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KATALOGOA

28 Domeinu Sistema Eragile. Pila konposatu bat.

DomainOS bakoitza arrazoibide plugin partekatuen eta MCP datu-geruzaren gainean eraikitako geruza mehe bat da. Domeinu zientifiko batentzat eraikiak — genomika, CRISPR, farmako-aurkikuntza, klinika — erabaki kritiko bakoitzean giza onarpen batekin.

DomainOS produktuak arrazoibide plugin partekatuen eta hash bidez egiaztatutako MCP datu-geruza baten gainean eraikitako sistema eragileak dira. Egin klik edozein txarteletan integratutako tresnak eta adibide bat ikusteko.

KATALOGOA

Domeinu bakoitza. Lan-fluxu bakoitza. Jatorri-manifestu bakarra.

Zazpi kategoria, 28 sistema eragile, 1.062+ trebetasun. Egin klik txartel batean integratutako tresnak, sarrerak eta irteerak eta adibide bat ikusteko.

Genomika eta aldaerak

8 produktu

Genomics & Variants

Beta

BIOos

Alignment, QC, RNA-seq

8 agente · 92 trebetasun · 3 MCP · 3 HITL ate

BIOos

Beta

8 agente

92 trebetasun

3 MCP

3 HITL ate

In

FASTQ · Reference genome · Sample sheet

Out

BAM/CRAM · MultiQC report · Count matrix

Integratutako tresnak

STAR BWA-MEM2 samtools MultiQC

MCP zerbitzariak

biocontext7 PubMed Knowledge Graph

Adibidea

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

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Genomics & Variants

Beta

GWASos

Association, fine-mapping

7 agente · 78 trebetasun · 3 MCP · 3 HITL ate

Ireki →

GWASos

Beta

7 agente

78 trebetasun

3 MCP

3 HITL ate

In

PLINK/VCF · Phenotype table · Covariates

Out

Summary stats · Manhattan plot · Credible sets

Integratutako tresnak

PLINK2 REGENIE SAIGE SuSiE

MCP zerbitzariak

biocontext7 PubMed Knowledge Graph

Adibidea

Run a biobank-scale association with calibrated inflation checks.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Genomics & Variants

Beta

varfx-os

Variant annotation

6 agente · 61 trebetasun · 3 MCP · 2 HITL ate

varfx-os

Beta

6 agente

61 trebetasun

3 MCP

2 HITL ate

In

VCF · Gene models

Out

Annotated VCF · Effect tiers · Evidence trail

Integratutako tresnak

VEP SnpEff AlphaMissense

MCP zerbitzariak

biocontext7 PubMed Knowledge Graph

Adibidea

Prioritize coding + regulatory variants with grounded effect calls.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Genomics & Variants

