Agent skill

Biopython Advanced

by aipoch in aipoch/medical-research-skills

Install Biopython Advanced

skills CLI

$ npx skills add aipoch/medical-research-skills --skill biopython-advanced -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills biopython-advanced --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Data Analysis/biopython-advanced' .claude/skills/biopython-advanced && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "biopython-advanced" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Data%20Analysis/biopython-advanced into .claude/skills/biopython-advanced/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biopython-advanced", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Data%20Analysis/biopython-advanced

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill biopython-advanced -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills biopython-advanced --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/'scientific-skills/Data Analysis/biopython-advanced' .agents/skills/biopython-advanced && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "biopython-advanced" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Data%20Analysis/biopython-advanced into .agents/skills/biopython-advanced/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biopython-advanced", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill biopython-advanced -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills biopython-advanced --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/'scientific-skills/Data Analysis/biopython-advanced' .cursor/skills/biopython-advanced && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "biopython-advanced" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Data%20Analysis/biopython-advanced into .cursor/skills/biopython-advanced/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biopython-advanced", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/aipoch/medical-research-skills.git --path 'scientific-skills/Data Analysis/biopython-advanced'

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill biopython-advanced -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills biopython-advanced --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/'scientific-skills/Data Analysis/biopython-advanced' .gemini/skills/biopython-advanced && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "biopython-advanced" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Data%20Analysis/biopython-advanced into .gemini/skills/biopython-advanced/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biopython-advanced", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install aipoch/medical-research-skills biopython-advanced

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add aipoch/medical-research-skills --skill biopython-advanced -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/'scientific-skills/Data Analysis/biopython-advanced' .github/skills/biopython-advanced && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "biopython-advanced" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Data%20Analysis/biopython-advanced into .github/skills/biopython-advanced/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biopython-advanced", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill biopython-advanced -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills biopython-advanced --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/'scientific-skills/Data Analysis/biopython-advanced' .opencode/skills/biopython-advanced && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "biopython-advanced" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Data%20Analysis/biopython-advanced into .opencode/skills/biopython-advanced/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biopython-advanced", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: biopython-advanced
GitHub stars: 2k
Token cost: ~1.6k tokens
SKILL.md length: 387 words
Files: 4 (incl. references)
Skills in repo: 567
Repo updated: Sep 17, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Works in 3 steps: Motif Statistics → Restriction Enzyme Cleavage Sites → Codon Usage Frequency (CDS)
You need extended bioinformatics analysis beyond basic sequence I/O and alignment
SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 1 more section
Calls python

What it does

Biopython Advanced is an agent skill from aipoch/medical-research-skills. Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended bioinformatics analysis beyond basic sequence I/O and alignment.

Its SKILL.md is about 1.6k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files, including reference files (for example `biopython-advanced_audit_result_v1.json`, `config/task_config.json` and `references/advanced.md`).

It sits in Research & Science, covering Bioinformatics. It works with Biopython. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

You need extended bioinformatics analysis beyond basic sequence I/O and alignment
Tasks that involve Bioinformatics

Example prompts

“/biopython-advanced”

Requirements

Python 3

Workflow steps

3 steps, taken from the step headings in SKILL.md.

Motif Statistics
Restriction Enzyme Cleavage Sites
Codon Usage Frequency (CDS)

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
- python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Biopython Advanced loads about 1.6k tokens when it runs, and up to ~5.3k if it reads all its reference files. Until then it costs about 64 tokens; SKILL.md has 387 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~64
When it runs · the whole SKILL.md, loaded when a task matches: ~1.6k
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~5.3k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 387 words, ~1,648 tokens.

Download SKILL.mdSave it as .claude/skills/biopython-advanced/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.

name: biopython-advanced
description: Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended bioinformatics analysis beyond basic sequence I/O and alignment.
license: MIT
author: AIPOCH

Source: https://github.com/aipoch/medical-research-skills

biopython-advanced

When to Use

You need motif discovery/statistics (e.g., PWM/consensus, motif counts across multiple sequences).
You want restriction enzyme site analysis (e.g., find cut sites for specific enzymes in a DNA sequence).
You need codon usage / sequence utility calculations (e.g., codon frequency from CDS, GC content, basic sequence stats).
You are working with population genetics (PopGen) utilities for advanced analyses.
You need advanced visualization such as GenomeDiagram-style plots for genomic features.

