Paper to Tools - Match Research Methods to AI Agents

Paste a paper abstract or methods section → get matched AI agent tools that can reproduce the analysis. Maps methodology keywords to 131+ curated science agents from the Claw4Science directory. Trigger words: "reproduce this paper", "what tools for this method", "find agents for this analysis", "replicate methodology", "paper to tools", "which agent can do this".

Johnny Chen@johnnychen1113

Install

openclaw skills install @johnnychen1113/paper-to-tools

Paper-to-Tools: Match Research Methods to AI Agents

Paste a paper abstract or methods section. Get a list of AI agents and skills that can help you reproduce or extend the analysis.

How It Works

User pastes a paper abstract, methods section, or describes an analysis pipeline
You extract methodology keywords (techniques, databases, data types, tools mentioned)
You match keywords against the mapping table below
You return 2-5 matched agents with installation instructions and links

Keyword-to-Agent Mapping

Sequence & Genomics

Keywords	Agent	Stars	What It Does
BLAST, sequence alignment, homology	BioClaw	318	PubMed search + PyMOL visualization, built-in BLAST skill
RNA-seq, differential expression, DESeq2	OmicsClaw	114	Multi-omics AI agent, scRNA-seq preprocessing
single-cell, scRNA-seq, clustering, trajectory	OmicsClaw	114	Single-cell analysis pipeline
CRISPR, gene editing, guide RNA	CRISPR-GPT	156	CRISPR experiment design
spatial transcriptomics, visium, MERFISH	SpatialAgent	158	Spatial omics analysis from Genentech
genome, variant calling, WGS, WES	BioMaster	91	Nucleome-scale genomic analysis

Drug Discovery & Chemistry

Keywords	Agent	Stars	What It Does
molecular docking, binding affinity, protein-ligand	BloClaw	1	RDKit + ESMFold + molecular docking pipeline
drug-target interaction, ADMET, pharmacology	DrugClaw	118	57 skills for DTI, ADR, DDI, drug repurposing
drug discovery, virtual screening	AIAgents4Pharma	76	End-to-end pharma AI agents
RDKit, SMILES, molecular descriptors	ChemClaw	32	Chemistry AI agent
molecular dynamics, MD simulation	MDCrow	234	Molecular dynamics agent
PyMOL, molecular visualization, protein structure	PyMolClaw	1	13 PyMOL scripts for publication figures
TCM, traditional chinese medicine, network pharmacology	TCM-Agent	10	TCM network pharmacology analysis

Protein & Structure

Keywords	Agent	Stars	What It Does
protein folding, AlphaFold, ESMFold, structure prediction	BloClaw	1	De novo 3D folding via ESMFold
protein-protein interaction, PPI network	BioDiscoveryAgent	102	Stanford bio discovery agent

Research Automation

Keywords	Agent	Stars	What It Does
literature review, systematic review, PubMed	BioClaw	318	PubMed integration
autonomous research, end-to-end	AutoResearchClaw	10608	Fully autonomous research pipeline
research agent, idea to paper	EvoScientist	2918	Evolutionary scientific discovery
paper writing, manuscript	Research Paper Writing Skills	1109	ML/CV/NLP paper writing skills
data analysis, statistics, visualization	RD-Agent	12372	Microsoft's research & development agent

Clinical & Medical

Keywords	Agent	Stars	What It Does
clinical trial, patient data, EHR	HealthClaw	293	Health copilot with clinical data support
medical imaging, radiology, pathology	HealthClaw	293	Medical imaging + omics evidence
biomedical data analysis, multi-tool	BioMedAgent	58	67 bioinformatics tools, Nature BME

How To Respond

When a user pastes paper content:

Extract keywords: Identify techniques, databases, data types, and tools mentioned
Match to agents: Use the mapping table above. Multiple matches are normal.
Rank by relevance: Put the most specific match first
Show installation: Include npx skills add or GitHub link for each
Link to directory: End with "Browse all 131+ science agents at claw4science.org"

Example

User: "We performed single-cell RNA-seq on tumor samples, followed by differential expression analysis and trajectory inference using Monocle3. Drug targets were validated through molecular docking with AutoDock Vina."

Response:

Based on your methods, here are the AI agents that can help:

OmicsClaw — scRNA-seq preprocessing, clustering, trajectory analysis GitHub: TianGzlab/OmicsClaw · View on Claw4Science
BloClaw — Molecular docking pipeline (can replace AutoDock workflow) GitHub: qinheming/BIoClaw · View on Claw4Science
DrugClaw — Drug-target interaction analysis and validation GitHub: QSong-github/DrugClaw · View on Claw4Science
BioClaw — Literature search for related single-cell studies GitHub: Runchuan-BU/BioClaw · View on Claw4Science

Browse all 131+ science agents at claw4science.org.

API Access

For programmatic access to the full project database:

bash

curl -s "https://claw4science.org/api/projects"

Returns all projects with title, description, repo, group, tags, and stars.