Biopython Bioinformatics
aiming-lab/AutoResearchClaw
Quick reference for Biopython work: sequence operations, SeqIO file parsing, BLAST searches, Entrez queries, phylogenetic trees and PDB structure analysis.
Unified biological database evidence owner. An agent skill from foryourhealth111-pixel/Vibe-Skills.
Install Bio Database Evidence
$ npx skills add foryourhealth111-pixel/Vibe-Skills --skill bio-database-evidence -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install foryourhealth111-pixel/Vibe-Skills bio-database-evidence --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/foryourhealth111-pixel/Vibe-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/bundled/skills/bio-database-evidence .claude/skills/bio-database-evidence && rm -rf skills-srcUse ~/.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/
Install the "bio-database-evidence" agent skill from https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/main/bundled/skills/bio-database-evidence into .claude/skills/bio-database-evidence/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-database-evidence", 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 install https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/main/bundled/skills/bio-database-evidenceType 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.
$ npx skills add foryourhealth111-pixel/Vibe-Skills --skill bio-database-evidence -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install foryourhealth111-pixel/Vibe-Skills bio-database-evidence --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/foryourhealth111-pixel/Vibe-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/bundled/skills/bio-database-evidence .agents/skills/bio-database-evidence && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-database-evidence" agent skill from https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/main/bundled/skills/bio-database-evidence into .agents/skills/bio-database-evidence/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-database-evidence", 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.
$ npx skills add foryourhealth111-pixel/Vibe-Skills --skill bio-database-evidence -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install foryourhealth111-pixel/Vibe-Skills bio-database-evidence --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/foryourhealth111-pixel/Vibe-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/bundled/skills/bio-database-evidence .cursor/skills/bio-database-evidence && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "bio-database-evidence" agent skill from https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/main/bundled/skills/bio-database-evidence into .cursor/skills/bio-database-evidence/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-database-evidence", 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 https://github.com/foryourhealth111-pixel/Vibe-Skills.git --path bundled/skills/bio-database-evidence--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add foryourhealth111-pixel/Vibe-Skills --skill bio-database-evidence -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install foryourhealth111-pixel/Vibe-Skills bio-database-evidence --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/foryourhealth111-pixel/Vibe-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/bundled/skills/bio-database-evidence .gemini/skills/bio-database-evidence && rm -rf skills-srcUse ~/.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/
Install the "bio-database-evidence" agent skill from https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/main/bundled/skills/bio-database-evidence into .gemini/skills/bio-database-evidence/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-database-evidence", 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.
$ gh skill install foryourhealth111-pixel/Vibe-Skills bio-database-evidenceInstalls 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).
$ npx skills add foryourhealth111-pixel/Vibe-Skills --skill bio-database-evidence -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/foryourhealth111-pixel/Vibe-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/bundled/skills/bio-database-evidence .github/skills/bio-database-evidence && rm -rf skills-srcUse ~/.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/
Install the "bio-database-evidence" agent skill from https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/main/bundled/skills/bio-database-evidence into .github/skills/bio-database-evidence/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-database-evidence", 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.
$ npx skills add foryourhealth111-pixel/Vibe-Skills --skill bio-database-evidence -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install foryourhealth111-pixel/Vibe-Skills bio-database-evidence --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/foryourhealth111-pixel/Vibe-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/bundled/skills/bio-database-evidence .opencode/skills/bio-database-evidence && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "bio-database-evidence" agent skill from https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/main/bundled/skills/bio-database-evidence into .opencode/skills/bio-database-evidence/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-database-evidence", 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
bio-database-evidence- GitHub stars
- 3.6k
- Token cost
- ~773 tokens
- SKILL.md length
- 311 words
- Files
- 2 (incl. references)
- Skills in repo
- 81
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Unified biological database evidence owner. An agent skill from foryourhealth111-pixel/Vibe-Skills.