Key Features

Motif analysis using Biopython’s Bio.motifs (counts, consensus, simple statistics).
Restriction analysis using Bio.Restriction (enzyme lookup, cut site detection).
Sequence utilities via Bio.SeqUtils (codon usage and related helpers).
Access to additional advanced tools such as CodonTable, SeqFeature, and IUPACData when needed.
Standardized workflow conventions:
- Write configuration to config/task_config.json as an intermediate artifact.
- Run tasks uniformly via python scripts/<task_name>.py.
- Avoid stacking many CLI flags; keep parameters in config files.
- Always use encoding="utf-8" for file I/O; JSON output uses ensure_ascii=False.

Dependencies

Required:

biopython (>=1.80)
numpy (>=1.21)

Optional (for reporting/plotting):

reportlab (>=3.6)
matplotlib (>=3.5)

Example Usage

The following examples are complete runnable scripts that follow the conventions:

configuration stored in config/task_config.json
invoked as python scripts/<task_name>.py
explicit UTF-8 encoding and ensure_ascii=False for JSON output

1) Motif Statistics

config/task_config.json

json

{
  "task": "motif_stats",
  "sequences": ["ATGCATGCATGC", "ATGCGTGCATGC", "ATGCATGTATGC"]
}

scripts/motif_stats.py

python

import json
from Bio import motifs
from Bio.Seq import Seq

def main():
    with open("config/task_config.json", "r", encoding="utf-8") as f:
        cfg = json.load(f)

    seqs = [Seq(s) for s in cfg["sequences"]]
    m = motifs.create(seqs)

    result = {
        "alphabet": str(m.alphabet),
        "length": m.length,
        "counts": {k: dict(v) for k, v in m.counts.items()},
        "consensus": str(m.consensus),
        "degenerate_consensus": str(m.degenerate_consensus),
    }

    with open("outputs/motif_stats.json", "w", encoding="utf-8") as f:
        json.dump(result, f, ensure_ascii=False, indent=2)

if __name__ == "__main__":
    main()

Run:

bash

python scripts/motif_stats.py

2) Restriction Enzyme Cleavage Sites

config/task_config.json

json

{
  "task": "restriction_sites",
  "sequence": "GAATTCGCGGAATTC",
  "enzymes": ["EcoRI", "BamHI"]
}

scripts/restriction_sites.py

python

import json
from Bio.Seq import Seq
from Bio.Restriction import RestrictionBatch

def main():
    with open("config/task_config.json", "r", encoding="utf-8") as f:
        cfg = json.load(f)

    seq = Seq(cfg["sequence"])
    batch = RestrictionBatch(cfg["enzymes"])
    analysis = batch.search(seq)

    # Convert enzyme keys to strings for JSON serialization
    result = {str(enzyme): positions for enzyme, positions in analysis.items()}

    with open("outputs/restriction_sites.json", "w", encoding="utf-8") as f:
        json.dump(result, f, ensure_ascii=False, indent=2)

if __name__ == "__main__":
    main()

Run:

bash

python scripts/restriction_sites.py

3) Codon Usage Frequency (CDS)

config/task_config.json

json

{
  "task": "codon_usage",
  "cds": "ATGGCTGCTGCTGCTTAA"
}

scripts/codon_usage.py

python

import json
from collections import Counter

def main():
    with open("config/task_config.json", "r", encoding="utf-8") as f:
        cfg = json.load(f)

    cds = cfg["cds"].upper().replace(" ", "").replace("\n", "")
    codons = [cds[i:i+3] for i in range(0, len(cds) - (len(cds) % 3), 3)]
    counts = Counter(codons)
    total = sum(counts.values()) or 1

    result = {
        "total_codons": total,
        "codon_counts": dict(sorted(counts.items())),
        "codon_frequencies": {k: v / total for k, v in sorted(counts.items())},
        "note": "This example computes raw codon frequencies from the provided CDS. Validate CDS frame and stop codons for your use case."
    }

    with open("outputs/codon_usage.json", "w", encoding="utf-8") as f:
        json.dump(result, f, ensure_ascii=False, indent=2)

if __name__ == "__main__":
    main()

