx

Both come from the one install, liulab-mbio, and share its version number.

Writing code for either one¶

Code that another method could use as it stands belongs in mbio. Code that holds one method's own choices belongs in synbio. CLAUDE.md in the repo gives the test and worked cases.