THE CATALOG
Each DomainOS is a thin shell over shared reasoning plugins and the MCP data layer. Purpose-built for a scientific domain — genomics, CRISPR, drug discovery, clinical, and beyond — with human gates on every critical decision.
DomainOS products are thin domain-specific operating systems built on shared reasoning plugins and a hash-verified MCP data layer. Flip any card below to see the tools it integrates and a worked example.
THE CATALOG
Seven categories, 28 operating systems, 1,062+ skills. Click a card to see its integrated tools, inputs and outputs, and an example workflow.
Genomics & Variants
8 productsGenomics & Variants
BetaAlignment, QC, RNA-seq
8 agents · 92 skills · 3 MCPs · 3 HITL gates
BIOos
Beta8 agents
92 skills
3 MCPs
3 HITL gates
FASTQ · Reference genome · Sample sheet
BAM/CRAM · MultiQC report · Count matrix
Tools integrated
MCP servers
Example
Align a 50-sample RNA-seq cohort with provenance-tracked QC gates.
Emits manifest.json · SHA-256 per artifact
Genomics & Variants
BetaAssociation, fine-mapping
7 agents · 78 skills · 3 MCPs · 3 HITL gates
GWASos
Beta7 agents
78 skills
3 MCPs
3 HITL gates
PLINK/VCF · Phenotype table · Covariates
Summary stats · Manhattan plot · Credible sets
Tools integrated
MCP servers
Example
Run a biobank-scale association with calibrated inflation checks.
Emits manifest.json · SHA-256 per artifact
Genomics & Variants
BetaVariant annotation
6 agents · 61 skills · 3 MCPs · 2 HITL gates
varfx-os
Beta6 agents
61 skills
3 MCPs
2 HITL gates
VCF · Gene models
Annotated VCF · Effect tiers · Evidence trail
Tools integrated
MCP servers
Example
Prioritize coding + regulatory variants with grounded effect calls.
Emits manifest.json · SHA-256 per artifact
Genomics & Variants
BetaStatistical fine-mapping
5 agents · 54 skills · 3 MCPs · 2 HITL gates
finemap-os
Beta5 agents
54 skills
3 MCPs
2 HITL gates
GWAS summary stats · LD reference
Credible sets · Posterior probs · Locus plots
Tools integrated
MCP servers
Example
Narrow a GWAS locus to a handful of credible causal variants.
Emits manifest.json · SHA-256 per artifact
Genomics & Variants
BetaPolygenic risk scores
4 agents · 47 skills · 3 MCPs · 2 HITL gates
prs-os
Beta4 agents
47 skills
3 MCPs
2 HITL gates
GWAS weights · Target genotypes
PRS per sample · Calibration plot · Ancestry audit
Tools integrated
MCP servers
Example
Derive a cross-ancestry PRS with bias and calibration diagnostics.
Emits manifest.json · SHA-256 per artifact
Genomics & Variants
BetaMendelian genetics
5 agents · 52 skills · 3 MCPs · 3 HITL gates
mendel-os
Beta5 agents
52 skills
3 MCPs
3 HITL gates
Pedigree · Trio VCF · HPO terms
Candidate variants · Inheritance fit · ACMG class
Tools integrated
MCP servers
Example
Narrow a trio exome to a ranked list of Mendelian candidates.
Emits manifest.json · SHA-256 per artifact
Genomics & Variants
BetaClinVar interpretation
4 agents · 39 skills · 3 MCPs · 3 HITL gates
clinvar-os
Beta4 agents
39 skills
3 MCPs
3 HITL gates
VCF · Variant IDs
ClinVar evidence · Conflict report · Citation trail
Tools integrated
MCP servers
Example
Audit clinical variant interpretations against latest ClinVar evidence.
Emits manifest.json · SHA-256 per artifact
Genomics & Variants
BetaONT, PacBio
5 agents · 58 skills · 3 MCPs · 2 HITL gates
longread-os
Beta5 agents
58 skills
3 MCPs
2 HITL gates
Nanopore / HiFi FASTQ · Reference
Phased BAM · SV VCF · Methylation BED
Tools integrated
MCP servers
Example
Phase a long-read genome and resolve structural variants end to end.
