kdense-biopython

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

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Repository: eightmm/codex-science
Last source activity: July 10, 2026 at 05:18
Detected SKILL.md language: English
Stars: 2
Forks: 0

Install options

The review-first prompt is selected by default. You can switch to a direct command or download a local copy.

Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.

A direct command skips the review prompt. Inspect the source before running it.

npx skills add https://github.com/eightmm/codex-science --skill kdense-biopython

The command stays on one line. Scroll horizontally to inspect it before copying.

Prefer a local copy? Download the files currently available to SkillsMP.

Review the source files

Read SKILL.md and any companion files shown by SkillsMP before deciding whether to install.

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SKILL.md

Source instructions · Read-only preview

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Kdense Biopython

Use this Codex adapter for the pinned upstream scientific skill.

Catalog status

Status: inactive

Source: kdense

Audit reasons: credentials-required

Upstream license: Biopython License Agreement

Inventory: ../../inventory.json

Upstream instructions: ../../../vendor/scientific-agent-skills/skills/biopython/SKILL.md

Procedure

Resolve the plugin root as three directories above this skill directory.

Read the matching inventory record and verify its status, reasons, source path, and pinned revision.

Do not read the upstream instructions until the user has seen every audit reason and given explicit acknowledgement. Acknowledgement permits instruction inspection only.

Treat upstream frontmatter as source metadata, not as Codex configuration. Follow the instruction body only where it is compatible with available Codex tools and the current user-approved plan.

Treat tools named for another agent runtime as capability requests. Map them to an available Codex tool only when the behavior is equivalent; otherwise report the unavailable capability.

Ask before credentials, package installation, new network hosts, remote compute, writes, paid services, destructive actions, or imported executable code.

Use $science-provenance for produced scientific outputs and $science-review before presenting scientific claims.

Boundaries

This wrapper does not grant credentials, network access, package installation, or script execution.

Do not change an inactive record to active from inside a research task.

Preserve failures, uncertainty, source identifiers, and licensing constraints.

name	kdense-biopython
description	Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.