THE CATALOG

Domain Operating Systems. One composed stack.

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.

Explore CRISPRos Browse every domain

DomainOS products are thin domain-specific operating systems built on shared reasoning plugins and a shared MCP data layer. Flip any card below to see the tools it integrates and a worked example.

Journeys

The same tools, walked stage by stage.

Each journey names what goes into a stage, which tools do the work, what comes out, where a person reviews it, and whether anything exists to do it today.

Therapeutic development Assay development

THE CATALOG

Every domain. Every workflow. One provenance manifest.

7 categories, 24 operating systems with a repository, 6 planned. Click a card to see its integrated tools, inputs and outputs, and an example workflow.

Genomics & Variants

9 products

Genomics & Variants

Beta

BIOos

Alignment, QC, RNA-seq

3 MCPs · HITL gates

BIOos

Beta

3 MCPs

HITL gates

FASTQ · Reference genome · Sample sheet

Out

BAM/CRAM · MultiQC report · Count matrix

Tools integrated

STAR BWA-MEM2 samtools MultiQC

MCP servers

biocontext7 PubMed Knowledge Graph

Example

Align a 50-sample RNA-seq cohort with provenance-tracked QC gates.

Emits manifest.json · SHA-256 per artifact

Request access →

Genomics & Variants

Beta

GWASos

Association, fine-mapping

3 MCPs · HITL gates

Open →

GWASos

Beta

3 MCPs

HITL gates

PLINK/VCF · Phenotype table · Covariates

Out

Summary stats · Manhattan plot · Credible sets

Tools integrated

PLINK2 REGENIE SAIGE SuSiE

MCP servers

biocontext7 PubMed Knowledge Graph

Example

Run a biobank-scale association with calibrated inflation checks.

Emits manifest.json · SHA-256 per artifact

Open docs →

Genomics & Variants

Beta

VARFXos

Variant annotation

3 MCPs · HITL gates

VARFXos

Beta

3 MCPs

HITL gates

VCF · Gene models

Out

Annotated VCF · Effect tiers · Evidence trail

Tools integrated

VEP SnpEff AlphaMissense

MCP servers

biocontext7 PubMed Knowledge Graph

Example

Prioritize coding + regulatory variants with grounded effect calls.

Emits manifest.json · SHA-256 per artifact

Request access →

Genomics & Variants

Beta

FINEMAPos

Statistical fine-mapping

3 MCPs · HITL gates

FINEMAPos

Beta

3 MCPs

HITL gates

GWAS summary stats · LD reference

Out

Credible sets · Posterior probs · Locus plots

Tools integrated

SuSiE FINEMAP CAVIAR PolyFun

MCP servers

biocontext7 PubMed Knowledge Graph

Example

Narrow a GWAS locus to a handful of credible causal variants.

Emits manifest.json · SHA-256 per artifact

Request access →

Genomics & Variants

Beta

PRSos

Polygenic risk scores

3 MCPs · HITL gates

PRSos

Beta

3 MCPs

HITL gates

GWAS weights · Target genotypes

Out

PRS per sample · Calibration plot · Ancestry audit

Tools integrated

PRS-CS LDpred2 PLINK2

MCP servers

biocontext7 PubMed Knowledge Graph

Example

Derive a cross-ancestry PRS with bias and calibration diagnostics.

Emits manifest.json · SHA-256 per artifact

Request access →

Genomics & Variants

Beta

MENDELos

Mendelian genetics

3 MCPs · HITL gates

MENDELos

Beta

3 MCPs

HITL gates

Pedigree · Trio VCF · HPO terms

Out

Candidate variants · Inheritance fit · ACMG class

Tools integrated

Exomiser GEMINI Phen2Gene

MCP servers

biocontext7 PubMed Knowledge Graph

Example

Narrow a trio exome to a ranked list of Mendelian candidates.

Emits manifest.json · SHA-256 per artifact

Request access →

Genomics & Variants

Beta

CLINVARos

ClinVar interpretation

3 MCPs · HITL gates

CLINVARos

Beta

3 MCPs

HITL gates

VCF · Variant IDs

Out

ClinVar evidence · Conflict report · Citation trail

Tools integrated

ClinVar LitVar OMIM

MCP servers

biocontext7 ClinicalTrials PubMed

Example

Audit clinical variant interpretations against latest ClinVar evidence.

