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Overview

The Research Memex methodology supports both GUI and CLI (command-line interface) approaches to agentic AI workflows. This guide helps you choose the right tools for your research needs.
GUI vs CLI: GUI tools like Cherry Studio are visual and beginner-friendly. CLI tools offer power, automation, and scriptability. Most researchers use BOTH - GUI for exploration, CLI for production workflows.

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The Tool Landscape

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GUI: Cherry Studio

  • Visual interface with buttons, panels, menus
  • Multi-model access through one app
  • Knowledge bases for PDF analysis
  • Beginner-friendly with no terminal needed
  • Full guide: Cherry Studio Setup

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CLI: Three Powerful Options

1. Claude Code (Premium)
  • Provider: Anthropic (paid)
  • Strength: Best reasoning quality
  • Cost: ~$20/mo
  • Full guide: Claude Code Setup
2. Gemini CLI (Free Power)
  • Provider: Google (free tier!)
  • Strength: 1M context, 1K req/day free
  • Cost: FREE (or pay for more)
  • Full guide: Gemini CLI Setup
3. OpenCode (Multi-Provider)
  • Provider: 75+ options (community)
  • Strength: Model flexibility, beautiful TUI
  • Cost: Pay per provider
  • Full guide: OpenCode Setup

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Comprehensive Comparison Table

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Feature Comparison

FeatureCherry StudioClaude CodeGemini CLIOpenCode
InterfaceGUICLICLITUI (visual CLI)
Model Access100+Claude onlyGemini only75+
Context WindowVaries200K1MVaries
Free TierVia providers❌ No✅ Yes (1K/day)Via providers
CostFree app$20/moFREEPay per provider
MCP Support✅ Full✅ Full✅ Full✅ Full
Project MemoryKnowledge BaseCLAUDE.mdGEMINI.mdConfig files
Slash Commands❌ No✅ Yes✅ Yes⚠️ Limited
Multi-Session✅ Tabs❌ Single❌ Single✅ Yes
Git Integration❌ No✅ Built-in⚠️ Basic⚠️ Basic
Open Source✅ Apache 2.0❌ No✅ Apache 2.0✅ MIT
Best ForExplorationPremium workBudget + powerFlexibility

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Cost Comparison

Monthly cost estimates (heavy research use):
ToolSetup CostMonthly CostNotes
Cherry StudioFree$5-30Via API providers
Claude CodeFree$20+Subscription + API
Gemini CLIFree$0-10Free tier often enough!
OpenCodeFree$5-50Depends on providers chosen
Budget strategy:
  • $0/month: Gemini CLI + Cherry Studio (free tiers)
  • $20/month: Add Claude Code for premium reasoning
  • $30/month: All tools + OpenCode with multiple providers

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Decision Matrix: Which Tool Should You Use?

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By Research Phase

Phase 1: Exploration & Learning → Cherry Studio (visual, easy, multi-model testing) Phase 2: Literature Analysis → Gemini CLI (1M context for 50+ papers, FREE!) Phase 3: Automation & Scale → OpenCode (multi-provider, cost optimization) Phase 4: Final Theory/Writing → Claude Code (premium reasoning quality)

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By Use Case

“I need to analyze 50+ papers comprehensively” → Gemini CLI (1M context window) “I want to compare GPT vs Claude vs Gemini vs DeepSeek” → OpenCode (75+ providers) “I need the absolute best reasoning quality” → Claude Code (Anthropic Sonnet 4.5) “I’m on a tight budget” → Gemini CLI (1K free requests/day) + Cherry Studio (free app) “I prefer visual interfaces” → Cherry Studio (GUI) “I want to automate everything” → Any CLI (all support automation) “I need maximum privacy (local processing)” → OpenCode + Ollama (run models locally)

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By Skill Level

Beginner:
  • Start: Cherry Studio (GUI, no terminal needed)
  • Then: Gemini CLI (gentle CLI introduction, free!)
Intermediate:
  • Add: OpenCode (experiment with providers)
  • Or: Claude Code (premium quality)
Advanced:
  • Use all 4 tools strategically
  • Right tool for each task
  • Optimize cost-quality-speed tradeoff

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Tool Combination Strategies

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Strategy 1: Budget Maximizer (Free/Minimal Cost)

