Researcher
Full TCM Research Study Design — From Herb to Publication in One Prompt
Key Takeaway
The TCM Biomedical Research Strategist skill designs complete network pharmacology research plans for herbal medicine — 11 mandatory sections, 14 analytical steps, 4 workload tiers. One prompt generates a study framework that would take a research team weeks to plan.
The Problem
You're a researcher interested in how Coptis chinensis (Huang Lian) might treat colorectal cancer through network pharmacology. You need a complete study design:
- Scientific question formulation
- Specific aims (2-4, independently answerable)
- Compound-target-pathway analysis workflow
- Database sources and inclusion criteria
- Statistical methods and validation plan
- Figure and table plan
- Timeline and resource requirements
Planning this study takes 2-4 weeks for an experienced researcher. For a junior researcher, it takes a month — and they'll likely miss critical methodological steps that reviewers catch during peer review.
The Solution
The TCM Biomedical Research Strategist skill generates publication-grade research plans from a single prompt. It covers everything from initial question formulation to validation design, with explicit decision points and risk assessment.
The Process
View details
You: Design a network pharmacology + molecular docking
study investigating how Coptis chinensis (Huang Lian)
treats colorectal cancer. Full research plan.
The agent produces an 11-section plan:
View details
§1. CORE SCIENTIFIC QUESTION
"How do the bioactive compounds of Coptis chinensis
(Huang Lian) modulate colorectal cancer progression
through multi-target, multi-pathway mechanisms
identifiable via network pharmacology and validated
by molecular docking?"
§2. SPECIFIC AIMS
Aim 1: Identify bioactive compounds and their
CRC-relevant targets through database mining
and network construction (DISCOVERY)
Aim 2: Characterize key pathways and hub genes
through enrichment analysis and PPI network
topology (MECHANISM)
Aim 3: Validate top compound-target pairs through
molecular docking and binding energy analysis
(VALIDATION)
Aim 4: Evaluate immune microenvironment modulation
by hub targets using immune deconvolution
(TRANSLATIONAL)
§3. OVERALL STUDY DESIGN
Type: Network pharmacology + WGCNA + immune
deconvolution + molecular docking
Logic chain (10 steps):
1. Compound identification (TCMSP, BATMAN-TCM)
2. Target prediction (SwissTargetPrediction, PharmMapper)
3. Disease gene collection (GeneCards, OMIM, DisGeNET)
4. Intersection analysis (Venn diagram)
5. PPI network (STRING → Cytoscape)
6. DEG analysis (GEO datasets, limma)
7. Pathway enrichment (GO + KEGG)
8. Hub gene identification (CytoHubba, MCODE)
9. Immune infiltration (CIBERSORT/ssGSEA)
10. Molecular docking (AutoDock Vina)
§4. STEP-BY-STEP ANALYTICAL PLAN
[14 steps, each with 9 fields: Tool, Input, Output,
Parameters, Thresholds, Alternatives, Decision Rules,
Expected Results, Failure Contingency]
...
§11. FOUR WORKLOAD TIERS
| Tier | Timeline | Figures | Suitable For |
|------|----------|---------|-------------|
| Lite | 2-4 weeks | 4-6 | Quick pilot |
| Standard | 4-8 weeks | 8-12 | Conventional pub |
| Advanced | 8-14 weeks | 12-18 | Competitive journal |
| Publication+ | 14+ weeks | 16-24 | High-impact |
The Results
| Metric | Manual Planning | AI Agent |
|---|---|---|
| Time to complete plan | 2-4 weeks | 30 minutes |
| Methodological completeness | Variable | 11 sections, 14 steps |
| Risk assessment included | Rarely | Always |
| Alternative methods documented | Sometimes | Every step |
| Reviewer-ready | After revisions | First draft |
Setup on MrChief
yamlShow code
skills:
- tcm-biomedical-research-strategist
- medical-research-toolkit
- pubmed
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