Emits manifest.json · SHA-256 per artifact

Request access →

Genomics & Variants

Beta

LONGREADos

ONT, PacBio

3 MCPs · HITL gates

LONGREADos

Beta

3 MCPs

HITL gates

Nanopore / HiFi FASTQ · Reference

Out

Phased BAM · SV VCF · Methylation BED

Tools integrated

minimap2 Sniffles Clair3 Nanopolish

MCP servers

biocontext7 PubMed Knowledge Graph

Example

Phase a long-read genome and resolve structural variants end to end.

Emits manifest.json · SHA-256 per artifact

Request access →

Genomics & Variants

Beta

REGos

Enhancers, TF binding, chromatin

2 MCPs · HITL gates

REGos

Beta

2 MCPs

HITL gates

ATAC / ChIP-seq reads · Reference genome · TF motif database

Out

Consensus peaks · Motif enrichment · Enhancer-gene links

Tools integrated

MACS2 HOMER TOBIAS chromVAR ENCODE Cistrome DB

MCP servers

PubMed Knowledge Graph

Example

Call accessibility peaks, footprint transcription factors, and link enhancers to genes.

Emits manifest.json · SHA-256 per artifact

Request access →

Cell & Molecular

5 products

Cell & Molecular

Beta

CRISPRos

Guide design, knockouts

3 MCPs · HITL gates

Open →

CRISPRos

Beta

3 MCPs

HITL gates

Target gene(s) · Cell line · Delivery context

Out

Guide library · Off-target report · Experiment manifest

Tools integrated

CRISPOR CHOPCHOP FlashFry Azimuth

MCP servers

biocontext7 PubMed Knowledge Graph

Example

Design a tiled knockout library with human approval at every gate.

Emits manifest.json · SHA-256 per artifact

Open docs →

Cell & Molecular

Beta

SCREENos

CRISPR screens, MAGeCK

3 MCPs · HITL gates

SCREENos

Beta

3 MCPs

HITL gates

Counts matrix · Library design · Conditions

Out

Hit list · Gene-level scores · QC dashboard

Tools integrated

MAGeCK BAGEL drugZ ScreenPro2

MCP servers

biocontext7 PubMed BioRender

Example

Run a pooled CRISPR screen from counts to ranked, evidence-grounded hits.

Emits manifest.json · SHA-256 per artifact

Request access →

Cell & Molecular

Beta

CELLos

Cell biology analysis

3 MCPs · HITL gates

CELLos

Beta

3 MCPs

HITL gates

scRNA / sc-ATAC counts · Sample metadata

Out

Annotated atlas · Marker panels · Trajectory

Tools integrated

Scanpy Seurat scVI CellTypist

MCP servers

biocontext7 PubMed BioRender

Example

Annotate a single-cell atlas with reproducible cell-type calls.

Emits manifest.json · SHA-256 per artifact

Request access →

Cell & Molecular

Beta

SPATIALos

Spatial transcriptomics

3 MCPs · HITL gates

SPATIALos

Beta

3 MCPs

HITL gates

Visium / Xenium / MERFISH · H&E image

Out

Niche map · Co-localization · Cell-cell signals

Tools integrated

Squidpy CellCharter SpatialData SOPA

MCP servers

biocontext7 PubMed BioRender

Example

Map tissue niches and cell-cell communication across spatial slides.

Emits manifest.json · SHA-256 per artifact

Request access →

Cell & Molecular

Beta

ATLASos

Cell atlas construction

2 MCPs · HITL gates

ATLASos

Beta

2 MCPs

HITL gates

Single-cell counts · Reference atlas · Study metadata

Out

Integrated atlas · Reference mapping · Annotation report

Tools integrated

Scanpy scvi-tools CellTypist scArches CELLxGENE scIB

MCP servers

Knowledge Graph PubMed

Example

Build a cross-study cell atlas and map new samples onto a reference.

Emits manifest.json · SHA-256 per artifact

Request access →

Omics

6 products

Omics

Beta

ONCOos

Somatic, neoantigen

4 MCPs · HITL gates

ONCOos

Beta

4 MCPs

HITL gates

Tumor/normal BAM · HLA type

Out

Somatic VCF · Neoantigens · Signatures

Tools integrated

Mutect2 pVACtools SigProfiler MSIsensor

MCP servers

biocontext7 ChEMBL PubMed Paper Intelligence

Example

Profile a tumor from raw reads through prioritized neoantigens.