Tools:
  • Cherry Studio (free app)
  • Gemini CLI (free 1K req/day)
Workflow:
  • Cherry Studio: Exploration, testing, learning
  • Gemini CLI: Heavy analysis (50+ papers), automation
Cost: $0-5/month

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Strategy 2: Quality Optimizer (Premium)

Tools:
  • Cherry Studio (multi-model testing)
  • Claude Code (premium reasoning)
  • Gemini CLI (massive context backup)
Workflow:
  • Cherry Studio: Quick tests, model comparison
  • Gemini CLI: Large-scale synthesis (free!)
  • Claude Code: Final theoretical work (paid quality)
Cost: $20-30/month

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Strategy 3: Model Experimenter (Flexibility)

Tools:
  • OpenCode (75+ providers)
  • Cherry Studio (visual multi-model)
  • Gemini CLI (free Google power)
Workflow:
  • OpenCode: Test 5+ models on same task
  • Cherry Studio: Visual comparison
  • Gemini CLI: Final choice if Google wins
Cost: $10-40/month (depends on experimentation)

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Strategy 4: Research Lab (Complete)

Tools:
  • All 4 tools configured
Workflow:
  • Cherry Studio: Student onboarding, teaching
  • Gemini CLI: RA heavy lifting (free!)
  • OpenCode: Model experiments, optimization
  • Claude Code: PI final review, theory building
Cost: $20-50/month

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Getting Started Recommendation

Week 1-2: Install Cherry Studio
  • Learn GUI basics
  • Test multiple models
  • Build knowledge bases
Week 3-4: Add Gemini CLI
  • Learn terminal basics
  • Try massive context (30+ papers)
  • Automate screening/extraction
Week 5+: Add OpenCode OR Claude Code
  • OpenCode if: Want flexibility, tight budget
  • Claude Code if: Need premium quality, budget allows
Not required: All 3 CLIs Recommended: Cherry Studio + At least 1 CLI (Gemini preferred for free tier)

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CLI Basics for Researchers

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Terminal Fundamentals

If you’re new to terminals: Navigate to project: 
cd ~/Documents/Research-Project    # Change directory
ls                                  # List files
pwd                                 # Show current location
mkdir new-folder                    # Create folder
Launch CLI tools: 
claude          # Launch Claude Code
gemini          # Launch Gemini CLI
opencode        # Launch OpenCode
Exit: 
exit            # Or Ctrl+D

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Environment Variables

What are they? Variables that store API keys securely. Set temporarily (current session): 
export GOOGLE_API_KEY="AIza..."
Set permanently: Add to ~/.zshrc (macOS) or ~/.bashrc (Linux): 
echo 'export GOOGLE_API_KEY="AIza..."' >> ~/.zshrc
source ~/.zshrc
Check if set: 
echo $GOOGLE_API_KEY

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Troubleshooting

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”I’ve never used terminal before”

Resources: Or stick with Cherry Studio (GUI) - it’s powerful enough!

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”Which tool should I start with?”

Decision tree:
  1. Comfortable with terminal?
    • No → Cherry Studio
    • Yes → Continue
  2. Budget?
    • $0 → Gemini CLI
    • $20+ → Claude Code
    • Flexible → OpenCode
  3. Need massive context (50+ papers)?
    • Yes → Gemini CLI (1M context)
    • No → Any tool works

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”Can I use multiple tools?”

Absolutely! Most researchers use:
  • GUI for exploration
  • CLI for automation
  • Both for different phases

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Next Steps

1. Choose your tool(s) using the decision matrix above 2. Follow detailed setup guide: 3. Learn agentic workflows: 4. Connect to research tools:

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Resources

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Comparison Articles

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Official Documentation

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Video Tutorials

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FAQ

Q: Do I need a CLI tool or is Cherry Studio enough? A: Cherry Studio is sufficient for the course! CLI tools are optional for students who want automation, scripting, or prefer terminal workflows. Q: Which CLI tool is best? A: Depends on priority:
  • Budget → Gemini CLI (free)
  • Quality → Claude Code (premium)
  • Flexibility → OpenCode (75+ providers)
Q: Can I switch between tools? A: Yes! All use markdown files and similar workflows. Easy to migrate. Q: Do these work with the same Zotero setup? A: Yes! All connect to your Zotero library via MCP servers configured in the Zotero Setup Guide. Q: Are CLI tools harder to learn? A: Initial learning curve, but automation benefits compound over time. Gemini CLI or OpenCode’s TUI are good starting points.
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