BIOos DomainOS¶
Status: Graduated (production, ADR-009)
Engine: bioinformatics-os
Domain: Evidence-locked AI bioinformatician (general dry-lab workbench)
General-purpose evidence-locked bioinformatics workbench built on 127+ biostack skills and 47K tools via biocontext7. Operates in three modes -- Explore (interactive EDA), Analyze (pipeline execution), Ship (reproducible export) -- and hosts the Shared Compiler that gates experiment designs for every DomainOS.
| Field | Value |
|---|---|
| Product | BIOos |
| Engine id | bioinformatics-os |
| Intent key | data_analysis |
| Repository | Hordago-Labs/bioinformatics-os |
| Plugin | bio-os |
| Maturity (registry) | Graduated (production, ADR-009) |
Overview¶
General-purpose evidence-locked bioinformatics workbench built on 127+ biostack skills and 47K tools via biocontext7. Operates in three modes -- Explore (interactive EDA), Analyze (pipeline execution), Ship (reproducible export) -- and hosts the Shared Compiler that gates experiment designs for every DomainOS.
Scientific approach¶
BIOos structures every run as 3 phases. Gates marked HITL require an explicit human-in-the-loop approval before the run advances.
| # | Phase | Gate | HITL |
|---|---|---|---|
| 1 | Explore | Interactive EDA; every claim references an artifact. | No |
| 2 | Analyze | Execute a reproducible pipeline. | No |
| 3 | Ship | Export an evidence-locked, reproducible bundle. | Yes |
Capabilities & evidence objects¶
Domain tools / skills
exploreanalyzeshipcompile
Evidence objects
| Object | Role | Consumer |
|---|---|---|
CompilerResult |
produces | hordago orchestrator (ACCEPT/REJECT/ITERATE/DEFER) |
provenance.json |
produces | evidence-audit |
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).
- Install the standalone
bio-osplugin (Hordago-Labs/bioinformatics-os) -- no Hordago platform required. - Invoke the domain skill with a BIOos intent (see the intent keywords below).
- Review the emitted artifacts under the run's output directory.
Intent keywords (route to this engine):
analyze analysis my data scrna-seq sc[- ]?rna(?:-seq)? \.h5ad \.vcf \.fastq \.bam \.csv \.tsv exploratory qc quality control
Worked example¶
Explore -> Analyze -> Ship an RNA-seq differential expression run
A user loads a counts matrix in Explore mode, iterates on QC and normalization, promotes to Analyze mode to run a reproducible DE pipeline, then Ships an evidence-locked bundle where every reported gene references a concrete artifact.
Validation & benchmarks¶
Benchmarks
- BixBench task coverage
- Shared Compiler ACCEPT/REJECT parity
Reproducibility. Ship mode emits a provenance-complete bundle; the Shared Compiler decision is deterministic.
Reference¶
MCP fallback servers (used when the plugin is unavailable): pubmed
Source documents
- BIOos spec:
docs/bioos-spec.md - Biostack integration:
references/biostack-integration.md
Composition¶
Platform opt-in
BIOos 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 |
Shared Compiler validates CRISPRos experiment designs. |
onco-os |
Provides the compile gate for experiment_design intents. |