Kenosian Protocol Platform

KPP Architecture

Computational infrastructure for longevity biology

Pipeline Overview

KPP processes biological data through a three-stage pipeline. Each stage produces verifiable outputs that feed directly into the next, with a TTTPS timestamp anchoring every result to a specific point in time.

Stage 0
Phenotypic Aging Analysis
Quantifies biological age from standard bloodwork. Anchors the baseline before any intervention.
In 9 blood markers + metadata
Out PhenoAge, telomere percentile, protocol recommendation, TTTPS timestamp
Stage 1, Option A
SynNotch Circuit Design
Designs a synthetic receptor circuit that selectively targets and clears senescent cells identified in Stage 0.
In Target receptor, payload gene
Out AND-gate circuit specification, TTTPS timestamp
Stage 2
Riboswitch Design
Designs RNA regulatory sequences that add post-transcriptional control to the Stage 1 circuit, a second layer of conditional expression.
In Target mRNA, trigger ligand
Out Candidate sequences, MFE, confidence scores, TTTPS timestamp
Full Pipeline
Longevity Protocol
Runs Stage 0 → 1 → 2 automatically and returns a three-link TTTPS chain that covers the entire computation from bloodwork to circuit output.
In Blood markers + circuit parameters
Out Consolidated report + 3-link TTTPS audit chain
Execution Flow
Full Pipeline: Request to Protocol

Internal execution order when calling POST /api/v1/longevity/protocol. Stages chain conditionally on bloodwork results.

Stage Reference
Stage 0: Phenotypic Aging Analysis
POST /api/v1/analyze/bloodwork
Item Detail
Biological context PhenoAge (Levine 2018) is a composite biomarker derived from clinical blood panels. It reliably outperforms chronological age as a predictor of all-cause mortality and disease risk. Telomere length percentile provides an orthogonal structural view of cellular aging. Together they define the intervention target before any therapeutic design begins.
Input parameters
wbcWhite blood cell count (10³/µL)
rbcRed blood cell count (10⁶/µL)
hemoglobinHemoglobin (g/dL)
plateletsPlatelet count (10³/µL)
glucoseFasting glucose (mg/dL)
creatinineSerum creatinine (mg/dL)
albuminSerum albumin (g/dL)
altAlanine aminotransferase (U/L)
total_cholesterolTotal cholesterol (mg/dL)
lymphocyte_pctLymphocyte percentage (%)
ageChronological age (years), used for delta computation
Output biological_age (years), telomere_percentile (0–100), phenoage_delta (chronological minus biological), recommended protocol stage (0–3), TTTPS timestamp
Downstream use The protocol recommendation maps directly to Stage 1 circuit targets. A delta < −5 years typically warrants senolytic intervention; the recommendation field encodes this as a structured enum for programmatic routing.
Stage 1: SynNotch AND-gate Senolytic Circuit
POST /api/v1/design/synnotch
Item Detail
Biological context Senescent cells accumulate with age and secrete a pro-inflammatory SASP (Senescence-Associated Secretory Phenotype). SynNotch is a synthetic receptor system that activates gene expression only when two surface markers are co-detected, reducing off-target cytotoxicity. The AND-gate architecture ensures the payload fires only in cells that present both the primary receptor and a co-ligand, a selectivity constraint not achievable with single-input receptors.
Input parameters
target_receptorPrimary surface marker on target senescent cells (e.g. p16INK4a, B2M)
payload_geneEffector gene to express upon AND-gate activation (e.g. CASP9, IL-2)
co_ligandOptional secondary marker for AND-gate specificity
cell_contextCell type background for promoter selection (T-cell, NK, fibroblast)
Output Full circuit specification: receptor binding domain, transmembrane linker, transcriptional activator, promoter cassette, payload expression construct, returned as structured JSON with optional SBOL-compatible annotation, plus TTTPS timestamp
Downstream use The circuit output passes directly into Stage 2. The payload_gene from Stage 1 becomes the target_mRNA for riboswitch design, adding a ligand-gated expression layer on top of the AND-gate logic.
Stage 2: RNA Riboswitch Design
POST /api/v1/design/riboswitch
Item Detail
Biological context Riboswitches are structured RNA elements in the 5' UTR that undergo conformational change upon small-molecule binding, controlling translation of the downstream ORF. Embedding a riboswitch upstream of the Stage 1 payload gene creates a third control layer: the circuit only activates (AND-gate), in the right cell (co-ligand), and when the exogenous ligand is present. This enables dose-titratable and temporally reversible control over therapeutic expression.
Input parameters
target_mrnamRNA to be regulated, typically the payload gene from Stage 1
trigger_ligandSmall molecule that triggers conformational switch (e.g. theophylline, tetracycline)
switch_typeON (ligand activates translation) or OFF (ligand suppresses translation)
n_candidatesNumber of candidate sequences to return (default 3)
Output For each candidate: nucleotide sequence, secondary structure dot-bracket notation, minimum free energy (MFE, kcal/mol), predicted switching efficiency (%), confidence score, TTTPS timestamp. Sequences ranked by MFE delta between apo and holo states.
Downstream use Candidate sequences are ready for synthesis and in-vitro validation. The MFE and confidence scores provide a ranked shortlist for experimental prioritization. All three outputs are included in the full-pipeline consolidated report.
Full Pipeline: Longevity Protocol
POST /api/v1/longevity/protocol
Item Detail
Biological context The longevity protocol endpoint chains Stage 0 → 1 → 2 in a single call. Intermediate results are passed automatically; the caller supplies all inputs upfront and receives a consolidated output plus a three-link TTTPS audit chain that anchors the entire computation to immutable timestamps.
Input parameters Union of Stage 0, 1, and 2 inputs. Blood markers are required. Circuit parameters (target_receptor, payload_gene, trigger_ligand) are required for the downstream stages. Absent parameters cause the pipeline to halt at the last completable stage and return partial results.
Output phenoage_result (Stage 0 output), circuit_design (Stage 1 output), riboswitch_candidates (Stage 2 output), tttps_chain (array of 3 timestamps, one per stage), pipeline_version
Downstream use The tttps_chain provides the audit record required for regulatory submissions. Each timestamp is independently verifiable against the KPP root certificate. FDA 21 CFR Part 11 and EU MDR audit trail requirements are satisfied by the chain alone, without additional logging infrastructure on the caller's side.
Audit Infrastructure
TTTPS Audit Chain

