Research-Stack/obsidian-vault/00-MAP/Getting Started.md

Getting Started with the Research Stack Obsidian Vault

Prerequisites

Before using this vault, you should:

1. Understand the Research Stack

   • Read 00-MAP/Core Concepts for fundamental principles
   • Review 01-LAYERS/00-Overview for architecture understanding
   • Familiarize yourself with basic Lean 4 concepts (if working with formal proofs)

2. Install Required Software

   • Obsidian (version 1.5.0 or later recommended)
   • Git (for version control)
   • Lean 4 (if working with formal proofs)

3. Understand Q16.16 Fixed-Point Arithmetic

   • The Research Stack uses Q16.16 for all computation
   • Read the arithmetic specification in core documentation
   • Understand Q16_16.ofNat, Q16_16.ofRatio, and Q16_16.ofInt constructors

Step-by-Step Setup

1. Open the Vault

1. Launch Obsidian
2. Click "Open folder as vault"
3. Navigate to /home/researcher/stack/obsidian-vault/
4. Wait for plugins to load (first time may take a moment)

2. Verify Plugin Installation

1. Open Settings (Ctrl/Cmd + ,)
2. Go to "Community Plugins"
3. Verify all plugins are enabled:
   • ✅ Templater
   • ✅ QuickAdd
   • ✅ Dataview
   • ✅ Advanced Tables
   • ✅ Excalidraw
   • ✅ Canvas
   • ✅ Tag Wrangler
   • ✅ Breadcrumbs
   • ✅ Workspaces

If any plugin is missing:

1. Click "Browse" in Community Plugins
2. Search for the plugin name
3. Install and enable it

3. Configure Templater

1. Open Settings → Templater
2. Verify "Template folder location" is set to: 08-TOOLS/01-Templates/
3. Check "Enable folder templates"
4. Verify folder templates are configured:
   • 01-LAYERS/*/01-Formal-Proofs → Formal Proof.md
   • 07-RESEARCH/01-Attack-Plans → Attack Plan.md
   • 07-RESEARCH/00-Milestones → Milestone.md
   • 01-LAYERS/*/03-Receipts → Receipt.md

4. Test Template Creation

1. Press Alt+Shift+F (or your configured hotkey)
2. Select "Formal Proof"
3. Fill in the prompts:
   • Title: "Test Theorem"
   • Layer: "L0 - Primordial"
   • Status: "Draft"
4. A new file should be created in 01-LAYERS/L0-Primordial/01-Formal-Proofs/

5. Test QuickAdd

1. Press Ctrl+Shift+P
2. Select "Create Formal Proof"
3. Fill in the required fields
4. Verify the note is created in the correct location

Your First Research Document

Creating a Formal Proof

1. Open Command Palette (Ctrl/Cmd + P)

2. Type "Templater: Open insert modal"

3. Select "Formal Proof"

4. Fill in the information:

   Title: My First Theorem
   Layer: L0 - Primordial
   Status: Draft
   

5. The template will generate:

   • YAML frontmatter with metadata
   • Overview section
   • Formal statement stub
   • Proof strategy outline
   • Receipt generation function
   • Tags

6. Write your theorem in the Formal Statement section:

   theorem myFirstTheorem [hypotheses] : conclusion :=
     sorry
   

7. Link to related documents:

   See also: [[Related Proof 1]] and [[Related Proof 2]]
   

8. Generate receipt when complete:

   def myFirstTheoremReceipt (state : State) : String :=
     "my_first_theorem:" ++ toString state.val ++ ","
   

Creating an Attack Plan

1. Use the Attack Plan template
2. Define clear success criteria
3. Break down into phases
4. Link to required formal proofs
5. Set target dates for each milestone
6. Track progress daily

Tracking a Milestone

1. Use the Milestone template
2. Define success metrics
3. Set timeline with key dates
4. Identify dependencies
5. Assign team responsibilities
6. Update progress regularly

Daily Workflow

Morning Routine

1. Open Dashboard (00-MAP/Dashboard.md)

2. Review active items:

   • Check attack plans due today
   • Review milestone progress
   • Note any blockers

3. Create Daily Standup:

   • Use Ctrl+Shift+P → "Create Daily Standup"
   • Fill in yesterday's progress
   • Plan today's work
   • Note any blockers

During the Day

1. Work on active items:

   • Update progress in attack plans
   • Add notes to formal proofs
   • Capture research findings

2. Use Quick Capture:

   • Ctrl+Shift+P → "Capture Research Note"
   • Quick ideas, observations, findings
   • Automatically tagged and timestamped

3. Update Progress:

   • Ctrl+Shift+P → "Add Progress Update"
   • Adds timestamped progress note to current file

Evening Wrap-Up

1. Update active documents:

   • Mark completed tasks
   • Update status if changed
   • Add any blockers encountered

2. Review tomorrow's plan:

   • Check what's scheduled
   • Prepare any needed resources
   • Note any deadlines approaching

