Genome Log

Genome Daily Logger

Track daily health data and get genetically-informed feedback. Every data point connects to the user's genetic profile — this isn't generic tracking, it's personalized monitoring that builds evidence over time for what works and what doesn't.

Two Modes

1. Conversational (Claude Code skill — default)

When the user mentions health data casually, extract and log it:

User says: "I took sertraline and alflorex this morning, feeling pretty anxious though" You do:

1. Read or create today's daily note (Daily/YYYY-MM-DD.md from Templates/_Daily.md)
2. Update: sertraline_50mg: true, alflorex: true, anxiety: 6 (ask for 0-10 if not clear)
3. Provide genetic context: "Anxiety 6 with FKBP5 C;T — cortisol may be running high. A 15-min walk would help both HRV and dopamine (DRD2)."

User says: "my stomach is killing me and nose is stuffed" You do:

1. Update symptoms: ask for gi_discomfort (0-10) and nasal_congestion (0-10)
2. Flag pattern: "GI + nasal together = classic histamine pattern (ABP1 3x het). What did you eat in the last 2 hours? Any aged cheese, canned fish, fermented food?"

User says: "what did I take today?" You do:

1. Read today's daily note, show current log
2. Flag anything missing from the usual stack

2. CLI (standalone script)

# Full interactive (all categories)
python3 scripts/daily_log.py

# Quick mode (supplements + medications only, ~15 sec)
python3 scripts/daily_log.py --quick

# Show today's log
python3 scripts/daily_log.py --show

# Specific date
python3 scripts/daily_log.py --date 2026-04-01

# Open in editor
python3 scripts/daily_log.py --edit

Script resolves vault from $GENOME_VAULT_ROOT, config/default.yaml, or auto-detects.

Daily Note Format

YAML frontmatter in Daily/YYYY-MM-DD.md:

medications:
  sertraline_50mg: true
supplements:
  methylfolate: true
  P5P: true
  alflorex: true
  # ... (full list in template)
symptoms:
  anxiety: null        # 0-10, null = not tracked
  gi_discomfort: null
  nasal_congestion: null
interventions:
  exercise: false      # boolean
  morning_walk: false
metrics:
  bristol_scale: null  # numeric
  sleep_hours: null
  caffeine_mg: null

• Boolean (medications, supplements, interventions): true/false
• Scale (symptoms): 0-10 where 0 = absent, 10 = worst
• Numeric (metrics): raw value, unit defined in Tracking Registry
• Null = not tracked today (different from false or 0)

Template pre-fills supplements as true (optimistic — untoggle what was missed).

Genetic Context Responses

When logging symptoms, provide brief genetic context — this is what makes this tracker different from any generic app. The user's profile is in .claude/CLAUDE.md (Key Genotype Quick Reference section). Key patterns:

Analysis Mode (/genome-log analyze or /log patterns)

Scans daily notes for patterns, correlations, and actionable insights.

CLI

python3 scripts/daily_analyze.py              # Last 14 days
python3 scripts/daily_analyze.py --days 30    # Last 30 days
python3 scripts/daily_analyze.py --json       # Machine-readable
python3 scripts/daily_analyze.py --save       # Save report to vault

What It Finds

1. Supplement adherence — % taken over period, flags <80%

2. Symptom trends — average, range, trend direction (improving/worsening/stable) by comparing first half vs second half of the period

3. Supplement → symptom correlations — "Days after taking P5P, anxiety averages 3.2; days without P5P, anxiety averages 5.8 (diff: 2.6 pts)" Requires ≥2 data points each way. Only surfaces differences ≥1.0 point.

4. Exercise effect — same correlation logic: "Next-day GI after exercise: 2.1; without: 4.8"

5. Pattern detection:

• GI ≥5 + nasal ≥5 same day → histamine pattern (ABP1)
• Anxiety ≥6 + no exercise → DRD2 dopamine unaddressed
• Morning stiffness ≥5 → HLA-B27 inflammatory flare
• Sleep quality <4 + caffeine >150mg → CYP1A2 overshoot

Conversational Analysis

When triggered via Claude Code, provide genetic-informed interpretation:

"Over the last 14 days, your GI discomfort averaged 5.2 and correlated with days you skipped P5P (avg 6.8 without vs 3.4 with). P5P is a DAO cofactor — your ABP1 3x het means DAO needs all the cofactor support it can get. Also noticed GI + nasal congestion co-occurred 4 times — classic histamine pattern. The elimination diet trial would give clearer data."

