screen-os DomainOS

Status: Scaffold (routing wired, skills pending)
Engine: screen-os
Domain: CRISPR & perturbation screens (MAGeCK, dropout, essentiality)

Functional-genomics screen DomainOS: MAGeCK analysis, essential-gene calling, dropout-screen analysis, and perturbation atlases. Routing is wired with status=scaffold; the sub-router checks 'crispr screen' before 'crispr' so screen intents land here rather than on CRISPRos.

Field	Value
Product	screen-os
Engine id	screen-os
Intent key	screen_os
Repository	Hordago-Labs/screen-os
Plugin	screen-os
Maturity (registry)	Scaffold (routing wired, skills pending)

Overview

Functional-genomics screen DomainOS: MAGeCK analysis, essential-gene calling, dropout-screen analysis, and perturbation atlases. Routing is wired with status=scaffold; the sub-router checks 'crispr screen' before 'crispr' so screen intents land here rather than on CRISPRos.

Scientific approach

screen-os structures every run as 4 phases. Gates marked HITL require an explicit human-in-the-loop approval before the run advances.

#	Phase	Gate	HITL
1	Count Matrix QC	QC the sgRNA count matrix.	No
2	Normalization	Normalize counts across conditions.	No
3	Enrichment Testing	Run MAGeCK enrichment/depletion.	No
4	Essentiality Calling	Call essential / dropout genes.	Yes

Capabilities & evidence objects

Domain tools / skills

• mageck
• essential-gene-calling
• dropout-analysis

Evidence objects

Object	Role	Consumer
result.json	planned	co-writer

Canonical artifacts (5-artifact contract)

Planned

The 5-artifact contract below is the target shape. Canonical-artifact emission is tracked as inherited debt (Wave 3C) and is not yet guaranteed.

Artifact	Description
result.json	Structured primary result payload for the domain run.
report.md	Human-readable narrative summary of the analysis.
provenance.json	Tool versions, reference data, and algorithm lineage for reproducibility.
gate_status.json	Per-phase gate pass/fail decisions.
session_summary.json	Session metadata for replay and audit.

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

Intent keywords (route to this engine):

crispr screen mageck essential gene perturbation screen genetic screen screen analysis gene essentiality dropout screen

Worked example

MAGeCK dropout screen (planned surface)

A user with an sgRNA count matrix asks for a dropout-screen analysis. The planned surface QCs and normalizes counts, runs MAGeCK enrichment testing, and calls essential genes. Until skills land, the engine degrades to the pubmed + chembl MCP fallback.

Validation & benchmarks

Benchmarks

• Planned: MAGeCK truth-set concordance

Reproducibility. Planned: provenance.json will pin library annotation and MAGeCK version.

Reference

MCP fallback servers (used when the plugin is unavailable): pubmed, chembl

Source documents

• Scaffold-domains ledger (screen-os): references/scaffold-domains.md

Composition

Platform opt-in

screen-os 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
crispr-system	Screen intents pre-empt CRISPRos via the sub-router ordering.