Emits manifest.json · SHA-256 per artifact
Cell & Molecular
4 productsCell & Molecular
BetaGuide design, knockouts
8 agents · 86 skills · 3 MCPs · 4 HITL gates
CRISPRos
Beta8 agents
86 skills
3 MCPs
4 HITL gates
Target gene(s) · Cell line · Delivery context
Guide library · Off-target report · Experiment manifest
Tools integrated
MCP servers
Example
Design a tiled knockout library with human approval at every gate.
Emits manifest.json · SHA-256 per artifact
Cell & Molecular
BetaCRISPR screens, MAGeCK
6 agents · 64 skills · 3 MCPs · 3 HITL gates
screen-os
Beta6 agents
64 skills
3 MCPs
3 HITL gates
Counts matrix · Library design · Conditions
Hit list · Gene-level scores · QC dashboard
Tools integrated
MCP servers
Example
Run a pooled CRISPR screen from counts to ranked, evidence-grounded hits.
Emits manifest.json · SHA-256 per artifact
Cell & Molecular
BetaCell biology analysis
6 agents · 71 skills · 3 MCPs · 2 HITL gates
cell-os
Beta6 agents
71 skills
3 MCPs
2 HITL gates
scRNA / sc-ATAC counts · Sample metadata
Annotated atlas · Marker panels · Trajectory
Tools integrated
MCP servers
Example
Annotate a single-cell atlas with reproducible cell-type calls.
Emits manifest.json · SHA-256 per artifact
Cell & Molecular
BetaSpatial transcriptomics
4 agents · 48 skills · 3 MCPs · 2 HITL gates
spatial-os
Beta4 agents
48 skills
3 MCPs
2 HITL gates
Visium / Xenium / MERFISH · H&E image
Niche map · Co-localization · Cell-cell signals
Tools integrated
MCP servers
Example
Map tissue niches and cell-cell communication across spatial slides.
Emits manifest.json · SHA-256 per artifact
Omics
5 productsOmics
BetaSomatic, neoantigen
6 agents · 68 skills · 4 MCPs · 3 HITL gates
onco-os
Beta6 agents
68 skills
4 MCPs
3 HITL gates
Tumor/normal BAM · HLA type
Somatic VCF · Neoantigens · Signatures
Tools integrated
MCP servers
Example
Profile a tumor from raw reads through prioritized neoantigens.
Emits manifest.json · SHA-256 per artifact
Omics
Beta16S, metagenomics
5 agents · 55 skills · 3 MCPs · 2 HITL gates
microbiome-os
Beta5 agents
55 skills
3 MCPs
2 HITL gates
16S / shotgun FASTQ · Sample metadata
ASV table · Taxonomy · Function profile
Tools integrated
MCP servers
Example
Go from raw microbiome reads to differential-abundance figures.
Emits manifest.json · SHA-256 per artifact
Omics
BetaMass spec
4 agents · 46 skills · 3 MCPs · 2 HITL gates
proteomics-os
Beta4 agents
46 skills
3 MCPs
2 HITL gates
RAW / mzML · Sample design
Protein matrix · PTM sites · Differential report
Tools integrated
MCP servers
Example
Quantify a label-free proteomics cohort with PTM-aware QC.
Emits manifest.json · SHA-256 per artifact
Omics
BetaMetabolomics
4 agents · 42 skills · 3 MCPs · 2 HITL gates
metab-os
Beta4 agents
42 skills
3 MCPs
2 HITL gates
LC-MS / NMR · Metadata
Feature table · Annotations · Pathway enrichment
Tools integrated
MCP servers
Example
Annotate and contextualize untargeted metabolomics features.
Emits manifest.json · SHA-256 per artifact
Omics
BetaImmune repertoire
4 agents · 44 skills · 3 MCPs · 2 HITL gates
immuno-os
Beta4 agents
44 skills
3 MCPs
2 HITL gates
TCR / BCR sequencing · Clonal metadata
Clonotype table · Diversity stats · V(D)J map
Tools integrated
MCP servers
Example
Characterize TCR/BCR repertoire dynamics across treatment arms.
