Home
cd ../playbooks
Academic ResearchBeginner

Research Ideation Generator

Generate research questions, hypotheses, and empirical strategies. Brainstorm ideas systematically with structured prompts that push beyond obvious approaches.

5 minutes
By communitySource
#research#brainstorming#ideation#hypotheses#creativity

You're staring at a blank page trying to come up with your next research question and everything feels either too incremental or too ambitious. Systematic ideation — structured brainstorming that pushes past obvious approaches — generates research directions you wouldn't reach through unstructured thinking alone.

Who it's for: PhD students developing dissertation proposals and research agendas, principal investigators identifying new research directions for grant proposals, postdocs pivoting into new research areas, research teams running structured brainstorming sessions, interdisciplinary researchers exploring connections between fields

Example

"Generate research directions at the intersection of NLP and healthcare" → Ideation package: 10 research questions ranked by novelty and feasibility, testable hypotheses for the top 5 questions, suggested empirical strategies with data requirements, literature gap analysis showing underexplored areas, and a research agenda framework for the next 2 years

CLAUDE.md Template

New here? 3-minute setup guide → | Already set up? Copy the template below.

# Research Ideation System

## Command
`/research-ideation [topic]` — Generate research ideas for a topic

## Ideation Framework

### Phase 1: Problem Space Exploration
Before generating ideas, understand the space:
1. What is the core phenomenon?
2. Why does it matter?
3. What's the current state of knowledge?
4. What are the key debates/tensions?

### Phase 2: Research Question Generation
Generate questions across dimensions:

**Descriptive Questions** (What is?)
- What is the prevalence/distribution of X?
- How does X vary across contexts?
- What are the components/dimensions of X?

**Causal Questions** (What causes?)
- Does X cause Y?
- What mediates the X→Y relationship?
- What moderates the X→Y relationship?

**Mechanism Questions** (How?)
- How does X produce Y?
- What is the process by which X operates?
- Why does X work in some contexts but not others?

**Normative Questions** (What should?)
- What is the optimal level of X?
- How should we design X?
- What interventions would improve X?

### Phase 3: Hypothesis Generation
For each research question, generate:
1. **Conventional hypothesis**: What most people would predict
2. **Contrarian hypothesis**: Opposite of conventional
3. **Contingent hypothesis**: "It depends on Z"
4. **Novel hypothesis**: Non-obvious prediction

### Phase 4: Empirical Strategy Brainstorm
For promising hypotheses:
- What data would test this?
- What's the ideal research design?
- What's a feasible alternative design?
- What are the main identification threats?

## Ideation Techniques

### Inversion
What if the opposite of conventional wisdom is true?

### Analogy Transfer
What works in field Y that hasn't been applied to field X?

### Boundary Exploration
What happens at the extremes? What's the smallest unit of analysis?

### Mechanism Deep Dive
Pick any relationship and ask "but how, exactly?"

### Counterfactual Thinking
What would the world look like if X didn't exist?

### Combination
What happens when A and B interact?

## Output Format

```
## Research Ideation: [Topic]

### Problem Space
[Brief characterization]

### Research Questions
1. [Question 1] — [Type: Descriptive/Causal/Mechanism/Normative]
2. [Question 2] — [Type]
3. [Question 3] — [Type]
...

### Most Promising Hypotheses
**Hypothesis 1**: [Statement]
- Rationale: [Why this might be true]
- Test: [How to test it]

**Hypothesis 2**: [Statement]
- Rationale: [Why]
- Test: [How]

### Non-Obvious Ideas
- [Idea that isn't immediately obvious]
- [Contrarian take]
- [Cross-domain insight]

### Gaps Identified
- [What hasn't been studied]
- [What's understudied]
```

## Quality Checks

Good research ideas should be:
- [ ] **Interesting**: Would people care about the answer?
- [ ] **Novel**: Not already answered definitively
- [ ] **Testable**: Can be empirically investigated
- [ ] **Meaningful**: Results would change how we think or act

Get new playbooks like this one

One email a week with new Claude Code workflows. Free, like everything here.

No spam. Unsubscribe anytime.

README.md

What This Does

This playbook helps generate research ideas systematically. Instead of staring at a blank page, use structured prompts to generate research questions, hypotheses, and empirical strategies. Claude pushes beyond obvious approaches to surface non-obvious ideas.

Prerequisites

  • Claude Code installed and configured
  • A research area or topic to explore

Research Ideation: [Topic]

Problem Space

[Brief characterization]

Research Questions

  1. [Question 1] — [Type: Descriptive/Causal/Mechanism/Normative]
  2. [Question 2] — [Type]
  3. [Question 3] — [Type] ...

