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Systems Biology Protocol Library
Last Updated 28 Jun 2026

Getting Started



Illustrative starting dashboard showing constrained minerals, energy and glycogen status alongside elevated toxic metals, immunological debt and sympathetic bias.
Example starting-state. The aim is to stabilise capacity before increasing biological load.

ON-BOARDING CONCEPTS

Start by protecting reserves

This is where the recovery journey starts.

Here we focus on just the initial stabilising moves: conserve glycogen, correct minerals, metals and redox capacity, correct cardiovascular and inflammatory issues that affect the autonomic nervous system and avoid pushing metabolic processes faster than the body can buffer.

The onboarding process is a sequenced approach and the goal is to create enough stability that later stages are more appropriate and easier to interpret, while avoiding unnecessary symptoms created by moving bottlenecks around or failing to adapt diet to a changing landscape.

Sometimes symptoms can be created by a hyper-vigilant autonomic nervous system, which predicts threats based on previous, outdated information. This may be observed as a common set of symptoms to a wide variety of inputs, even at near-placebo doses, and usually settles within a few days. Slow titration helps.

Illustrative onboarding trajectory showing capacity improving, stored load falling and initial immune activity as a glycogen storage challenge.
Expected onboarding trajectory. Improvement can include a temporary immune and glycogen-storage challenge. Dietary carbohydrate, pacing and electrolytes are the practical buffers.
Illustrative trace showing perceived energy, glycogen stores and adrenaline over time as glycogen is depleted and replenished.
Glycogen and perceived energy. Adrenaline can temporarily mask low reserve while glycogen stores are depleted. Carbohydrates, pacing and electrolytes help restore reserve and reduce sympathetic pressure, usually after a "dead battery" transition state.

Before You Start

Things you will need

Most on-boarding steps rely on the same practical scaffolding: baseline patient data, a printed run-sheet and completed product ordering links. Explore all of these before working through the implementation sequence.

Baseline tests Send these first where possible, then use follow-up testing to interpret changes. Starter daily schedules Jump to the compounded-nutrient or separate-supplement run-sheet choice below. Ordering spreadsheet Jump to the starter ordering spreadsheet and region selector below.

Starter path

Overview

These are outlines of the concepts described in detail further down, in the protocol on-boarding sequence:

1

Pacing

Pacing protects glycogen and avoids the acidaemia-related spiral that can worsen electrolyte and mineral depletion.
2

Maintain lymph flow

Use gentle lymphatic support before restoring mitochondrial metabolism and immune activity.
3

Stabilise carb intake

As glycolysis and immune activity increase, glycogen storage can become a practical load to manage.
4

Stabilise minerals and redox

Introduce electrolytes, antioxidants and cofactors slowly enough that the response remains interpretable.
5

Cardiovascular health is essential

A focus on structural, immune, inflammatory processes, oxidative stress, histamine and the nervous system.
6

Para-/sympathetic signalling cascade

Check nasal breathing patterns, sleep and inflammation.

Detailed sequence

Please follow these steps with care and accuracy

This section contains a structured, logical starting order which is designed to minimise the introduction of unnecessary symptoms. Notes for each area are provided to help navigate this process.

Orientation: a gentle approach
Needed here Baseline tests Starter schedule Ordering spreadsheet
This protocol is a comprehensive framework which addresses how to quantify and remediate different aspects of chronic diseases that share mitochondrial dysfunction as a common feature. 

However, the protocol also spans over 250 printable pages - so it's also completely understandable if you find yourself feeling a bit overwhelmed by the volume of new information needing to be absorbed.. likely while still battling brain fog and energy envelope issues, chronic feelings of fight/flight and other challenges.

Removing some or all of these debilitating issues should help improve the absorption and retention of new information. The focus of this section is to order and integrate JUST the essential items needed to get started on stabilising the key metabolic pathways. You can integrate them using the order described below, also noted in the daily schedules / run-sheets provided at the end of this section, along with a product ordering spreadsheet.