Emits manifest.json · SHA-256 per artifact
Imaging & Structure
2 productsImaging & Structure
BetaAlphaFold, docking
5 agents · 59 skills · 4 MCPs · 2 HITL gates
struct-os
Beta5 agents
59 skills
4 MCPs
2 HITL gates
Sequence · Ligand SMILES · Target PDB
Predicted structure · Pocket map · Docked poses
Tools integrated
MCP servers
Example
Fold a target, find its pocket, and screen candidate binders.
Emits manifest.json · SHA-256 per artifact
Imaging & Structure
BetaMicroscopy
5 agents · 51 skills · 3 MCPs · 2 HITL gates
bioimage-os
Beta5 agents
51 skills
3 MCPs
2 HITL gates
TIFF / OME-Zarr · Channel metadata
Segmentation · Morphometrics · Tracking
Tools integrated
MCP servers
Example
Segment and quantify phenotypes across high-content imaging plates.
Emits manifest.json · SHA-256 per artifact
Clinical & Regulatory
3 productsClinical & Regulatory
BetaRare disease, ACMG
5 agents · 57 skills · 3 MCPs · 4 HITL gates
rare-os
Beta5 agents
57 skills
3 MCPs
4 HITL gates
Proband VCF · HPO phenotypes · Trio (optional)
ACMG classification · Candidate list · Report draft
Tools integrated
MCP servers
Example
Generate an ACMG-graded rare disease report with traceable evidence.
Emits manifest.json · SHA-256 per artifact
Clinical & Regulatory
BetaEHR, PyHealth
4 agents · 49 skills · 3 MCPs · 3 HITL gates
clinical-os
Beta4 agents
49 skills
3 MCPs
3 HITL gates
FHIR / OMOP CDM · Cohort criteria
Cohort table · Endpoint schedule · Audit log
Tools integrated
MCP servers
Example
Build an OMOP cohort with endpoints that survive regulatory audit.
Emits manifest.json · SHA-256 per artifact
Clinical & Regulatory
BetaISO 13485, FDA QMSR
4 agents · 41 skills · 3 MCPs · 4 HITL gates
reg-os
Beta4 agents
41 skills
3 MCPs
4 HITL gates
Requirements · Test records · Change log
DHF package · Traceability matrix · Submission draft
Tools integrated
MCP servers
Example
Compile a design-history file with claim-to-evidence traceability.
Emits manifest.json · SHA-256 per artifact
Drug Discovery
3 productsDrug Discovery
BetaCheminformatics
5 agents · 50 skills · 3 MCPs · 2 HITL gates
chem-os
Beta5 agents
50 skills
3 MCPs
2 HITL gates
SMILES · Assay readouts
Property table · Scaffold map · SAR summary
Tools integrated
MCP servers
Example
Triage a library and pull out scaffold-level SAR trends.
Emits manifest.json · SHA-256 per artifact
Drug Discovery
BetaADMET prediction
4 agents · 45 skills · 3 MCPs · 3 HITL gates
admet-os
Beta4 agents
45 skills
3 MCPs
3 HITL gates
SMILES · Reference compounds
ADMET profile · Alert flags · Confidence bands
Tools integrated
MCP servers
Example
Profile ADMET liabilities with calibrated uncertainty, not point estimates.
Emits manifest.json · SHA-256 per artifact
Drug Discovery
BetaVirtual screening
4 agents · 48 skills · 3 MCPs · 2 HITL gates
virtual-screen-os
Beta4 agents
48 skills
3 MCPs
2 HITL gates
Target structure · Compound library
Ranked hits · Pose library · Enrichment report
Tools integrated
MCP servers
Example
Dock a million compounds and surface high-confidence candidates.
Emits manifest.json · SHA-256 per artifact
Systems & Networks
3 productsSystems & Networks
BetaSystems biology
4 agents · 43 skills · 3 MCPs · 2 HITL gates
systems-os
Beta4 agents
43 skills
3 MCPs
2 HITL gates
Expression matrix · Perturbation data
Causal graph · Intervention plan · Model fit
Tools integrated
MCP servers
Example
Build a causal systems model that predicts perturbation response.