Most Promising Hypotheses

Hypothesis 1: [Statement]

  • Rationale: [Why this might be true]
  • Test: [How to test it]

Hypothesis 2: [Statement]

  • Rationale: [Why]
  • Test: [How]

Non-Obvious Ideas

  • [Idea that isn't immediately obvious]
  • [Contrarian take]
  • [Cross-domain insight]

Gaps Identified

  • [What hasn't been studied]
  • [What's understudied]

## Quality Checks

Good research ideas should be:
- [ ] **Interesting**: Would people care about the answer?
- [ ] **Novel**: Not already answered definitively
- [ ] **Testable**: Can be empirically investigated
- [ ] **Meaningful**: Results would change how we think or act

Step-by-Step Setup

Step 1: Add to your research CLAUDE.md

Add the template above to your research folder's CLAUDE.md.

Step 2: Test with a topic

/research-ideation [your research area]

Or simply:

Generate research ideas about [topic]. Use the ideation framework.

Example Usage

User:

"/research-ideation AI adoption in healthcare"

Claude:

Research Ideation: AI Adoption in Healthcare

Problem Space

AI tools (diagnostic, administrative, clinical decision support) are becoming available in healthcare, but adoption is uneven. Key tensions: accuracy vs explainability, efficiency vs job displacement, innovation vs regulation.

Research Questions

Descriptive

  1. What predicts which hospitals adopt AI early vs late? — Descriptive
  2. How do clinicians' mental models of AI accuracy compare to actual accuracy? — Descriptive

Causal 3. Does AI diagnostic assistance improve or harm physician decision-making? — Causal 4. Does exposure to AI errors affect future trust calibration? — Causal

Mechanism 5. How do clinicians integrate AI recommendations with their own judgment? — Mechanism 6. Why do some physicians override AI more than others? — Mechanism

Normative 7. What level of AI explanation is optimal for different clinical decisions? — Normative 8. How should liability be allocated when AI contributes to errors? — Normative

Most Promising Hypotheses

Hypothesis 1: AI assistance helps average physicians more than experts

  • Rationale: Experts have strong priors; AI provides less marginal information
  • Test: Compare diagnostic accuracy improvement across experience levels

Hypothesis 2: AI explanation length has an inverse-U relationship with trust

  • Rationale: Too little = black box distrust; too much = cognitive overload
  • Test: Experiment varying explanation detail, measuring adoption

Hypothesis 3: AI adoption is higher for "defensive" diagnoses (ruling out) than "offensive" (ruling in)

  • Rationale: Liability asymmetry — missing a diagnosis is worse than over-testing
  • Test: Compare adoption rates by diagnosis type

Non-Obvious Ideas

  • Automation complacency as hidden cost: Physicians may stop developing skills they delegate to AI, creating fragility
  • AI as scapegoat: Physicians might adopt AI not for accuracy but for blame-shifting ("the AI suggested it")
  • Inverse selection: Hospitals that most need AI (under-resourced, overworked) may be least able to implement it

Gaps Identified

  • Long-term effects on physician skill development
  • Patient preferences for AI involvement in their care
  • How AI errors affect downstream patient trust in medicine broadly

Tips

  • Push for contrarian ideas: Explicitly ask "What if the opposite were true?"
  • Cross-domain insights: Ask "What does [other field] know about this that healthcare hasn't applied?"
  • Quantity first: Generate 10-15 questions before evaluating. Don't self-censor early.
  • Test feasibility later: Ideation phase is about possibility, not practicality.

Troubleshooting

Problem: Ideas feel generic/obvious

Solution: Go deeper. For any idea, ask "Yes, but specifically how?" or "What's the second-order effect?"

Problem: Can't generate contrarian ideas

Solution: List the assumptions behind conventional wisdom. What if each assumption were wrong?

Problem: Ideas aren't testable

Solution: Add "How would you test this?" as a required component for each hypothesis. Untestable ideas get cut.

$Related Playbooks

Academic Research

Scientific Adaptyv

Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein ...

10 minutes
Intermediate
Academic Research

Scientific Alphafold Database

Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

10 minutes
Intermediate
Academic Research

Scientific Anndata

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; f...

10 minutes
Intermediate
Academic Research

Scientific Arboreto

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships a...

10 minutes
Intermediate
Academic Research

Scientific Benchling Integration

Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

10 minutes
Intermediate
Academic Research

Scientific Bindingdb Database

Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activit...

5 minutes
Beginner
Academic Research

Scientific Biopython

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation...

10 minutes
Intermediate
Academic Research

Scientific Biorxiv Database

Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.

5 minutes
Beginner
Academic Research

Scientific Bioservices

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick singl...

10 minutes
Intermediate
Academic Research

Scientific Brenda Database

Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.

5 minutes
Beginner
Academic Research

Scientific Cbioportal Database

Query cBioPortal for cancer genomics data including somatic mutations, copy number alterations, gene expression, and survival data across hundreds of cancer studies. Essential for cancer target validation, oncogene/tumor suppressor analysis, and p...

5 minutes
Beginner
Academic Research

Scientific Cellxgene Census

Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For ana...

10 minutes
Intermediate

Browse all Academic Research playbooks →