Systems Biology Protocol Library

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Patient Clinician Technical

The Disease Model

(Preliminary) Data Analysis

Protocol Shortcuts

Getting Started Introduction Remineralisation & Toxic Metals Electrolytes Diet Living Without Chronic Dysbiosis Structural Issues Sympathetic Overdrive, Glycogen, MCAS and Dysautonomia Rapid Withdrawal, Hypo/Hyper-metabolism 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

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

↳ Toxic metals chelation

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

4.4 (Optional) Bulk DIY minerals

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

(Preliminary) Data Analysis

Protocol Shortcuts

Getting Started Introduction Remineralisation & Toxic Metals Electrolytes Diet Living Without Chronic Dysbiosis Structural Issues Sympathetic Overdrive, Glycogen, MCAS and Dysautonomia Rapid Withdrawal, Hypo/Hyper-metabolism NotebookLM AI Assistance Single Page View (for printing / PDF)

Meal Planner Electrolyte Calculator Find an Oligoscan Practitioner Oligoscan PDF Processor Universal OAT Tool Metabolic Pathway Overlay Biomesight Analysis Antimicrobial Library

Last Updated 9 Jun 2026

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Compass

Help find your way into Born Free

Introduction↗ Getting Started↗ Protocol Helper Wizard↗ Disease model↗ Videos and presentations↗

Schedules and ordering

Starter

Starter schedules↗ Starter ordering↗

Full protocol

Full daily supplement schedule↗ Full supplement ordering guide↗

These links explain the schedules. Compass does not choose one for you.

Electrolyte amounts

Electrolyte calculator↗ Electrolyte guidance↗

Food and gut

Diet guidance↗ Meal Planner↗ Living without chronic dysbiosis↗

Tests and result tools

Before a test

Collect your data↗ Find an Oligoscan practitioner↗

Result tools

Oligoscan PDF Processor↗ Universal OAT Tool↗ Biomesight Analysis↗ Metabolic Pathway Overlay↗

Other topics and resources

Topic guides

Remineralisation↗ Chest pain and slipped rib syndrome↗ Cortisol, limbic system and glycogen↗ Rapid withdrawal↗

More resources

NotebookLM setup guide↗ Printable protocol↗ Frequently asked questions↗ Research references↗

Clinician education: register interest with CSI ↗