Ideally after sending off your baseline tests, you may help stabilise critical parts of the metabolism and help avoid unwanted MCAS + other symptoms by;
1. Pacing appropriately
Needed here Pacing section
1. Pacing appropriately, to avoid low glycogen promoting the acidaemia-related spiral towards progressive electrolyte and mineral depletion, resulting in progressive baseline worsening (see 2.2.4 The importance of pacing).
2. Working on lymph flow
Needed here Lymphatic maintenance
2. Working on your lymph flow - (see 2.2.2 Lymphatic maintenance - this is especially important if addressing the nutrient deficiencies allows immune activity to initially increase, which is progressively more likely when these deficiencies are severe.)

Notes:
i) Failure to maintain lymphatic flow can result in compartment-specific pressure buildup, eg. intracranial pressure.
ii) For severe patients, this may need to be actioned by carers and/or professionals. Sensitivity to touch may initially prevent performing this necessary step, however it should be actioned as soon as possible.
3. Food, dysbiosis phases and glycogen support
Purpose Buffer energy availability while dysbiosis work and nutrient repletion change demand.
Needed here Diet guidance, dysbiosis phasing and carbohydrate planning.
Watch for More immune activity increasing carbohydrate and electrolyte needs.
Needed here Diet GI dysbiosis phases Meal Planner
3. Consuming the suggested food items in 2.2.1 Diet, while also integrating the phases described in 2.2.3 Living without chronic dysbiosis - Gastrointestinal biofilms and pathogens. A new Meal Planner tool has also been added to help you reach targets safely.

Notes:
i) Eat strategically to ensure glycogen stores are being appropriately supported - in this model, restoring insulin sensitivity and glycogen synthesis may increase carbohydrate tolerance and need. Some people may rapidly require >200-250g of net carbohydrates / day, or (much) more, absorbed over >3-6 meals / snacks, as the metabolism improves, to avoid sympathetic reflex. In a "crash", hourly "snacks" of 15g net carbs can be very helpful. In metabolic syndrome and type 2/3 diabetes contexts, treat this as staged metabolic repletion rather than generic high-carbohydrate advice; track glucose responses and use clinician guidance if insulin-dependent, using glucose-lowering medication, prone to hypoglycaemia, or managing eating-disorder risk. [134] [135] Carbohydrate needs reflect (immune) activity levels and other factors. A number of the supplements included below will help glycogen homeostasis.
ii) The initial goal is a low-inflammatory, low-histamine, low-oxalate diet - ideally, one that avoids triggering foods - however this doesn't need to be "perfect", just "good enough". This will later expand to include a wide array of plants, their helpful polyphenols, microbiome nourishing fibres / starches and numerous other useful compounds, whilst accompanying targeted, staged probiotics that focus on butyrate production and epithelial integrity, before repopulating lactobacillus, bifidobacterium, oxalobacter and other helpful species. 
4a. Electrolytes, resveratrol, ashwagandha and magnesium gel
Purpose Stabilise the redox and mineral + metal terrain before larger metabolic shifts.
Needed here Electrolyte targets, DIY sipper/shots, run-sheet and ordering links.
Watch for GI response, calcium sensitivity, adrenergic shift and carbohydrate need.
Needed here Electrolytes DIY sipper/shots Electrolyte Calculator Starter schedule Ordering spreadsheet

Electrolyte recipe

4. Stabilise the redox and mineral terrain. This includes VERY SLOWLY introducing:

a) electrolytes (see 4.1 Electrolytes), taken slowly over the day, by making a daily / weekly recipe of specific electrolytes and amino acids to put in a 500ml drink bottle and slowly sip / pour a "shot" into a glass, top up with water and drink between meals (see 4.3 DIY "sipper / shots"). You can start at eg. 1/8 daily doses and slowly increase.

Daily targets

The daily targets for each electrolyte compound used are also listed in the daily schedules at the end of this page.

These are daily protocol targets for staged repletion, not generic supplement advice. Adjust for dietary intake, kidney function, medications, blood pressure/volume status, and baseline/follow-up testing; as with the rest of the protocol, use clinician supervision where there is kidney, cardiac, endocrine, pregnancy, medication, or severe illness complexity.

