borzoi skill | PlugMCP

borzoi

by aipoch5.0k

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Download skill resources/skills/borzoi/SKILL.md on GitHub

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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:

SKILL.md loads `johahi/borzoi-replicate-0` — a PyTorch port of Calico's

Borzoi ("ported weights (with permission)"). The HuggingFace model card

for that exact artifact states `License: cc-by-4.0`. Calico's CODE repo is

Apache-2.0, but the weights the skill downloads carry CC-BY-4.0. The model

card is where the license is declared (info_url — not a ToU page).

verified 2026-06-30

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+

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

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

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)

borzoi

Install

Related skills

SKILL.md loads `johahi/borzoi-replicate-0` — a PyTorch port of Calico's

Borzoi ("ported weights (with permission)"). The HuggingFace model card

for that exact artifact states `License: cc-by-4.0`. Calico's CODE repo is

Apache-2.0, but the weights the skill downloads carry CC-BY-4.0. The model

card is where the license is declared (info_url — not a ToU page).

verified 2026-06-30

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

How to run

Output format

Remote compute

Troubleshooting

Install

Related skills

SKILL.md loads johahi/borzoi-replicate-0 — a PyTorch port of Calico's

Borzoi ("ported weights (with permission)"). The HuggingFace model card

for that exact artifact states License: cc-by-4.0. Calico's CODE repo is

Apache-2.0, but the weights the skill downloads carry CC-BY-4.0. The model

card is where the license is declared (info_url — not a ToU page).

verified 2026-06-30

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

How to run

Output format

Remote compute

Troubleshooting

SKILL.md loads `johahi/borzoi-replicate-0` — a PyTorch port of Calico's

for that exact artifact states `License: cc-by-4.0`. Calico's CODE repo is