- Works in 5 steps: Identify the biological entity type:… → Pick the narrowest source that answers… → Preserve source names, query terms,… → …
- Gene annotation
- SKILL.md covers Use This Skill For, Do Not Use This Skill For, Workflow and Source Guide
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Bio Database Evidence is an agent skill from foryourhealth111-pixel/Vibe-Skills. Unified biological database evidence owner. Use for gene annotation, variant clinical significance, cancer mutation evidence, GWAS trait associations, pathway mapping, target-disease evidence, protein structures, protein interaction networks, reference single-cell census queries, and cross-database biological ID mapping. Do not use for full single-cell analysis, bulk RNA-seq differential expression, BAM/VCF processing, protein embedding models, metabolic flux modeling, genomic interval ML, or flow-cytometry file…
Its SKILL.md is about 770 tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files, including reference files (for example `references/database-evidence-sources.md`).
It sits in Research & Science, covering Bioinformatics and Protein structure and design. The repository describes itself as: Intelligent Skill routing and workflow orchestration for AI agents — +21.12 pp reward, −29.6% tokens on SkillsBench with DeepSeekV4Flash-VE. The licence is Apache-2.0.
When your agent uses it
- Gene annotation
- Variant clinical significance
- Cancer mutation evidence
- GWAS trait associations
Example prompts
- “/bio-database-evidence”
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Identify the biological entity type: gene, transcript, variant, pathway, target, protein structure, protein interaction, trait…
- Pick the narrowest source that answers the evidence question.
- Preserve source names, query terms, access dates, identifiers, and API caveats in the result.
- Return evidence in a table when comparing multiple sources.
- State when authentication, license, rate limits, or non-public access restricts a source.
What it can do on your machine
Read from SKILL.md and the folder at commit ddcaa2a. 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
No scripts in the folder and no shell commands in SKILL.md.
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
Bio Database Evidence loads about 773 tokens when it runs, and up to ~1.4k if it reads all its reference files. Until then it costs about 137 tokens; SKILL.md has 311 words of instructions outside code blocks.
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 foryourhealth111-pixel/Vibe-Skills at commit ddcaa2a, republished under its Apache-2.0 licence (© foryourhealth111-pixel). 311 words, ~773 tokens.
Download SKILL.mdSave it as
.claude/skills/bio-database-evidence/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.- name
- bio-database-evidence
- description
- Unified biological database evidence owner. Use for gene annotation, variant clinical significance, cancer mutation evidence, GWAS trait associations, pathway mapping, target-disease evidence, protein structures, protein interaction networks, reference single-cell census queries, and cross-database biological ID mapping. Do not use for full single-cell analysis, bulk RNA-seq differential expression, BAM/VCF processing, protein embedding models, metabolic flux modeling, genomic interval ML, or flow-cytometry file parsing.
Bio Database Evidence
Use This Skill For
Use this skill when the main task is biological database lookup, annotation, or evidence gathering across one or more biological sources:
- Gene annotation, identifiers, RefSeq, Ensembl IDs, orthologs, VEP, GO, and genomic coordinates.
- Variant clinical significance, VUS interpretation support, ClinVar review status, cancer mutations, and COSMIC evidence.
- GWAS Catalog trait associations, rs IDs, p-values, summary statistics, and genetic epidemiology evidence.
- Pathway mapping, ID conversion, KEGG pathways, Reactome enrichment, disease pathways, and pathway evidence.
- Target-disease association evidence, tractability, safety, known drugs, and Open Targets evidence.
- Protein structure evidence from AlphaFold DB or RCSB PDB, including UniProt IDs, mmCIF/PDB downloads, pLDDT, PAE, and structure metadata.
- Protein-protein interaction evidence, STRING networks, hub proteins, and enrichment evidence.
- Reference single-cell data lookup from CELLxGENE Census when the user asks for census metadata or expression data, not full downstream analysis.
- Cross-database biological ID mapping and evidence tables across multiple resources.
Do Not Use This Skill For
- Single-cell RNA-seq analysis, clustering, UMAP, marker genes, cell annotation, AnnData/h5ad container editing, or scVI/scANVI batch-correction planning. Use
scanpy. - Bulk RNA-seq differential expression. Use
pydeseq2. - BAM, SAM, CRAM, VCF, pileup, coverage, or region extraction as a primary file-processing task.
- deepTools signal-track processing and heatmaps.
- Protein language models, embeddings, inverse folding, or protein-design workflows.
- Constraint-based metabolic modeling, FBA, or metabolic-engineering simulation.
- BED/genomic interval embeddings, genomic-region ML, or gene regulatory network inference.
- FCS or flow-cytometry file parsing.