These targets allow for minimal dietary intakes and can be further adjusted around consistent dietary intake patterns, using this calculator tool:

Magnesium Glycerophosphate - 4g total powder (500mg elemental magnesium, 638mg phosphorous) / day. Can also be taken sublingually for higher repletion efficacy.
Calcium Aspartate - 5.5g total powder (750mg elemental calcium) / day.
Potassium Citrate - 13g total powder (4940mg elemental potassium) / day.
Sodium Bicarbonate - 5g total powder (1350mg elemental sodium & 3650mg bicarbonate) / day.
Sodium Chloride - 5-7g total powder (2730mg elemental sodium & 4270mg chloride) / day.

Resveratrol

Resveratrol can be very slowly added here (not in the "sipper/shots" recipe) 3x/day - initially starting at 50mg and increasing to 500mg per dose, to help protect against additional lactic acid being created by unblocking bottlenecks in glycolysis (correcting phosphate, magnesium, etc) while the TCA cycle is less efficient. This may improve insulin sensitivity and expose any hypothyroidism -> hepatic gluconeogenesis impairment, presenting as postprandial somnolence, brain fog, hunger, anxiety.

Ashwagandha

Ashwagandha can be very slowly added here (not in the "sipper/shots" recipe), starting with an evening dose of 25-50mg (1/10th capsule) and working up to a full evening dose before adding a morning dose, which shouldn't need much titration. Ashwagandha may affect stress, sleep, endocrine, immune, and thyroid-related pathways, but it is not appropriate for everyone. Avoid during pregnancy or breastfeeding, and like the rest of this protocol, use medical guidance with thyroid disease, autoimmune disease, liver disease, planned surgery, sedatives, anticonvulsants, immunosuppressants, diabetes or blood-pressure medicines, thyroid hormone, or hormone-sensitive prostate cancer risk.

Thyroid hormone option

An alternative option to Ashwagandha that your doctor may consider is thyroid hormone replacement. In the disease model, (levo)thyroxine (T4) may be more appropriate where iodine is low and selenium is normal, while triiodothyronine (T3) may be more relevant where selenium is low, regardless of iodine status.

Thyroid hormones are usually started and titrated gradually under medical supervision, guided by symptoms, thyroid blood tests and cardiovascular risk. Some people notice improved energy levels or functionality quite quickly, but as dosing increases and endogenous thyroid synthesis is suppressed, there can be a temporary step backwards or a need for prompt dose review and adjustment. Your doctor can advise how best to manage this process, including whether split dosing, such as early morning and early afternoon dosing, is appropriate.

Magnesium gel

Liberally applying the magnesium gel after showering, can be highly effective for magnesium absorption and is included in the schedule.

Notes and cautions

Notes:

i) Consuming too much at once may cause diarrhoea, headaches, nausea, water retention and/or rapid urination. With severe dysbiosis, some electrolyte forms can also act as biofilm breakers and trigger immune activity in the form of temporary nausea and diarrhoea, even at smaller doses. Within the protocol this may sometimes be interpreted as a transient response, but persistent, severe, dehydrating, bloody, febrile, or otherwise concerning symptoms should prompt dose reduction/cessation and clinical review. If symptoms persist, try to isolate the trigger and consider swapping out forms. eg. Potassium citrate can be swapped for potassium chloride.

ii) Calcium and, to a lesser extent, potassium may temporarily increase adrenergic / glutamatergic sensitivity and need to be increased more slowly than the other electrolytes. Calcium sensitivity needs to be tested and managed carefully. Where adrenergic, dopaminergic or related auto-antibody patterns are suspected, treat this as a clinical caution rather than a proven predictor, and replete slowly while tracking symptoms. (see 4.1 Electrolytes)

iii) Starting magnesium and/or phosphate may support glucose handling, ATP production and glycogen synthesis where deficiency or refeeding-like physiology is present. [84] [88] Experiencing symptoms that resemble hypoglycaemic events or diabetic "hangry" mood alterations may indicate more dietary carbohydrates are needed.

iv) This recipe can also be combined with eg. green or other tea, lemon juice, lime juice, acai, berry, etc for flavour. The glycine added in the next step sweetens the flavour considerably.

v) Shake before each use.

vi) Ashwagandha is known to trigger anhedonia symptoms in some people, which is expected to resolve as neurotransmitters re-balance from less sympathetic drive, over 2 weeks. There are also potential interactions with SSRIs and some general cautions for excessive serotonin. However, ashwagandha has also been studied for OCD in SSRI-using patients without adverse effects.