Run:

bash

python scripts/codon_usage.py

Show full SKILL.md (171 more words)Show less

Implementation Details

Configuration-first execution
- All task parameters are stored in config/task_config.json to keep CLI invocation stable and reproducible.
- Scripts read the config as the single source of truth and write results to outputs/*.json.
Motif statistics (Bio.motifs)
- A motif is created from aligned sequences of equal length.
- Outputs typically include:
  - counts: per-position nucleotide counts
  - consensus and degenerate_consensus: derived consensus sequences
- If sequences differ in length, you must align/trim/pad them before motif creation.
Restriction analysis (Bio.Restriction)
- RestrictionBatch(enzymes).search(seq) returns cut positions per enzyme.
- Enzyme objects are converted to strings for JSON serialization.
Codon usage
- The example computes codon frequencies by splitting the CDS into triplets in-frame.
- Practical considerations:
  - Ensure the CDS length is a multiple of 3 (or decide how to handle remainder bases).
  - Confirm the correct reading frame and whether to include terminal stop codons.
  - For organism-specific codon usage tables, integrate Bio.Data.CodonTable as needed.
I/O requirements
- Always open files with encoding="utf-8".
- Use json.dump(..., ensure_ascii=False) to preserve non-ASCII characters in outputs.
Further reference
- See references/advanced.md for additional notes and module coverage (motifs/PopGen/SeqUtils/Restriction/Cluster, GenomeDiagram, CodonTable/SeqFeature/IUPACData).

Files

SKILL.md and 3 other files (references) in scientific-skills/Data Analysis/biopython-advanced of aipoch/medical-research-skills.

SKILL.md
biopython-advanced_audit_result_v1.json
config/task_config.json
references/advanced.md

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Biopython Advanced next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Biopython Advanced compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Biopython Advanced this skillaipoch/medical-research-skills	2k	—	~1.6k	Automated safety check: Pass	MIT	20 days ago
Bio Alignment IoGPTomics/bioSkills	1.2k	3 repos	~4.9k	Automated safety check: Pass	MIT	1 mo ago
Biopython Bioinformaticsaiming-lab/AutoResearchClaw	15k	—	~810	Automated safety check: Pass	MIT	1 mo ago
Bio Write SequencesGPTomics/bioSkills	1.2k	3 repos	~2.1k	Automated safety check: Pass	MIT	1 mo ago
Biopythondavila7/claude-code-templates	32k	13 repos	~3.4k	Automated safety check: Pass	MIT	today
Ggetdavila7/claude-code-templates	32k	11 repos	~6.3k	Automated safety check: Pass	MIT	today

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Questions about Biopython Advanced

What does Biopython Advanced do?

Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended bioinformatics analysis…. Biopython Advanced is an agent skill from aipoch/medical-research-skills. Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended bioinformatics analysis beyond basic sequence I/O and alignment.

When should I use Biopython Advanced?

Biopython Advanced fits situations like: you need extended bioinformatics analysis beyond basic sequence I/O and alignment; tasks that involve Bioinformatics.

How do I install Biopython Advanced in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill biopython-advanced -a claude-code`. Or copy the skill folder (scientific-skills/Data Analysis/biopython-advanced in aipoch/medical-research-skills) into .claude/skills/biopython-advanced in your project. Claude Code loads it when a task matches its description.

How do I install Biopython Advanced in Codex?

Run `npx skills add aipoch/medical-research-skills --skill biopython-advanced -a codex`. Or copy the skill folder (scientific-skills/Data Analysis/biopython-advanced in aipoch/medical-research-skills) into .agents/skills/biopython-advanced in your project. Codex loads it when a task matches its description.

Can I use Biopython Advanced in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill biopython-advanced -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/biopython-advanced, .gemini/skills/biopython-advanced, .github/skills/biopython-advanced and .opencode/skills/biopython-advanced in your project.

What does Biopython Advanced need to run?

Going by SKILL.md and its folder, Biopython Advanced needs the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Biopython Advanced access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Biopython Advanced safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Biopython Advanced use?

Biopython Advanced is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Biopython Advanced use?

About 1.6k tokens (SKILL.md is roughly 6.6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 3.7k tokens, read only when the agent opens those files.

What are the alternatives to Biopython Advanced?

Skills that share tags, products or a category with Biopython Advanced: Bio Alignment Io (GPTomics/bioSkills, 1.2k stars), Biopython Bioinformatics (aiming-lab/AutoResearchClaw, 15k stars), Bio Write Sequences (GPTomics/bioSkills, 1.2k stars) and Biopython (davila7/claude-code-templates, 32k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Biopython Advanced?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,973 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Biopython Advanced

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

biopython-advanced

When to Use

Key Features

Dependencies

Example Usage

1) Motif Statistics

2) Restriction Enzyme Cleavage Sites

3) Codon Usage Frequency (CDS)

Implementation Details

Files

Compare with similar skills

Similar skills

More from aipoch/medical-research-skills

Related

Questions about Biopython Advanced