borzoi

name	borzoi
description	Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. Use this skill when: (1) Scoring the regulatory effect of a variant on expression/accessibility, (2) Generating predicted coverage tracks for a locus, (3) Prioritising non-coding variants by predicted track delta.
license	Apache-2.0
category	biomodels
requirements	["gpu"]
metadata	{"third_party":[{"kind":"weights","name":"Borzoi (PyTorch port)","provider":"Calico Life Sciences","license":"CC-BY-4.0","info_url":"https://huggingface.co/johahi/borzoi-replicate-0"}]}

Borzoi — DNA → Functional Track Prediction

Prerequisites

Requirement	Minimum	Recommended
Python	3.10+	3.11
CUDA	12.1+	12.4+
GPU VRAM	16 GB	24 GB+

How to run

from borzoi_pytorch import Borzoi

model = Borzoi.from_pretrained("johahi/borzoi-replicate-0").cuda().eval()
# input: (batch, 4, 524288) one-hot DNA  → output: (batch, tracks, 6144) bins

Borzoi consumes ~524 kb one-hot windows and emits binned predictions across 7,611 human tracks (the separate 2,608-track mouse head is off by default; enable via enable_mouse_head=True and select with forward(..., is_human=False)). For variant scoring, run ref/alt windows centred on the variant and compare per-track output.

Output format

(B, T, L) tensor — T tracks × L 32-bp bins. Track metadata (assay, biosample) is in borzoi_pytorch.pytorch_borzoi_model.TRACKS_DF (or model.tracks_df when using the AnnotatedBorzoi subclass) — the base Borzoi model has no targets attribute.

Remote compute

Needs ≥24 GB VRAM and either pre-cached HF weights or egress to huggingface.co. Read compute_details({provider, mode:'read'}) for an environment with borzoi-pytorch, then:

c = host.compute.create(provider)
job = c.submitJob(
    intent="Borzoi track prediction for 1 locus — 1×GPU, ~2 min",
    inputs=[{"src": "borzoi_run.py", "dstFilename": "borzoi_run.py"}],
    command="python3 borzoi_run.py",   # env selection is host-specific — see compute_details for your provider
    outputs=["tracks.npz"],
    timeoutSeconds=1800,
)
print(job.job_id)   # cell ends here — kernel never blocks on compute

Then call the wait_for_notification brain-tool. When the compute_done notification arrives, act on its payload:

save_artifacts(payload["featured_files"])   # paths under hpc/<job_id>/

For the full result dict (output_files, remote_workdir, …), re-enter the kernel: c.attachJob(job_id).result() then c.close(). See the remote-compute-ssh / remote-compute-modal skill for the orchestration details.

If the provider exposes a weight-cache mount, point HF_HOME at it inside borzoi_run.py (path is in compute_details).

Troubleshooting

Symptom	Cause	Fix
module has no __version__	Package exposes no attr	Use importlib.metadata.version("borzoi-pytorch")
Shape mismatch on input	Wrong window length	Pad/crop to 524288 bp (fixed; not exposed as a model attribute)

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Next: combine track deltas with evo2 likelihood deltas for a two-axis variant prioritisation.