4b. Antioxidants and mitochondrial cofactors
Needed here Starter schedule Ordering spreadsheet Rapid-withdrawal watch

        b) antioxidants and mitochondrial cofactors (Vitamin C, Vitamin E, R-ALA, CoQ10, and Glutathione donors like NAC, Serine -> Glycine), taken 2-3x/day. 

Notes:
i) These may need TINY doses, initially, eg. 50-100mg of Vitamin C, NAC, Serine, Glycine and CoQ10. Introduce these individually. 
ii) Vitamin E and R-ALA are normally less sensitive. R-ALA and Glutathione donors may increase insulin sensitivity, exposing any hypothyroidism -> impaired hepatic gluconeogenesis. Serine can unblock a methylation bottleneck, creating a temporarily adrenergic shift in metabolism. For people with severe neuropsychiatric symptom susceptibility, this may need a slow titration.   
4c. Carnitine, creatine, uridine, D-ribose, taurine and inosine
Needed here DIY sipper/shots Electrolyte Calculator

        c) (usually less slowly) L-carnitine / acetyl L-carnitine, creatine (for fatty acid transport and ATP-PC pathway), Uridine monophosphate (sublingually - ramping up from 10, to typically 50-100mg, 2x/day) and similar slowly ramp up of D-ribose, starting at 500mg, to 10g, added to the daily DIY "sipper/shot" recipe. Slowly add in the other DIY "sipper/shot" recipe ingredients, eg. Taurine, Hyaluronic acid, N-acetylglucosamine. SLOWLY titrate a morning sublingual dose of Inosine from 10mg to 50-100mg range. The sources for these components support their roles in fatty-acid transport, creatine/phosphocreatine energy buffering, D-ribose/CFS pilot context, uridine/nucleotide physiology, and taurine safety/microbiome interactions; the low-dose ramping schedule is protocol titration and should be individualised. [100] [113] [114] [115] [116] [117] 

Notes:
i) Expect insulin sensitivity and glycogen synthesis to increase with Uridine, D-Ribose and Inosine - be prepared to increase intakes of carbohydrates to facilitate glycogen synthesis and potentially sodium + other electrolytes, towards their daily targets. This may also expose any hypothyroidism -> hepatic gluconeogenesis impairment, presenting as postprandial somnolence, brain fog, hunger, anxiety.
ii) Inosine is also an immune stimulant, and may trigger some initial immune activity - keep the dose low, eg. 50-100mg. Hold at this dose until Stage 2 of the protocol, or otherwise metabolically ready for an increased immune activity phase. If an "unmanageable" level of immune system response presents. If symptoms become difficult to tolerate, reduce the dose to 25-50mg and reassess.  
iii) Taurine may cause GI discomfort in some people, particularly where bile-acid handling or microbiome ecology is abnormal; lower-dose or sublingual use can be considered if tolerated. [118] [119] [120]
4d. Correcting mineral cofactor deficiencies and excess toxic metals
Needed here Remineralisation Ordering spreadsheet Starter schedule

d) Adding mineral cofactors like Zinc, Copper, Iron, Manganese, Selenium, Iodine, Lithium, Rubidium, Cobalt, Boron, and Molybdenum, etc. This helps balance the neurotransmitter synthesis pathway (and precursors), lowers the burden on ALDH and MAO pathways and reduces oxidative stress, allowing safer processing of neurotransmitter metabolites. [82] [138] (see 2.3.2 Remineralisation).

MiADMSA can be started at 5mg (active) / 27mg total (about 1/20 of a 100mg (active) capsule / 550mg total) and titrated for severe / sensitive patients; otherwise, 100mg every 3 days may be used. Maintain sufficient hydration and urinary excretion. Early data and protocol experience suggest that between 5-10 x 100mg doses may be sufficient for many people to achieve a highly functional metabolic shift. Chelation is an active intervention, so use clinician guidance where there is kidney, liver, pregnancy, medication, or severe illness complexity.

