liulab-mbio

Molecular biology design and analysis tools for DNA sequences, enzymes, primers and cloning.

Set it up

This repo uses pixi and nothing else — no pip, no conda, no uv. Clone it, then:

pixi install

Use it

Plan a Golden Gate cloning job from a vector file and an insert file:

pixi run mbio cloning goldengate plan vector.dna insert.dna --out plan/

Four files land in plan/. product.dna is the assembled plasmid, with its features and primers marked. primers.tsv is the oligos to order. protocol.json is the protocol written as data. protocol.html is the page made from that data, one page you can follow at the bench: reagents, reaction tables, programs, expected bands and troubleshooting.

If you edit protocol.json, turn it back into a page:

pixi run mbio protocol render plan/protocol.json

The same thing from Python:

from mbio.cloning.goldengate import plan_assembly

plan = plan_assembly("vector.dna", "insert.dna")
plan.write("plan/")

Sequence files are read into one shared model, whatever their format:

from mbio.io import read_record

record = read_record("vector.dna")

One wheel, two import packages. mbio is the general toolkit above; synbio holds the lab's own named methods and has its own command, so a barcoded combinatorial library is planned with pixi run synbio igga plan.

A primer pair can also be checked against a whole genome, so you learn where else it would amplify before you order it: check primers on a genome.

The docs have a worked example: GFP into pUC19, with the protocol it writes.

Check your work

pixi run check

That runs the linters, the type checker and the tests. It reports every failure at once, so read to the bottom before you fix anything.

Read the docs

The site is at https://liuhlab.github.io/liulab-mbio/. Build it yourself with pixi run docs-build.

Set up your agent

Skills for coding agents live in skills/. Link them into each agent's own folder:

python skills/install.py --target all

If you work on the lab's clusters, add the shared plugin once per machine:

/plugin marketplace add liuhlab/liulab-compute-skills
/plugin install lab-compute@liulab