Gemini CLI Setup Guide

node --version

npm install -g @google/gemini-cli

gemini --version

cd ~/your-research-project
gemini

echo $GOOGLE_API_KEY  # Should display your key

cd ~/Research-Project
gemini

What are the key components of a systematic literature review?

# Research Project: [YOUR TOPIC]

## Project Goal
[Describe your research objective]

## File Structure
- /literature/ - Papers in markdown format
- /analysis/ - Data and synthesis
- /drafts/ - Paper sections
- /outputs/ - Final exports

## Research Protocol
- Citation style: APA 7th Edition
- Analysis approach: [Your methodology]
- Quality checks: [Your criteria]

## Key Context
- Research domain: [Your field]
- Theoretical framework: [Your approach]
- Target audience: [Journal or academic level]

"Analyze all papers in @/literature/ (contains 47 papers).
Identify the 5 most common theoretical frameworks used.
For each framework, list which papers use it and how
their applications differ."

"Review my complete dissertation in @/drafts/ (6 chapters, ~40K words).
Check for:
- Argument coherence across chapters
- Citation coverage and balance
- Transition quality between sections
- Theoretical consistency throughout"

"Using Sequential Thinking, synthesize all 47 papers in @/literature/:
1. Extract all theoretical constructs mentioned
2. Map relationships between constructs
3. Identify consensus vs contradictory findings
4. Propose an integrated framework
5. Suggest future research directions"

{
  "mcpServers": {
    "zotero": {
      "command": "zotero-mcp",
      "args": [],
      "env": {
        "ZOTERO_LOCAL": "true"
      }
    },
    "filesystem": {
      "command": "mcp-server-filesystem",
      "args": ["/Users/[username]/Research"]
    }
  }
}

"Search my Zotero library for papers on organizational scaling
published after 2023. Show titles, authors, and citation keys."

"Read all markdown files in @/literature/ and create a master
bibliography in APA 7th format."

mkdir -p .gemini/commands

Create a structured summary of this paper:

Paper: $ARGUMENTS

## Summary Format
- **Citation**: [Author(s), Year, Title]
- **Research Question**:
- **Methodology**:
- **Sample**:
- **Key Findings**: (3-5 bullets)
- **Theoretical Contribution**:
- **Limitations**:
- **Future Research**:

Use academic language, cite page numbers.

Analyze these papers for common themes:

Papers: $ARGUMENTS

## Thematic Analysis
1. Identify 5-7 major themes
2. For each theme:
   - List papers that discuss it
   - Summarize key arguments
   - Note points of agreement/disagreement
   - Assess theoretical depth

Output as structured markdown.

"I'm providing my complete literature set (47 papers in @/literature/).

Phase 1: Read all papers and extract:
- Research questions
- Methodologies
- Key findings
- Theoretical frameworks

Phase 2: Identify patterns:
- Which methods are most common?
- What theories dominate?
- Where are the contradictions?

Phase 3: Gap analysis:
- What questions aren't being asked?
- What methods are underused?
- What theories need development?

Work through this systematically and save outputs to @/analysis/"

"Verify this claim across all papers in @/literature/:
'Organizational scaling requires both strategy and structure.'

Show which papers support, contradict, or nuance this claim.
Provide specific page references."

"Based on all papers in @/literature/, propose a novel
theoretical framework integrating:
- Key constructs identified across papers
- Relationships between constructs
- Boundary conditions
- Testable propositions

Use the 1M context to ensure nothing is missed!"

"Analyze all 47 papers in @/literature/ in the background.
Extract methodologies and create comparison table.
Notify when complete."

"Chain these actions:
1. Read all papers in @/literature/
2. Extract theoretical frameworks
3. Create comparison matrix
4. Identify most and least used theories
5. Save analysis to @/outputs/framework_analysis.md"

mkdir Systematic-Review-Gemini
cd Systematic-Review-Gemini
gemini

# Systematic Literature Review: AI in Education

## Goal
Synthesize 50+ papers on AI's impact on student learning (2020-2025)

## File Structure
- /literature/ - All 50 papers as markdown
- /analysis/ - Thematic analysis, extraction tables
- /synthesis/ - Draft sections

## Protocol
- Citation: APA 7th
- Inclusion: Peer-reviewed, empirical, English
- Analysis: Thematic synthesis + meta-analysis

## Context Advantage
With 1M tokens, I can load ALL 50 papers simultaneously for:
- Comprehensive thematic analysis
- Cross-paper validation
- Gap identification across entire corpus

"Read all 50 papers in @/literature/ (approx 800K tokens).

Task: Comprehensive meta-synthesis
1. Extract all reported effect sizes
2. Group by intervention type
3. Analyze by student age group
4. Identify methodological patterns
5. Flag contradictory findings
6. Propose integrated theory

Save complete analysis to @/analysis/meta_synthesis.md"

"Load my complete dissertation from @/drafts/ (6 chapters, 45K words).

Review for:
- Argument coherence across all chapters
- Citation balance (am I over-citing certain papers?)
- Theoretical consistency
- Transition quality between chapters
- Missing literature I should address

Provide chapter-by-chapter feedback."

"Analyze all papers in @/literature/ for research gaps.

Systematically check:
- Methodological gaps (which methods are underused?)
- Theoretical gaps (which theories lack development?)
- Empirical gaps (which contexts are understudied?)
- Temporal gaps (what recent trends aren't covered?)

For each gap, assess significance and feasibility."

"I claim: 'AI tools improve student outcomes but reduce
critical thinking skills.'

Search all 50 papers in @/literature/:
- Which support this claim? (quote specific findings)
- Which contradict it? (provide counter-evidence)
- Which nuance it? (add boundary conditions)

Build an evidence table with page references."