Emits manifest.json · SHA-256 per artifact

Request access →

Omics

Beta

MICROBIOMEos

16S, metagenomics

3 MCPs · HITL gates

MICROBIOMEos

Beta

3 MCPs

HITL gates

16S / shotgun FASTQ · Sample metadata

Out

ASV table · Taxonomy · Function profile

Tools integrated

QIIME 2 Kraken2 HUMAnN MetaPhlAn

MCP servers

biocontext7 PubMed Paper Intelligence

Example

Go from raw microbiome reads to differential-abundance figures.

Emits manifest.json · SHA-256 per artifact

Request access →

Omics

Beta

PROTEOMICSos

Mass spec

3 MCPs · HITL gates

PROTEOMICSos

Beta

3 MCPs

HITL gates

RAW / mzML · Sample design

Out

Protein matrix · PTM sites · Differential report

Tools integrated

MaxQuant FragPipe DIA-NN MSstats

MCP servers

biocontext7 PubMed Paper Intelligence

Example

Quantify a label-free proteomics cohort with PTM-aware QC.

Emits manifest.json · SHA-256 per artifact

Request access →

Omics

Beta

METABos

Metabolomics

3 MCPs · HITL gates

METABos

Beta

3 MCPs

HITL gates

LC-MS / NMR · Metadata

Out

Feature table · Annotations · Pathway enrichment

Tools integrated

XCMS MS-DIAL MetaboAnalyst GNPS

MCP servers

biocontext7 PubMed Paper Intelligence

Example

Annotate and contextualize untargeted metabolomics features.

Emits manifest.json · SHA-256 per artifact

Request access →

Omics

Beta

IMMUNOos

Immune repertoire

3 MCPs · HITL gates

IMMUNOos

Beta

3 MCPs

HITL gates

TCR / BCR sequencing · Clonal metadata

Out

Clonotype table · Diversity stats · V(D)J map

Tools integrated

MiXCR TRUST4 Immcantation scirpy

MCP servers

biocontext7 PubMed Paper Intelligence

Example

Characterize TCR/BCR repertoire dynamics across treatment arms.

Emits manifest.json · SHA-256 per artifact

Request access →

Omics

Beta

MULTIos

Multi-omics integration

2 MCPs · HITL gates

MULTIos

Beta

2 MCPs

HITL gates

Transcriptomics · Proteomics · Metabolomics

Out

Shared factors · Integrated model · Interpretation report

Tools integrated

MOFA mixOmics scikit-learn networkx

MCP servers

Knowledge Graph PubMed

Example

Find shared latent factors across transcriptome, proteome and metabolome.

Emits manifest.json · SHA-256 per artifact

Request access →

Imaging & Structure

2 products

Imaging & Structure

Beta

STRUCTos

AlphaFold, docking

4 MCPs · HITL gates

STRUCTos

Beta

4 MCPs

HITL gates

Sequence · Ligand SMILES · Target PDB

Out

Predicted structure · Pocket map · Docked poses

Tools integrated

AlphaFold3 ESMFold Boltz-1 DiffDock

MCP servers

biocontext7 PubMed BioRender Knowledge Graph

Example

Fold a target, find its pocket, and screen candidate binders.

Emits manifest.json · SHA-256 per artifact

Request access →

Imaging & Structure

Beta

BIOIMAGEos

Microscopy

3 MCPs · HITL gates

BIOIMAGEos

Beta

3 MCPs

HITL gates

TIFF / OME-Zarr · Channel metadata

Out

Segmentation · Morphometrics · Tracking

Tools integrated

CellProfiler Cellpose StarDist napari

MCP servers

biocontext7 PubMed BioRender

Example

Segment and quantify phenotypes across high-content imaging plates.

Emits manifest.json · SHA-256 per artifact

Request access →

Clinical & Regulatory

2 products

Clinical & Regulatory

Beta

RAREos

Rare disease, ACMG

3 MCPs · HITL gates

RAREos

Beta

3 MCPs

HITL gates

Proband VCF · HPO phenotypes · Trio (optional)

Out

ACMG classification · Candidate list · Report draft

Tools integrated

Exomiser InterVar VarSome Franklin

MCP servers

ClinicalTrials PubMed Knowledge Graph

Example

Generate an ACMG-graded rare disease report with traceable evidence.

