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Practitioner Toolkit

Section umbrella for the practitioner-side wiki: how a single researcher (institutional or independent) works rigorously at kitchen-table or personal scale. Three sub-buckets, each with a distinct character.

Three-tier structure

  1. Self-Experiments — n=1 personal protocols + active in-progress experiments. Brian doing things on himself, with discipline.
  2. DIY Capability Builds — kitchen-table / home / minimal-equipment procedures that enable self-experimentation (and, in several cases, double as Open Enzyme platform infrastructure).
  3. Rigor Disciplines — cross-cutting methodology that applies to all research modes: literature mining, evidence verification, falsification, AI-driven-discovery prior art. Pages live in their topical homes elsewhere on the wiki; cross-linked here.

Self-Experiments (n=1)

Personal protocols and in-progress n=1 work.

  • self-experiment-protocol.md — biomarker monitoring framework: blood panels (CBC / CMP / UA / hs-CRP / LDH / HbA1c), 16S stool, daily diary, red-flag halt criteria; specialty biomarkers (C3 / C4 / CH50 / C5a CP0; urinary LTE4 CP6a)
  • personal-genome-protocol.md — kitchen-table sequencing as both personal genome project AND Open Enzyme strain-QC infrastructure; gout pharmacogenomic query list (HLA-B*58:01, ABCG2 Q141K, SLC2A9, URAT1, PDZK1, MEFV)
  • PERT-timing self-experiment (April 2026 → ongoing) — BoulderBio dose/timing n=1; documented inline in digestive-enzyme-optimization.md. Splits dose-finding from formulation question for the engineered-platform endgame.

DIY Capability Builds

Kitchen-table / minimal-equipment procedures. Several of these double as platform infrastructure for the engineered-strain library.

  • koji-home-fermentation.md — wild-type small-batch koji protocol (koji-kin → koji rice → shio-koji / amazake); pre-engineering baseline + n=1 trial bed for the EPI co-target.
  • enzyme-quantification-protocol.md — tiered methods for measuring amylase / protease / lipase activity (kitchen → smartphone colorimetry → community-college bench → outsourced contract assay).
  • engineered-koji-protocol.md — engineering-stage protocol for A. oryzae multi-enzyme fermentation; bridges DIY-bio capability into platform engineering.
  • medicinal-mushroom-extract-sops.md — planned extract characterization SOPs (GLPP, cordycepin, ergothioneine); operator-independent reproducibility tolerances.
  • Low-cost liquid-handling automation (Picolab prior art, 2026-05-19). Picolab v2 is an MIT-licensed prototype that repurposes an Ender-style printer gantry into a syringe liquid handler with a FastAPI backend, React dashboard, G-code motion planner, calibration store, camera-assisted OpenAI agent workspace, and operator approval gate before hardware execution. For Open Enzyme, this belongs in the capability-build lane: plausible infrastructure for repeatable tube-scale colorimetric assays, serial dilutions, and quantification-ladder.md Tier ⅔ method development. It is not a sterile, clinical, or production liquid handler. Dedicated page threshold: create low-cost-lab-automation.md only after there is OE-specific analysis of bill of materials, positional/volume accuracy, contamination controls, assay compatibility, and first automatable protocols. (Engineering prior art; source: Picolab v2 repository)
  • Sequencing capability (sub-bucket of personal-genome-protocol.md) — MinION + Dorado + Flye / Clair3 pipeline for personal genome AND CRISPR integration verification, off-target indel screening, plasmid validation, released-strain genome QC.

Rigor Disciplines (cross-cutting)

Methodology that applies to all research modes — wet-lab, computational, literature, and self-experiment alike. Pages live in their topical homes elsewhere; cross-linked here for discoverability.

  • manual-literature-mining.md — five-rule protocol for safe LLM literature use (safe primitives only, anchor to meta.json, grep-verify all numbers, never propagate map / reduce summaries, cite line-anchored). Surfaced 2026-05-05 after documented Paperclip map operator hallucination.
  • chembl-cross-check.md — quarterly ChEMBL v34 cross-reference of stack compounds; separates direct-inhibitor claims from pathway-modulator claims (e.g., quercetin → 5-LOX, not NLRP3).
  • linter-design.md — two-linter architecture (Document Lint always-on; Falsification Lint on-demand per-hypothesis with killshot menus, failure-mode ontology, survival scoring).
  • tcm-modern-rigor-intersection.md — six-rule methodology for evidence-leveling traditional-medicine claims (chokepoint mapping, ChEMBL cross-check, bioavailability-honest framing, formula decomposition, standardized-extract specification, falsification-card discipline).
  • autonomous-screening-methodology.md — peer-track methodology page on ClockBase Agent (Ying et al. bioRxiv v3, late 2025 / early 2026); transferable patterns for comp-NNN: search-space sizing, composite-score ranking across orthogonal predictors, hypothesis-then-verify, autonomy boundary, N-of-M concordance for wet-lab handoff.
  • cross-validation.md — thesis stress-test discipline; risk matrix across all tracks; identifies true blockers vs. surmountable obstacles.

Section conventions

  • Evidence-level discipline applies. Every personal-protocol claim gets the standard wiki tagging (Clinical Trial / Animal Model / In Vitro / Mechanistic Extrapolation). n=1 is its own evidence level — useful for personal-protocol decisions, weak for population claims.
  • Privacy-by-default. Self-experiment data is private unless explicitly published. Genetic data in particular is governed by the privacy gradient in personal-genome-protocol.md.
  • Project crossover where applicable. Several self-experiment / DIY-bio capabilities (sequencing, fermentation, enzyme assays) double as Open Enzyme platform infrastructure. Pages flag this crossover explicitly.
  • Pre-commit grep-verify gate (CLAUDE.md §4) applies to load-bearing numbers in all three sub-buckets equally.

Open questions

  • Promote to a wiki/practitioner-toolkit/ subfolder? Currently 2 LIVE pages in Self-Experiments, 4–5 in DIY Capability Builds, 6 cross-linked in Rigor Disciplines. Promote when the LIVE count exceeds ~10 and the flat structure becomes unwieldy.
  • Pharmacogenomic priors → self-experiment monitoring. Should findings from personal-genome-protocol.md feed self-experiment-protocol.md as priors? (e.g., "ABCG2 Q141K homozygote → blunted allopurinol response → adjust biomarker monitoring cadence.") Likely yes; integration not yet drafted.
  • Compound self-trial sub-bucket. Once the first compound self-trial protocol is written, add a sub-bucket inside Self-Experiments. Candidates from the existing wiki: BHB / ketogenic-state, butyrate, theaflavins, KPV, BPC-157.
  • DIY-bio capability gaps. What's missing? Likely candidates: home tissue culture (Caco-2 / HepG2 for permeability + HDAC activity assays); home Western blot equivalent (smartphone-based dot blot? lateral flow strip protocol?); home ELISA equivalent for IL-1β / hs-CRP; low-cost liquid-handling automation that can make serial dilutions and colorimetric assay setup operator-independent. Each would unlock a tier of comp-NNN follow-ups.

Why this section exists

Open Enzyme is, structurally, a single-researcher project (Brian as platform / engineering, three PhD-level collaborator roles being recruited per team.md). The practitioner toolkit is what lets that scale stay rigorous: explicit personal protocols with halt criteria, capability builds that work at kitchen-table scale, and rigor disciplines that prevent single-operator failure modes (hallucination, post-hoc rationalization, evidence-level slippage). The three tiers reinforce each other.