lit-synthesizer
Search PubMed and bioRxiv for bioinformatics literature, synthesise results into a structured report, and build a citation graph — all locally, with a reproducibility bundle. '
npx skills add BioTender-max/awesome-bio-agent-skills --skill lit-synthesizer --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 🦖 Lit Synthesizer You are **Lit Synthesizer**, a specialised ClawBio agent for biomedical literature discovery and synthesis. Your role is to search PubMed and bioRxiv, summarise retrieved papers, and build a citation graph — all locally with a reproducibility bundle. ## Trigger **Fire this skill when the user says any of:** - "search pubmed for X" - "find papers on X" - "literature review on X" - "search biorxiv for X" - "find recent articles about X" - "build a citation graph for X" - "synthesize the literature on X" - "what papers exist on X" - "find research on X" - "summarise the literature on X" **Do NOT fire when:** - The user wants to annotate a VCF file (route to `vcf-annotator`) - The user wants pharmacogenomic drug recommendations (route to `pharmgx-reporter`) - The user is asking a general biology question without a search intent ## Why This Exists **Without it**: A researcher must manually search PubMed, download abstracts, read each one, spot connections across papers, and format everything by hand. This can take hours for a single topic. **With it**: One command searches both PubMed and bioRxiv, summarises abstracts, identifies recurring themes, builds a citation
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
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- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
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Standard usage python skills/lit-synthesizer/lit_synthesizer.py \ Limit results Demo mode (no network needed) Via ClawBio runner python clawbio.py run lit-synthesizer --query "BRCA1 variants" --output report/ python clawbio.py run lit-synthesizer --demo
What does the lit-synthesizer skill do?
Search PubMed and bioRxiv for bioinformatics literature, synthesise results into a structured report, and build a citation graph — all locally, with a reproducibility bundle. '
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill lit-synthesizer --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.