Every API call returns a TTTPS (TLS Time Token Protocol Specification) timestamp, a cryptographically signed record binding the computation output to a precise point in time.

T: Time
Temporal Anchor
UTC timestamp at computation completion. Precision: sub-millisecond. Signed by Kenosian root CA.
L: Logic
Output Digest
SHA-256 hash of the full response payload. Any modification to results invalidates the digest.
S: Sync
Chain Integrity
Links to the previous timestamp in a pipeline sequence. Breaks if intermediate results are altered.
Verification
Independent Check
Any party with the Kenosian public key can verify a timestamp offline, without contacting KPP servers.

For the full pipeline endpoint, the response contains a tttps_chain array with three entries, one per stage. Regulators can verify the chain to confirm that Stage 2 riboswitch candidates were derived from the specific Stage 0 blood values in the same computation, with no opportunity to substitute intermediate results. This satisfies FDA 21 CFR Part 11 electronic records requirements and EU MDR Annex II documentation obligations without additional infrastructure on the caller side.

Quick Start
# Install
pip install httpx

import httpx

client = httpx.Client(
    base_url="https://kpp.kenosian.com",
    headers={"X-API-Key": "your-key"}
)

# Stage 0: Biological age
stage0 = client.post("/api/v1/analyze/bloodwork", json={
    "age":               52,
    "wbc":               5.8,
    "rbc":               4.6,
    "hemoglobin":        14.2,
    "platelets":         220,
    "glucose":           94,
    "creatinine":        0.9,
    "albumin":           4.1,
    "alt":               22,
    "total_cholesterol": 188,
    "lymphocyte_pct":    28.4
})

bio_age = stage0.json()["biological_age"]   # e.g. 44.7
delta   = stage0.json()["phenoage_delta"]   # +7.3 years younger
ts0     = stage0.json()["tttps_timestamp"] # TTTPS anchor

# Stage 1: Senolytic circuit design
stage1 = client.post("/api/v1/design/synnotch", json={
    "target_receptor": "p16INK4a",
    "payload_gene":    "CASP9",
    "co_ligand":       "B2M",
    "cell_context":    "NK"
})

# Stage 2: Riboswitch for conditional payload control
stage2 = client.post("/api/v1/design/riboswitch", json={
    "target_mrna":    "CASP9",
    "trigger_ligand": "theophylline",
    "switch_type":    "ON",
    "n_candidates":   3
})

candidates = stage2.json()["candidates"]
# [{"sequence": "GCUCG...", "mfe": -44.1, "confidence": 0.87}, ...]

# Or run all three stages in a single call
full = client.post("/api/v1/longevity/protocol", json={
    # bloodwork params + circuit params combined
    "age": 52, "wbc": 5.8,  # ... all bloodwork fields
    "target_receptor": "p16INK4a",
    "payload_gene":    "CASP9",
    "trigger_ligand":  "theophylline"
})

chain = full.json()["tttps_chain"]  # 3-link audit record
TTTPS
Time
Integrity
sealed
“TTTPS-sealed” — the time-integrity standard (proposed)

Every computation in the KPP pipeline is sealed at ingestion: operator-independent Roughtime timestamp, SHA-256 + HMAC over inputs and outputs, Ed25519 signature. A proposed trust mark that the when, what, and who of each computation are tamper-rejecting. Conditional on TTTPS being adopted as the standard, with Kenosian as the root of trust.

Illustrative mark for explanation only. Any trust authority, mark, or “sealed” status is conditional (“could / if adopted”) and would operate under the Kenosian root — not a present-day certification program.