codonfm-embed SKILL.md skillA
This file is byte-identical to the first copy the registry indexed, one of 3 indexed copies. Same content hash, so the same checks give both the same grade.
codonfm-embed from nvidia-bionemo/bionemo-agent-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add nvidia-bionemo/bionemo-agent-toolkit/codonfm-embed@git:20261009.084a18cPins git:20261009.084a18c in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- nvidia-bionemo/bionemo-agent-toolkit
- Path
skills/bionemo-agent-toolkit/skills/codonfm-embed/SKILL.md- Versions recorded
- 1
- Latest version
- git:20261009.084a18c, committed Oct 9, 2026
- Size
- 9,557 bytes
- Repository stars
- 503
- License
- a license file GitHub does not identify
Validate coding-sequence CSVs, extract public CodonFM/Encodon embeddings, and choose checkpoints for downstream property modeling.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Extract public Encodon embeddings ## Purpose Extract one frozen CLS vector per coding sequence with public Encodon v1. Support input validation, command preparation, extraction, and checkpoint selection for translation efficiency, expression, or mRNA stability modeling. Extraction does not automatically train a downstream regressor. ## Prerequisites - Validation needs Python 3 standard library only; no GPU, weights, or API key. - Execution needs the public CodonFM checkout, its `requirements.txt` environment, a compatible NVIDIA GPU, and local checkpoint weights. A metadata JSON is not a checkpoint. A `.safetensors` file needs its sibling `config.json`; `.ckpt` checkpoints are also supported by the public loader. - Run `python -m src.runner` from the CodonFM repository root. In an isolated workspace, use supplied source artifacts; source paths below are relative to that checkout or source archive, not this skill directory. ## Inputs Input source precedence: explicit user prompt arguments, then supplied files/checkpoint metadata, then inspected public runner defaults. Resolve conflicting model names and checkpoint metadata before execution. Supplied 80M …
Read the whole file at its exact version.
How to install
mdr add nvidia-bionemo/bionemo-agent-toolkit/codonfm-embed@sha256:0d8d430a48a1f0c6The line at the top of this page pins the label git:20261009.084a18c, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_hckt5fgetvjr3qrt)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Oct 9, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (9557 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
nvidia-bionemo/bionemo-agent-toolkit · 503 stars · license a license file GitHub does not identify · pushed 2026-11-05 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_hckt5fgetvjr3qrt GET https://markdownregistry.com/api/v1/resolve?ref=nvidia-bionemo/bionemo-agent-toolkit/codonfm-embed GET https://markdownregistry.com/api/v1/blob/0d8d430a48a1f0c63325b06e05d3dd6c948063d6625df65100d0c162f39a24a7
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
More from nvidia-bionemo/bionemo-agent-toolkit
Every file in nvidia-bionemo/bionemo-agent-toolkit