Working with Formal Proofs

Structure of a Formal Proof Document

---
title: "Theorem Name"
type: "formal-proof"
layer: "L0"
status: "draft"
---

# Theorem Name

## Overview
Brief description of what this theorem proves.

## Formal Statement
```lean
theorem theoremName [hypotheses] : conclusion :=
  sorry  -- TODO: Complete proof

Proof Strategy

1. Step one of the proof
2. Step two of the proof
3. Step three of the proof

Key Lemmas

• Lemma 1
• Lemma 2

Receipt Generation

def theoremNameReceipt (state : State) : String :=
  "theorem_name:" ++ toString state.val ++ ","

Verification Status

• Formal Verification: Pending
• Code Review: Pending
• Testing: Pending

### Linking Proofs

Create connections between proofs using wiki-links:
- `[[Dependency Theorem]]` - Link to a theorem this one depends on
- `[[Related Theorem]]` - Link to a related theorem
- `[[Used In Application]]` - Link to where this theorem is applied

### Proof Status Tracking

Use tags to track status:
- `#status-draft` - Initial creation
- `#status-in-progress` - Being worked on
- `#status-proven` - Proof complete (with sorry)
- `#status-verified` - Fully verified with complete proof

## Working with Receipts

### Receipt Structure

Each receipt document follows this structure:

```markdown
---
title: "Receipt Name"
type: "receipt"
schema: "receipt_v1"
status: "valid"
---

# Receipt: Receipt Name

## Receipt Metadata
```json
{
  "schema": "receipt_v1",
  "version": "1.0.0",
  "generated_at_utc": "2024-05-19T10:00:00Z"
}

Claim Boundary

What this receipt proves and its limitations.

Observation Layer

Measurements and observations made.

Decision Layer

Decisions based on observations.

Action Layer

Actions taken based on decisions.

Result Layer

Results of those actions.

### Receipt Dimensions

All receipts must include these dimensions:
- **C (Crossing Matrix)** - Topological state
- **σ (Sidon Slack)** - Address budget headroom
- **k (Step Count)** - Iteration count
- **ε_seq (Residual Series)** - Error measurements
- **t (Timing)** - Execution timing
- **∅_scars (Scar Absence)** - Failure record status

## Advanced Features

### Using Dataview Queries

Create dynamic tables and lists:

```dataview
TABLE status, priority
FROM #attack-plan
WHERE status = "active"
SORT priority DESC

Graph View

1. Press Ctrl/Cmd + G to open graph view
2. See connections between all documents
3. Use filters to focus on specific layers or types
4. Drag nodes to reorganize

Canvas

1. Create visual diagrams using Canvas
2. Add notes, images, and links
3. Connect elements with arrows
4. Save canvas files in appropriate folders

Excalidraw

1. Use for hand-drawn style diagrams
2. Good for architecture sketches
3. Can embed in other notes
4. Export as images for reports

Best Practices

Naming Conventions

• Formal Proofs: TheoremName.md (PascalCase)
• Attack Plans: Attack-Plan-Name.md (Kebab-case)
• Milestones: Milestone-Name.md (Kebab-case)
• Receipts: Receipt-Name.md (Kebab-case)

Tagging Strategy

Always include:

• Layer tag: #layer-L0 through #layer-L6
• Type tag: #formal-proof, #attack-plan, #milestone, #receipt
• Status tag: #status-draft, #status-active, #status-completed

Linking Strategy

• Link to prerequisites (upward dependencies)
• Link to related work (sideways connections)
• Link to applications (downstream uses)
• Link to receipts (validation artifacts)

Content Guidelines

1. Be Specific: Include exact Lean code, not just descriptions
2. Be Complete: Document assumptions, limitations, and edge cases
3. Be Current: Update status and progress regularly
4. Be Connected: Link to related documents generously

Troubleshooting

Common Issues

Templates not working

• Check Templater settings
• Verify template folder path
• Ensure <%* %> blocks are correct

Dataview queries not updating

• Use "Dataview: Force refresh all views"
• Check query syntax
• Verify frontmatter fields exist

Graph view too crowded

• Use local graph view (sidebar)
• Apply filters by tag or folder
• Adjust graph settings

QuickAdd not responding

• Check QuickAdd settings
• Verify command configurations
• Restart Obsidian if needed

Getting Help

1. Check this guide first
2. Review 00-MAP/Core Concepts for terminology
3. Look at existing documents for examples
4. Check Obsidian community forums for plugin-specific issues

Tips and Tricks

Keyboard Shortcuts

Shortcut	Action
Ctrl/Cmd + O	Quick switcher
Ctrl/Cmd + P	Command palette
Ctrl/Cmd + G	Graph view
Alt + Shift + F	Insert template
Ctrl + Shift + P	QuickAdd menu
Ctrl/Cmd + E	Toggle edit/preview
Ctrl/Cmd + B	Bold text
Ctrl/Cmd + I	Italic text

Productivity Hacks

1. Daily Notes: Create a daily note each morning for scratch thoughts
2. Zettelkasten: Use atomic notes with unique IDs for research findings
3. MOCs (Maps of Content): Create index notes for complex topics
4. Fleeting Notes: Use QuickAdd for quick captures throughout the day
5. Literature Notes: Keep notes on papers and references in 09-REFERENCES/

Organization Tips

1. Inbox: Use root level for temporary/quick notes
2. Processing: Move notes to appropriate folders after processing
3. Archiving: Move completed items to 10-ARCHIVE/
4. Review: Weekly review of all active items
5. Cleanup: Monthly cleanup of stale links and unused files

Next Steps

After completing this guide:

1. Your First Formal Proof - Create a complete formal proof document
2. Your First Attack Plan - Plan a research initiative
3. Dashboard Tutorial - Learn to use the dashboard effectively
4. Advanced Queries - Master Dataview for complex reports

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This guide is a living document. Update it as you discover better workflows.

#getting-started #tutorial #obsidian-vault