Msa Search Nim — Agent Skill by NVIDIA

From the author

Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM. Use for homolog search, UniRef30/ColabFold env searches, A3M or FASTA alignments, paired MSA search for complexes, PDB70 structural templates, hosted NVIDIA API calls, or local Docker deployment. For local deployment, download the databases in parallel with aria2c and launch via NIM_MODEL_NAME (the recommended default fast path, ~14 min vs over 80 min for the built-in downloader); a plain docker run uses the slow built-in downloader.

— the description by NVIDIA

Install

Get the skill from its source (we cannot redistribute it):
https://github.com/NVIDIA/skills/tree/fce3cca4170be75e82c64920654d56ee2811b005/skills/bionemo-msa-search-nim

Documentation by NVIDIA

The licence of this skill does not allow us to copy its documentation. Read it at the source

Files

BENCHMARK.md(opens on GitHub)Not mirrored: opens on GitHub6.9 KiB
SKILL.md(opens on GitHub)Not mirrored: opens on GitHub17.8 KiB
config/skillspector-baseline.yml(opens on GitHub)Not mirrored: opens on GitHub2.0 KiB
evals/config.yml(opens on GitHub)Not mirrored: opens on GitHub117 B
evals/evals.json(opens on GitHub)Not mirrored: opens on GitHub7.2 KiB
evals/trigger_evals.json(opens on GitHub)Not mirrored: opens on GitHub2.2 KiB
references/api.md(opens on GitHub)Not mirrored: opens on GitHub6.3 KiB
references/examples.md(opens on GitHub)Not mirrored: opens on GitHub2.1 KiB
references/parameters.md(opens on GitHub)Not mirrored: opens on GitHub1.8 KiB
references/science.md(opens on GitHub)Not mirrored: opens on GitHub1.1 KiB
references/validation.md(opens on GitHub)Not mirrored: opens on GitHub2.0 KiB
scripts/hosted_search.py(opens on GitHub)ScriptNot mirrored: opens on GitHub7.8 KiB
skill-card.md(opens on GitHub)Not mirrored: opens on GitHub4.3 KiB
skill.oms.sig(opens on GitHub)Not mirrored: opens on GitHub6.8 KiB
tests/test_hosted_search.py(opens on GitHub)ScriptNot mirrored: opens on GitHub16.1 KiB

Requirements and compatibility

Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta

“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.

Needs: Declares allowed tools, Needs network access, Needs an API key, Needs a command-line tool, Needs Python, Needs Node.js

The author says: requests>=2.28

Security

What our scanner noticed· Medium risk

Large base64-encoded blobs
Instructions that use the network
Scripts that your agent may run

This skill includes scripts that your agent may run. Read them before you use it.

A static scan is not a guarantee. Skills are third-party content: review a skill before you let an agent use it.

Scvi Tools
K-Dense· Community
A toolkit for fitting probabilistic generative models to single-cell omics data, including RNA, ATAC, and multimodal integration.
Science and researchClaude CodeClaude appsOpenAI Codex+14 more
MITLow riskGitHub stars of the source repository56.4k
Onekgpd
K-Dense· Community
Query individual-level genotype data and variants from the 1000 Genomes Project cohort.
Science and researchClaude CodeClaude appsOpenAI Codex+14 more
MITLow riskHas scriptsGitHub stars of the source repository56.4k
Geniml
K-Dense· Community
A toolkit for managing local genomic interval workflows, including BED validation, consensus universe construction, and model planning.
Science and researchClaude CodeClaude appsOpenAI Codex+14 more
MITLow riskHas scriptsGitHub stars of the source repository56.4k
Latchbio Integration
K-Dense· Community
Develop, register, and operate bioinformatics workflows on the Latch platform using the Python SDK and CLI.
Science and researchClaude CodeClaude appsOpenAI Codex+14 more
MITLow riskHas scriptsGitHub stars of the source repository56.4k
Diffdock
K-Dense· Community
Perform protein-small-molecule docking and pose generation using the DiffDock and DiffDock-L models.
Science and researchClaude CodeClaude appsOpenAI Codex+14 more
MITLow riskHas scriptsGitHub stars of the source repository56.4k
Neuropixels Analysis
K-Dense· Community
End-to-end analysis pipeline for Neuropixels extracellular electrophysiology recordings using SpikeInterface.
Science and researchClaude CodeClaude appsOpenAI Codex+14 more
MITLow riskHas scriptsGitHub stars of the source repository56.4k