ZeqGene — Expression Analysis

Protein folding, ecosystems, neural, gene expression.

• Protocol ID — zeq-gene-express
• Category — Biology
• Endpoint — POST /api/bio/gene/expression
• Auth — api-key
• Rate limit — 10/min
• Version — 1.0
• Precision — ≤0.1% (KO42-enforced)

What it does

Gene expression time-series analysis using ZeqShift projection. Map gene expression oscillations onto the HulyaPulse timescale to detect circadian and ultradian rhythms.

Signature

Request

POST /api/bio/gene/expression

Param	Type	Required	Default	Description
expressionData	array	✓	—	Array of { geneId, timepoints, values }.
referenceGenes	array		—	Housekeeping genes for normalization.

Response

{ normalized, oscillatingGenes, periods, phases, clusters, hulyaPulseAlignment }

Runnable example

curl -sS -X POST \
  -H "Authorization: Bearer $ZEQ_API_KEY" \
  -H "Content-Type: application/json" \
  -d '{
  "expressionData": [],
  "referenceGenes": []
}' \
  "https://api.zeq.dev/api/bio/gene/expression"

Integrate

1. Domain solver — compose with KO42 + two additional operators from the matching family for pulse-coherent results.
2. Digital twin — pipe sensor data into this protocol every Zeqond to keep the model phase-locked with the system.
3. Alert threshold — flag results whose error_pct exceeds 0.1% as out-of-spec events for the operations layer.

Seeds

• Near — wrap /api/bio/gene/expression in a language SDK so builders can call it in three lines.
• Medium — publish a reference integration demonstrating ZeqGene — Expression Analysis alongside a real workload, with pulse-aligned metrics.
• Far — propose ZeqGene — Expression Analysis as an open reference standard so other runtimes can implement it verbatim against the Zeq paper.

Papers

• Zeq paper — https://doi.org/10.5281/zenodo.18158152
• Framework paper — https://doi.org/10.5281/zenodo.15825138

Middleware active. Kernel on the 1.287 Hz HulyaPulse. Awaiting next Zeqond.