Emits manifest.json · SHA-256 per artifact
Systems & Networks
BetaPathway analysis
4 agents · 40 skills · 3 MCPs · 2 HITL gates
pathway-os
Beta4 agents
40 skills
3 MCPs
2 HITL gates
Gene lists · Expression data
Enriched pathways · Network figure · Citation trail
Tools integrated
MCP servers
Example
Convert a gene hit list into a pathway narrative grounded in citations.
Emits manifest.json · SHA-256 per artifact
Systems & Networks
BetaGene regulatory networks
4 agents · 46 skills · 3 MCPs · 2 HITL gates
grn-os
Beta4 agents
46 skills
3 MCPs
2 HITL gates
scRNA + ATAC · TF motif database
Regulon set · TF targets · Perturbation predictions
Tools integrated
MCP servers
Example
Infer TF regulons from multiomic data and simulate knockouts.
Emits manifest.json · SHA-256 per artifact
28 Domain Operating Systems · Counts as of Q2 2026 · Click any card for integrations and example workflows
THE REASONING LAYER
DomainOS products dispatch to a shared reasoning layer: five plugins Claude composes on every run. Each solves one hard scientific problem well.
Reasoning Plugin
BetaCompiles scientific writing
Compiles submission-grade papers, grants, biosketches, and CVs from structured intent and lab data. Every output compiled from artifacts, with claim-to-evidence tracking and venue formatting.
34 skills · 5 agents · 3 MCPs
co-writer
Compiles scientific writing
34 skills
5 agents
3 MCPs
Signature skills
Agents
MCP servers
Example
Compile an R01 renewal from lab data, prior papers, and aims — every sentence cited to a source artifact.
Emits: claim-to-evidence map + manifest.json
Reasoning Plugin
BetaGenerates and critiques hypotheses
Hypothesis-driven research assistant. Generates, critiques, and evaluates hypotheses using the Swanson ABC model across a 6-phase pipeline — Scout → Generate → Critique → Scan → Plan → Review — with Elo tournament ranking.
8 skills · 7 agents · 4 MCPs
co-scientist
Generates and critiques hypotheses
8 skills
7 agents
4 MCPs
Signature skills
Agents
MCP servers
Example
Explore 'cold target' hypotheses for a rare disease with Elo-ranked debate between generator and critic agents.
Emits: HypothesisIR + DebateRecord + Elo ranking
Reasoning Plugin
BetaAudits scientific reasoning
Scientific reasoning plugin for Claude Code. Runs as automatic background observations and an explicit deep mode — uncertainty calibration, causal skepticism, drift auditing, epistemic diagnostics.
7 skills · 9 agents · 2 MCPs
sophia-claudette
Audits scientific reasoning
7 skills
9 agents
2 MCPs
Signature skills
Agents
MCP servers
Example
Flag correlation-vs-causation drift in a mid-flight manuscript before it ships to peer review.
Emits: epistemic card + drift log
Reasoning Plugin
BetaExtracts and tracks claims
Extracts structured claims from scientific papers, builds evidence graphs, and queries claim relationships. Seven-stage ingestion: ingest → extract → normalize → dedup → link → tag → upsert. Provenance is never fabricated.
12 skills · 3 agents · 4 MCPs
paper-intelligence
Extracts and tracks claims
12 skills
3 agents
4 MCPs
Signature skills
Agents
MCP servers
Example
Ingest 40 papers on BRCA1 synthetic lethality and surface contradictions across the claim graph.
Emits: claim graph + provenance chain per claim
Reasoning Plugin
BetaUnifies biomedical knowledge
Universal biomedical knowledge graph infrastructure. Neo4j graph + DuckDB columnar + SQLite FTS5 text search, Biolink Model schema, namespace-isolated across pi, t1d, gwas, crispr, tools, hyp, skill.
5 skills · 1 agents · 4 MCPs
knowledge-graph
Unifies biomedical knowledge
5 skills
1 agents
4 MCPs
Signature skills
Agents
MCP servers
Example
Unify GWAS loci, tissue expression, and drug targets into one queryable graph for target selection.
Emits: Biolink-schema graph + citation edges
We work with research labs, biotechs, government programs, and life-science industry teams. Tell us the domain; we'll map the right DomainOS, engines, and human gates.