PectaSol (optional) can be started at 0.5g and titrated to 5g before meals. PectaSol may trigger reactions in some people.

Notes:
i) Many of the minerals require non-standard routes for absorption, eg. sublingual, liposomal, DMSO-carrier.
ii) Remineralisation will be severely limited if acidaemia / acidosis is still present.
iii) Immunological debt is likely to become a focus for the system as the mineral + toxic metal balance is improved. Immune activity, inflammation, pain, rashes, etc are expected and carbohydrate needs may increase to help maintain functionality during immune response and new baseline metabolism.
iv) Expect glucose metabolism to rapidly improve and net carbohydrate needs to rapidly increase to >200g / day, to avoid glycogen insufficiency. The examples below show approximate 2200 kcal day structures for omnivore, vegetarian and vegan diets that spread carbohydrate intake across the day. Treat them as adaptable starting points rather than fixed prescriptions: adjust around current diet phase, histamine / oxalate tolerance, glucose response, kidney function, medication context and clinician guidance. During immune activity, carbohydrate and electrolyte needs may rise further.

Omnivore examples
Vegetarian examples
Vegan examples

Example diet plans

Example 1 of 3
Download example 1
4e. Active B1/B2 and compounded nutrients
Needed here Compounded nutrients Starter schedule Rapid-withdrawal watch

         e) Introducing Vitamins B1 and B2 in active or near-active forms - such as TPP / cocarboxylase and FMN / R5P. These support mitochondrial redox balance, glycolysis, and the pentose phosphate pathway; the active-form dose range below is protocol-specific titration rather than a guaranteed clinical correction. [136] [137] [127] Depending on the severity of dysbiosis / acetaldehyde burden, the total daily B1 dosing can range from 50-600mg of the active form, cocarboxylase / thiamine pyrophosphate (not to be confused with eg. thiamine or thiamine HCL which would require much higher doses), starting from a low dose. 

Notes:
i) Compounded nutrients are available (see 4.2 Compounded nutrients) and replace a wide range of individual supplements. The compounded nutrients are potent, therefore starting at eg. 1/8th doses, may be helpful to soften / slow the metabolic shift when restoring severe deficiencies. 
ii) B vitamin titration options for patients with severe neuropsychiatric sensitivity are also discussed.
iii) Additional B1, in any form, can be added for further acetaldehyde adduct-forming and detoxification support, later - noting the impact of rapid removal of acetaldehyde -> endogenous morphine. (see 2.3.4 Rapid withdrawal, hypo-/hypermetabolism) 
iv) Adding B1 can increase B9 transporter activity and SAMe availability, allowing some adrenergic signalling increase unless B2 and NAD+ are restored in balance - start slowly.
4f. Other B vitamins, methylation and monoamine cautions
Needed here Starter schedule Vitamin Q context Rapid-withdrawal watch

        f) Slowly layer in Vitamins B5, B6 (as P5P), Biotin, D-Chiro Inositol, B9 and B12 (as methylcobalamin or hydroxocobalamin) only after upstream redox stress is under better control. 

Notes:
i) B1, B9 and B12 can increase methylation -> SAMe availability, unblocking epinephrine synthesis at PNMT and also COMT activity, leading to hyper-adrenergic signalling if TOO MUCH is introduced quickly, ie. without sufficient B2 for MAO and NAD+ (and redox) for ALDH. 
ii) In the context of unresolved aldehyde or monoamine overload, these can also be disruptive (unless P5P is eg. dissolved in DMSO, bypassing impaired alkaline phosphatase (ALP) and pyridoxal kinase (PK) steps) and BH4 synthesis (dietary queuine - see "Vitamin Q deficiency").
NB. Acetaldehyde, NAD redox and rapid withdrawal
Needed here Rapid withdrawal Starter schedule

NB. Reducing acetaldehyde burden and/or restoring NAD+:NADH status may improve several downstream metabolic bottlenecks; within the disease model, effects on ALDH/dopamine/THP/endogenous-morphine pathways remain a proposed mechanism built from component evidence. [13] [30] [68] [82]
Stay keenly observant for rapid withdrawal symptoms and manage them proactively.

