Skip to content

CRISPRos DomainOS

Status: Production
Engine: crispr-system
Domain: CRISPR gene editing (wet lab -> dry lab design)

Evidence-locked CRISPR experiment design engine. Takes a target gene, cell line, and organism through guide design, off-target analysis, and a mandatory human-in-the-loop experiment-design gate before emitting the full 5-artifact contract. The reference-grade DomainOS all other engines are lifted toward.

Field Value
Product CRISPRos
Engine id crispr-system
Intent key crispros
Repository Hordago-Labs/crispr-system
Plugin crispr-system
Maturity (registry) Production

Overview

Evidence-locked CRISPR experiment design engine. Takes a target gene, cell line, and organism through guide design, off-target analysis, and a mandatory human-in-the-loop experiment-design gate before emitting the full 5-artifact contract. The reference-grade DomainOS all other engines are lifted toward.

Scientific approach

CRISPRos structures every run as 5 phases. Gates marked HITL require an explicit human-in-the-loop approval before the run advances.

# Phase Gate HITL
1 Target Validation Confirm gene, cell line, organism. No
2 Guide Design Select candidate guide RNAs. No
3 Off-Target Analysis Review off-target predictions. No
4 Experiment Design Approve experimental plan. Yes
5 Safety Review Acknowledge safety concerns (SV40 Large T gate for HEK293T + TP53). Yes

Capabilities & evidence objects

Domain tools / skills

  • experiment-runner
  • guide-designer
  • off-target-analyzer
  • safety-reviewer

Evidence objects

Object Role Consumer
result.json produces co-writer
report.md produces co-writer
provenance.json produces evidence-audit
gate_status.json produces hordago orchestrator

Canonical artifacts (5-artifact contract)

Emitted

CRISPRos emits the full 5-artifact contract on every completed run.

Artifact Description
result.json Guide sequences, efficiency scores, off-target predictions.
report.md Human-readable experiment design summary.
provenance.json Tool versions, reference genome, scoring algorithm lineage.
gate_status.json Phase gate pass/fail decisions.
session_summary.json Session metadata for reproducibility.

Standalone quickstart

Zero platform dependency

This quickstart runs the DomainOS standalone. The Hordago platform is not required; platform composition is opt-in (see Composition below).

  1. Install the standalone crispr-system plugin (Hordago-Labs/crispr-system) -- no Hordago platform required.
  2. Invoke the domain skill with a CRISPRos intent (see the intent keywords below).
  3. Review the emitted artifacts under the run's output directory.

Intent keywords (route to this engine):

crispros crispr.?os\b crispr pipeline crispr workflow crispr-system cas9 experiment validated crispr crispr production

Worked example

Knock out TP53 in HEK293T

A user asks to design a TP53 knockout in HEK293T. CRISPRos validates the target, designs candidate guides, scores off-targets, then halts at the Experiment Design HITL gate. Because the cell line is HEK293T and the target is TP53, the SV40 Large T antigen safety gate fires in Safety Review. On approval, the engine emits all five canonical artifacts.

Validation & benchmarks

Benchmarks

  • Off-target scoring parity against reference genome pins
  • Guide-efficiency scoring regression suite

Reproducibility. provenance.json pins reference genome build and scoring algorithm lineage so a run is byte-reproducible from the bundle.

Reference

MCP fallback servers (used when the plugin is unavailable): pubmed, open-targets

Source documents

  • DomainOS registry (CRISPRos section): references/domain-os-registry.md
  • ADR-002 routing symmetry: docs/adr/002-domain-os-routing-symmetry.md

Composition

Platform opt-in

CRISPRos runs standalone. When composed under the Hordago platform it gains cross-domain routing, the Shared Compiler gate, and evidence-audit provenance enforcement. Platform composition is opt-in; the quickstart above has zero platform dependency.

Cross-domain dependencies

Engine Relationship
screen-os Screen intents ('crispr screen', 'mageck') route to screen-os, not CRISPRos; the sub-router checks 'crispr screen' before 'crispr'.
bioinformatics-os Shared Compiler validates the experiment design before execution.