Workflow
- Identify the biological entity type: gene, transcript, variant, pathway, target, protein structure, protein interaction, trait association, or reference cell population.
- Pick the narrowest source that answers the evidence question.
- Preserve source names, query terms, access dates, identifiers, and API caveats in the result.
- Return evidence in a table when comparing multiple sources.
- State when authentication, license, rate limits, or non-public access restricts a source.
Source Guide
See references/database-evidence-sources.md for source-specific boundaries and query notes.
© foryourhealth111-pixel, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 1 other file (references) in bundled/skills/bio-database-evidence of foryourhealth111-pixel/Vibe-Skills.
- SKILL.md
- references/database-evidence-sources.md
Open the folder on GitHubat commit ddcaa2a
Compare with similar skills
Bio Database Evidence 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Bio Database Evidence this skillforyourhealth111-pixel/Vibe-Skills | 3.6k | — | ~773 | Automated safety check: Pass | Apache-2.0 | |
| Biopython Bioinformaticsaiming-lab/AutoResearchClaw | 15k | — | ~810 | Automated safety check: Pass | MIT | |
| Ggetdavila7/claude-code-templates | 33k | 10 repos | ~6.3k | Automated safety check: Pass | MIT | |
| Tooluniverseynulihao/AgentSkillOS | 618 | 2 repos | ~2.5k | Automated safety check: Pass | None | |
| Hugging ScienceK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~2.9k | Automated safety check: Notes | MIT | |
| Bio Entrez LinkGPTomics/bioSkills | 1.2k | 2 repos | ~3.8k | Automated safety check: Pass | MIT |
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Discovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog.
Bio Entrez Link
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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink).
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Related
Categories
Questions about Bio Database Evidence
What does Bio Database Evidence do?
Unified biological database evidence owner. An agent skill from foryourhealth111-pixel/Vibe-Skills. Bio Database Evidence is an agent skill from foryourhealth111-pixel/Vibe-Skills. Unified biological database evidence owner.
When should I use Bio Database Evidence?
Bio Database Evidence fits situations like: gene annotation; variant clinical significance; cancer mutation evidence; GWAS trait associations.
How do I install Bio Database Evidence in Claude Code?
Run `npx skills add foryourhealth111-pixel/Vibe-Skills --skill bio-database-evidence -a claude-code`. Or copy the skill folder (bundled/skills/bio-database-evidence in foryourhealth111-pixel/Vibe-Skills) into .claude/skills/bio-database-evidence in your project. Claude Code loads it when a task matches its description.
How do I install Bio Database Evidence in Codex?
Run `npx skills add foryourhealth111-pixel/Vibe-Skills --skill bio-database-evidence -a codex`. Or copy the skill folder (bundled/skills/bio-database-evidence in foryourhealth111-pixel/Vibe-Skills) into .agents/skills/bio-database-evidence in your project. Codex loads it when a task matches its description.
Can I use Bio Database Evidence 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 foryourhealth111-pixel/Vibe-Skills --skill bio-database-evidence -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-database-evidence, .gemini/skills/bio-database-evidence, .github/skills/bio-database-evidence and .opencode/skills/bio-database-evidence in your project.
What does Bio Database Evidence need to run?
SKILL.md names no scripts, command-line tools or credentials: Bio Database Evidence is instructions for the agent only.
Does Bio Database Evidence 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 Bio Database Evidence 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 Bio Database Evidence use?
Bio Database Evidence is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Bio Database Evidence use?
About 773 tokens (SKILL.md is roughly 3.1k 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 578 tokens, read only when the agent opens those files.
What are the alternatives to Bio Database Evidence?
Skills that share tags, products or a category with Bio Database Evidence: Biopython Bioinformatics (aiming-lab/AutoResearchClaw, 15k stars), Gget (davila7/claude-code-templates, 33k stars), Tooluniverse (ynulihao/AgentSkillOS, 618 stars) and Hugging Science (K-Dense-AI/scientific-agent-skills, 48k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Database Evidence?
foryourhealth111-pixel (a GitHub user) maintains it in foryourhealth111-pixel/Vibe-Skills, which has 3,627 GitHub stars. The repository holds 81 skills in this directory. The repository was last updated on August 31, 2026.
Source: foryourhealth111-pixel/Vibe-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.