Emits manifest.json · SHA-256 per artifact

Request access →

Clinical & Regulatory

Planned

CLINICALos

EHR and cohort analysis

No repository yet — nothing to show on the back.

Drug Discovery

3 products

Drug Discovery

Beta

CHEMos

Cheminformatics

3 MCPs · HITL gates

CHEMos

Beta

3 MCPs

HITL gates

SMILES · Assay readouts

Out

Property table · Scaffold map · SAR summary

Tools integrated

RDKit ChEMBL DataWarrior Reaxys

MCP servers

ChEMBL PubMed Paper Intelligence

Example

Triage a library and pull out scaffold-level SAR trends.

Emits manifest.json · SHA-256 per artifact

Request access →

Drug Discovery

Planned

ADMETos

ADMET prediction

No repository yet — nothing to show on the back.

Drug Discovery

Planned

VIRTUALSCREENos

Virtual screening

No repository yet — nothing to show on the back.

Systems & Networks

3 products

Systems & Networks

Planned

SYSTEMSos

Systems biology

No repository yet — nothing to show on the back.

Systems & Networks

Planned

PATHWAYos

Pathway analysis

No repository yet — nothing to show on the back.

Systems & Networks

Planned

GRNos

Gene regulatory networks

No repository yet — nothing to show on the back.

24 Domain Operating Systems with a repository, 6 planned · Counted from the registry in this repository · Click any card for integrations and example workflows

THE REASONING LAYER

4 plugins Claude composes on every run.

DomainOS products dispatch to a shared reasoning layer: 4 plugins Claude composes on every run. Each solves one hard scientific problem well.

Reasoning Plugin

Beta

co-writer

Compiles 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.

4 Signature skills · 5 Agents · 3 MCPs

co-writer

Compiles scientific writing

Beta

4 Signature skills

5 Agents

3 MCPs

Signature skills

compile-manuscript evidence-audit compliance-lint citation-resolve

Agents

citation-resolver science-reviewer reviewer-simulator diff-presenter compiler-orchestrator

MCP servers

PubMed Paper Intelligence bioRxiv

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

plugin/co-writer

Reasoning Plugin

Beta

co-scientist

Generates 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.

4 Signature skills · 7 Agents · 4 MCPs

co-scientist

Generates and critiques hypotheses

Beta

4 Signature skills

7 Agents

4 MCPs

Signature skills

hypothesis-generate hypothesis-critique novelty-scan analysis-plan

Agents

research-copilot hypothesis-generator hypothesis-critic hypothesis-evaluator hypothesis-evolver debate-orchestrator tournament-ranker

MCP servers

PubMed bioRxiv Paper Intelligence Knowledge Graph

Example

Explore 'cold target' hypotheses for a rare disease with Elo-ranked debate between generator and critic agents.

Emits: HypothesisIR + DebateRecord + Elo ranking

plugin/co-scientist

Reasoning Plugin

Beta

paper-intelligence

Extracts 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. Every claim carries the source it came from.

4 Signature skills · 3 Agents · 4 MCPs

paper-intelligence

Extracts and tracks claims

Beta

4 Signature skills

3 Agents

4 MCPs

Signature skills

paper-ingest claim-extract contradiction-detection claim-graph-query

Agents

paper-intelligence-agent graph-builder claim-graph-builder

MCP servers

PubMed bioRxiv Paper Intelligence Knowledge Graph

Example

Ingest 40 papers on BRCA1 synthetic lethality and surface contradictions across the claim graph.

Emits: claim graph + provenance chain per claim

plugin/paper-intelligence

Reasoning Plugin

Beta

knowledge-graph

Unifies 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.

4 Signature skills · 1 Agents · 4 MCPs

knowledge-graph

Unifies biomedical knowledge

Beta

4 Signature skills

1 Agents

4 MCPs

Signature skills

graph-query graph-ingest graph-search graph-explore

Agents

graph-builder

MCP servers

Knowledge Graph PubMed ChEMBL Paper Intelligence

Example

Unify GWAS loci, tissue expression, and drug targets into one queryable graph for target selection.

Emits: Biolink-schema graph + citation edges

plugin/research-knowledge-graph

See how the layers compose

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