When to Suggest Analysis

• After 7+ daily notes exist
• When user asks "is X helping?"
• When symptoms are trending worse
• Weekly (Sunday evening via weekly-learn daemon)
• Before prescriber visits (to bring data)

Definitions & Dashboard

• Tracking Registry: Protocols/Tracking Registry.md — all item IDs, doses, gene links
• Adherence Dashboard: Meta/Supplement Adherence.md — auto-calculated via Dataview
• Template: Templates/_Daily.md — daily note template with all fields

Adding New Tracked Items

1. Add definition to Protocols/Tracking Registry.md (ID, name, scale, gene basis)
2. Add field to Templates/_Daily.md in the right category
3. Existing daily notes don't need updating — missing fields default to null

Setup Mode

First-time setup or when changing what to track.

Interactive Setup (/genome-log setup or CLI --setup)

Walks through each category and asks what to track:

1. MEDICATIONS
   Current: sertraline 50mg
   Add medication? (name + dose, or Enter to skip): _
   
2. SUPPLEMENTS
   Suggested from genetic profile:
     ✓ Methylfolate 400mcg (MTHFR A1298C + MTRR G;G)
     ✓ P5P 25mg (ALPL C;C — DAO + GABA cofactor)
     ✓ Mg glycinate 400mg (GABA-A, general cofactor)
     ✓ Omega-3 EPA/DHA ≤2g (FADS1/2 het)
     ✓ D3+K2 (VDR variants)
     ✓ B12 methylcobalamin (MTRR G;G)
     ✓ NAC 600mg (IL1B, antioxidant)
     ✓ Vitamin C 500mg (DAO cofactor)
   Currently taking:
     ✓ Alflorex (IBS-D, started 2026-03-30)
     ✓ Sertraline 50mg
   Add more? (name + dose, or Enter to finish): _
   Remove any? (name, or Enter to keep all): _

3. SYMPTOMS
   Suggested for your profile:
     ✓ anxiety (FKBP5, SLC6A4, COMT)
     ✓ gi_discomfort (ATG16L1, ABP1)
     ✓ nasal_congestion (ABP1, IL1B — VMR)
     ✓ sleep_quality (PER3, CYP1A2)
     ✓ fatigue (ALPL, MTRR)
     ✓ morning_stiffness (HLA-B27, IL1B)
   Add custom symptom? (name, or Enter): _

4. INTERVENTIONS
   Suggested:
     ✓ exercise
     ✓ morning_walk
     ✓ breathing (FKBP5 cortisol management)
     ✓ resistant_starch (ATG16L1 butyrate)
     ✓ low_histamine_day (elimination protocol)
     ✓ saline_rinse (VMR)
   Add custom? _

5. METRICS
   Suggested:
     ✓ bristol_scale (IBS-D)
     ✓ sleep_hours (FKBP5 cortisol debt threshold: <6h)
     ✓ caffeine_mg (CYP1A2 ≤150mg)
     ✓ steps (auto from Health MCP when available)
   Add custom? _

Setup generates:

• Updated Templates/_Daily.md with chosen fields
• Updated Protocols/Tracking Registry.md with definitions + gene links
• First daily note for today

CLI Setup

python3 scripts/daily_log.py --setup

Same interactive flow in the terminal. Can also be run non-interactively:

# Add a supplement
python3 scripts/daily_log.py --add-supplement "Lasea 80mg" --timing evening

# Add a symptom
python3 scripts/daily_log.py --add-symptom "joint_pain" --scale 0-10

# Remove an item
python3 scripts/daily_log.py --remove "butyzol"

# Show current tracking config
python3 scripts/daily_log.py --config

Partial Updates

The user doesn't need to fill everything at once. Common patterns:

• Morning: "took my supplements" → update supplement booleans only
• Afternoon: "stomach hurts" → update gi_discomfort score
• Evening: "did 30 min calisthenics" → update exercise: true, add note
• Before bed: "log symptoms" → full symptom pass

Each update reads the existing daily note and merges — never overwrites previous entries.