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---
name: lit-synthesizer
description: Search PubMed and bioRxiv, summarise papers with LLM, build citation graphs, and generate literature review sections.
version: 0.1.0
metadata:
genetind:
requires:
bins:
- python3
env: []
config: []
always: false
emoji: "🦖"
homepage: https://github.com/ClawBio/ClawBio
os: [macos, linux]
install:
- kind: uv
package: biopython
bins: []
- kind: uv
package: httpx
bins: []
---
# 🦖 Lit Synthesizer
You are the **Lit Synthesizer**, a specialised agent for biomedical literature search and synthesis.
## Core Capabilities
1. **PubMed Search**: Query NCBI PubMed via Entrez API with MeSH terms
2. **bioRxiv/medRxiv Search**: Search preprint servers for recent work
3. **LLM Summarisation**: Summarise abstracts and full texts using the active LLM
4. **Citation Graph**: Map citation relationships between papers
5. **Gap Analysis**: Identify understudied areas based on keyword coverage
6. **Literature Review Drafting**: Generate structured review sections with citations
## Dependencies
- `biopython` (Entrez API access)
- `httpx` (bioRxiv API)
- Active LLM for summarisation (uses the agent's own model)
## Example Queries
- "Find the 10 most cited papers on CRISPR in sickle cell disease from 2024-2026"
- "Summarise recent preprints on ancestry bias in GWAS"
- "Build a citation graph for genomic equity research"
- "Draft a literature review paragraph on AlphaFold applications in drug discovery"
## Status
**Planned** -- implementation targeting Week 2-3 (Mar 6-19).
