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Systems Biology Protocol Library
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Contents
1
Overview
1.1
Summary
1.2
Disclaimer
1.3
Contents
1.4
Introduction
2
The protocol
↳ Severe neuropsych onboarding
↳ Getting started
2.1
Collect your data
2.1.1
Blood tests
2.1.2
Intracellular minerals
2.1.3
Organic Acids Test (OAT)
2.1.4
Cronometer
2.1.5
Microbiome testing
↳ Fermenting species identification
2.2
Lifestyle changes
2.2.1
Diet
↳ Feeding energy pathways
↳ Standard mixed diets vs ketogenic diets
↳ Active Vitamin A deficiency
↳ Vitamin Q deficiency
↳ Strategic eating
2.2.2
Lymphatic maintenance
2.2.3
Living without chronic dysbiosis
↳ Nasopharynx
↳ Gastrointestinal biofilms and pathogens
↳ Mammary glands, lactiferous ducts
↳ Parasites
↳ Glycocalyx
↳ Interventions
↳ Binders
↳ Bacteriophages
↳ DIY antiseptic recipe
↳ Biofilm breakers
↳ Protective probiotics
↳ Prebiotics
↳ Herbal anti-microbials
↳ Prescription anti-microbials
↳ Environment
2.2.4
The importance of “pacing”
↳ Acidaemia: a key influence in disease progression
↳ NADPH: a reductive "currency", powered by TCA cycle flux
2.2.5
Structural issues
2.2.6
Cortisol, limbic system, glycogen and IFN-γ
↳ Histamine triggers glycogen redistribution
↳ Sympathetic overdrive
↳ Anxiety, isolation, and phobia
2.2.7
Reproductive health, menstrual cycles, UTIs and PSSD
2.2.8
Sleep
2.2.9
PEM prevention and recovery
2.3
Daily schedule
↳ 2.3A Alternative – [no compounded nutrients]
↳ 2.3B Alternative – [no DIY shake]
↳ 2.3C Alternative – [no DIY shake or compounded nutrients]
↳ 2.3D Starter Schedule [compounded nutrients]
↳ 2.3E Starter Schedule [without compounded nutrients]
2.3.1
Herxheimer / die-off / acetaldehyde support
↳ Methylene Blue - "A lifeguard for the NAD+ pool"
2.3.2
Remineralisation
2.3.3
Blood-flow, hypoxia and fibrin-amyloid
2.3.4
Rapid withdrawal, hypo/hypermetabolism
2.4
Optional follow-up
2.5
Ongoing preventative maintenance
3
Rationale for protocol inclusions and general notes
4
Calculating supplement doses
4.1
Electrolytes
4.2
Compounded nutrients
4.3
DIY powder
5
Ordering supplements
5.1
Bacteriophage lookup
6
FAQ
7
Changelog
8
References
Protocol Tools
Meal Planner
Electrolyte Calculator
Find an Oligoscan Practitioner
Oligoscan PDF Processor
Universal OAT Tool
Metabolic Pathway Overlay
Biomesight Analysis
Antimicrobial Library
The Disease Model
Protocol
Getting started
NotebookLM AI Assistance
Single Page View (for printing / PDF)
Tools
Meal Planner
Electrolyte Calculator
Find an Oligoscan Practitioner
Oligoscan PDF Processor
Universal OAT Tool
Metabolic Pathway Overlay
Biomesight Analysis
Antimicrobial Library
Videos
Theme:
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System
Light
Dark
Last Updated 11 Feb 2026
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