# Genome Model Runner + Registry

> Agent-facing counterpart to the [human project page](/projects/genome-model-runner/).

## Record metadata

- Record: 012
- Slug: genome-model-runner
- Domain: Science
- Domain code: SC
- Type: Research workbench
- Status: Active
- Period: 2026
- Portfolio role: Research infrastructure
- Publication state: Public-safe technical record
- Case-study readiness: Draftable
- Compendium edition: 0.4

## Summary

A manifest-first workbench for running genomic evidence tools through explicit, reusable contracts.

## Overview

Genomic research tools rarely arrive as interchangeable components. They use different input conventions, produce different kinds of evidence, and often leave their operational limits in prose that a workflow cannot enforce.

A FastAPI and React workbench paired with a registry of tool manifests describing inputs, outputs, limits, provenance, and execution contracts.

Purpose: Make heterogeneous genetics tools easier to run, compare, audit, and compose into safe research workflows.

## The problem behind the project

Genomic tools often arrive as incompatible scripts, services, or models. A common contract makes it possible to assemble repeatable workflows without hiding what each component can and cannot establish.

Genome Model Runner and its registry address that integration layer. The registry describes what a tool accepts, what it returns, how it should be invoked, and what its output can establish; the runner turns those declarations into inspectable workflows.

Bioinformatics researchers and expert reviewers benefit most directly. Patients benefit only indirectly after appropriate validation and clinical governance.

## How it took shape

Prepared CSV and VCF intake, normalization, registry manifests, workflow orchestration, public evidence adapters, structured result tables, JSON exports, and reviewer-packet generation.

The current workbench combines a FastAPI service, a React interface, prepared CSV and VCF intake, normalization, manifests, adapters, tables, JSON exports, and reviewer packets. Initial evidence paths include FH-oriented sources such as ClinVar, gnomAD, and ClinGen.

Josiah set the modular runner-and-registry direction, selected the initial evidence workflow, defined safety requirements, and directed agent-assisted implementation.

Runnable adapters currently cover selected FH, ClinVar, gnomAD, and ClinGen paths and can generate inspectable workflow outputs.

## What the project means now

The registry's most important function is not discoverability but epistemic discipline. A model or database entry should travel with its assumptions, version, provenance, and limits so that composition does not quietly turn several narrow tools into one unjustifiably confident system.

It is not a universal model host, a validated clinical pipeline, or a substitute for expert review. Tool coverage and input handling remain intentionally narrow.

A registry becomes valuable when it records operational and epistemic limits, not merely how to invoke a tool.

Harden manifests and validation, add reproducible benchmark cases, and connect new tools only when their evidence boundary is explicit.

## Publication and interpretation notes

- Current classification: Active
- Portfolio readiness: Draftable
- Publication boundary: Public-safe technical record

## Additional agent context

This is a concrete infrastructure component beneath the broader medical-variant methodology. Keep research and clinical claims separate.

## Related project records

- [Medical Variant Triage Methodology](/projects/genomic-evidence-orchestration/llm/) — A deterministic-first methodology for carrying raw genetic data as far as reliable evidence allows before expert interpretation.
- [FH Variant Triage](/projects/fh-variant-triage/llm/) — An open research workflow for prioritizing uncertain variants in familial hypercholesterolemia genes.

## Navigation

- [Complete project index](/projects/llm/)
- [Human version of this record](/projects/genome-model-runner/)
- [About Josiah's working method](/about/llm/)
- [Agent discovery map](/llms.txt)