4g. NAD+ pool support and methylene blue
Needed here Methylene blue detail Rapid-withdrawal watch Starter schedule

Then;
        g) Introducing NAD+ pool support (apigenin - P38 inhibitor), NAD+:NADH redox support (0.05-0.3mg of methylene blue, once per day), and

Notes:
i) Start at 0.05mg (50mcg) of methylene blue per day and slowly increase every 2-3 days until ANY metabolic shift is observed. Hold at that dose and look to decrease towards 50mcg, when appropriate. Safety note: most formal warnings and case reports involve doses orders of magnitude higher than used here, and usually intravenous methylene blue. However, methylene blue is pharmacologically active and has recognised drug-interaction and contraindication issues, so check the detailed methylene blue section before starting, especially if using serotonergic medicines, opioids, dextromethorphan, or if G6PD status is unknown. [77] [78] Prepare and dose carefully.

ii) "MORE IS NOT MORE." THE MITOCHONDRIAL SUPPORTING EFFECT OF METHYLENE BLUE IS LOST AT HIGHER DOSE RANGES.
iii) Expect and watch for alcohol / opioid withdrawal symptoms. Manage them proactively.
iv) The microdose range here is protocol-derived from nM-level mitochondrial/cell-culture methylene-blue work and oral pharmacokinetic scaling. It should be read as model-based dose reasoning, not as a clinically validated oral microdose range. [111] [112] [81]

4h. Sublingual NAD+
Needed here Rapid-withdrawal watch Starter schedule

        h) Adding active vitamin B3, as sublingual NAD+ (NOT precursors - niacin, nicotinamide / niacinamide, nicotinamide riboside / mononucleotide) at 5-10mg doses, 2x/day and increase to 20-40mg 2x/day. 

Notes:
i) Expect and watch for alcohol / opioid withdrawal symptoms. Manage them proactively. (see 2.3.4 Rapid withdrawal, hypo- / hyper metabolism)

5. Blood-flow, hypoxia and structural contributors
Needed here Blood-flow/hypoxia Structural issues Cortisol/glycogen
5. Testing for and addressing blood-flow / hypoxia -> acidaemia issues - especially relating to chronic infection, thoracic outlet syndrome and cranial instability, affecting the CNS alarm signalling cascade (see 2.3.3 Blood-flow, hypoxia and fibrin-amyloid, 2.2.5 Structural issues and 2.2.6 Cortisol, limbic system, glycogen and IFN-gamma).
6. Histamine and sympathetic overdrive influences
Needed here Cortisol/glycogen Nasopharynx

6. Start working on identifying and addressing any/all other influences affecting histamine and/or sympathetic overdrive (see 2.2.6 Cortisol, limbic system, glycogen and IFN-gamma). 
 
Notes:
i) Unrestricted, deep nasal breathing without localised inflammation is a basic requirement for parasympathetic signalling (see also 2.2.3 Living without chronic dysbiosis - Nasopharynx).

(PRINTABLE) SPREADSHEET RESOURCES

Schedules and ordering links

Use these (optional) focused starter resources before moving into the full protocol schedule and full product-ordering pathway.

"Starter" daily schedule / run-sheets

Once you have sufficiently stabilised, the full Stage 1, 2 and 3 schedule options are available in 2.3 Daily supplement schedule. For onboarding, use the simpler starter run-sheet and DIY sipper daily recipe that matches how you intend to source nutrients.

I plan to start the protocol:

Using compounded nutrients Using separate store-bought supplements

"Starter" product ordering links

If you are already committed to completing the whole protocol, the full primary-pathway product list is in 5 Ordering products. For now, the table below exports a smaller starter-items spreadsheet.

Download the spreadsheet below

1. Choose shipping region

Select the relevant region from the drop-down menu before exporting.

2. Export Excel or CSV

Use Excel for a working spreadsheet, or CSV for a plain data export.

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