borzoi

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.

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Repository: aipoch/open-science
Last source activity: August 11, 2026 at 16:51
Detected SKILL.md language: English
Stars: 3,699
Forks: 235

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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

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

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)

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"}]}

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

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"}]}

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

borzoi

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Borzoi — DNA → Functional Track Prediction

Prerequisites

Borzoi — DNA → Functional Track Prediction

Prerequisites

How to run

Output format

Remote compute

Troubleshooting

borzoi

Source facts

Install options

Review the source files

More from this repository

More from this repository

Borzoi — DNA → Functional Track Prediction

Prerequisites

Borzoi — DNA → Functional Track Prediction

Prerequisites

How to run

Output format

Remote compute

Troubleshooting