Beta

finemap-os

Statistical fine-mapping

5 agente · 54 trebetasun · 3 MCP · 2 HITL ate

finemap-os

Beta

5 agente

54 trebetasun

3 MCP

2 HITL ate

In

GWAS summary stats · LD reference

Out

Credible sets · Posterior probs · Locus plots

Integratutako tresnak

SuSiE FINEMAP CAVIAR PolyFun

MCP zerbitzariak

biocontext7 PubMed Knowledge Graph

Adibidea

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

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Genomics & Variants

Beta

prs-os

Polygenic risk scores

4 agente · 47 trebetasun · 3 MCP · 2 HITL ate

prs-os

Beta

4 agente

47 trebetasun

3 MCP

2 HITL ate

In

GWAS weights · Target genotypes

Out

PRS per sample · Calibration plot · Ancestry audit

Integratutako tresnak

PRS-CS LDpred2 PLINK2

MCP zerbitzariak

biocontext7 PubMed Knowledge Graph

Adibidea

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

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Genomics & Variants

Beta

mendel-os

Mendelian genetics

5 agente · 52 trebetasun · 3 MCP · 3 HITL ate

mendel-os

Beta

5 agente

52 trebetasun

3 MCP

3 HITL ate

In

Pedigree · Trio VCF · HPO terms

Out

Candidate variants · Inheritance fit · ACMG class

Integratutako tresnak

Exomiser GEMINI Phen2Gene

MCP zerbitzariak

biocontext7 PubMed Knowledge Graph

Adibidea

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

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Genomics & Variants

Beta

clinvar-os

ClinVar interpretation

4 agente · 39 trebetasun · 3 MCP · 3 HITL ate

clinvar-os

Beta

4 agente

39 trebetasun

3 MCP

3 HITL ate

In

VCF · Variant IDs

Out

ClinVar evidence · Conflict report · Citation trail

Integratutako tresnak

ClinVar LitVar OMIM

MCP zerbitzariak

biocontext7 ClinicalTrials PubMed

Adibidea

Audit clinical variant interpretations against latest ClinVar evidence.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Genomics & Variants

Beta

longread-os

ONT, PacBio

5 agente · 58 trebetasun · 3 MCP · 2 HITL ate

longread-os

Beta

5 agente

58 trebetasun

3 MCP

2 HITL ate

In

Nanopore / HiFi FASTQ · Reference

Out

Phased BAM · SV VCF · Methylation BED

Integratutako tresnak

minimap2 Sniffles Clair3 Nanopolish

MCP zerbitzariak

biocontext7 PubMed Knowledge Graph

Adibidea

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

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Zelula eta molekularra

4 produktu

Cell & Molecular

Beta

CRISPRos

Guide design, knockouts

8 agente · 86 trebetasun · 3 MCP · 4 HITL ate

Ireki →

CRISPRos

Beta

8 agente

86 trebetasun

3 MCP

4 HITL ate

In

Target gene(s) · Cell line · Delivery context

Out

Guide library · Off-target report · Experiment manifest

Integratutako tresnak

CRISPOR CHOPCHOP FlashFry Azimuth

MCP zerbitzariak

biocontext7 PubMed Knowledge Graph

Adibidea

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

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Cell & Molecular

Beta

screen-os

CRISPR screens, MAGeCK

6 agente · 64 trebetasun · 3 MCP · 3 HITL ate

screen-os

Beta

6 agente

64 trebetasun

3 MCP

3 HITL ate

In

Counts matrix · Library design · Conditions

Out

Hit list · Gene-level scores · QC dashboard

Integratutako tresnak

MAGeCK BAGEL drugZ ScreenPro2

MCP zerbitzariak

biocontext7 PubMed BioRender

Adibidea

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

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Cell & Molecular

Beta

cell-os

Cell biology analysis

6 agente · 71 trebetasun · 3 MCP · 2 HITL ate

cell-os

Beta

6 agente

71 trebetasun

3 MCP

2 HITL ate

In

scRNA / sc-ATAC counts · Sample metadata

Out

Annotated atlas · Marker panels · Trajectory

Integratutako tresnak

Scanpy Seurat scVI CellTypist

MCP zerbitzariak

biocontext7 PubMed BioRender

Adibidea

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

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Cell & Molecular

Beta

spatial-os

Spatial transcriptomics

4 agente · 48 trebetasun · 3 MCP · 2 HITL ate

spatial-os

Beta

4 agente

48 trebetasun

3 MCP

2 HITL ate

In

Visium / Xenium / MERFISH · H&E image

Out

Niche map · Co-localization · Cell-cell signals

Integratutako tresnak

Squidpy CellCharter SpatialData SOPA

MCP zerbitzariak

biocontext7 PubMed BioRender

Adibidea

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

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Omikak

5 produktu

Omics

Beta

onco-os

Somatic, neoantigen

6 agente · 68 trebetasun · 4 MCP · 3 HITL ate

onco-os

Beta

6 agente

68 trebetasun

4 MCP

3 HITL ate

In

Tumor/normal BAM · HLA type

Out

Somatic VCF · Neoantigens · Signatures

Integratutako tresnak

Mutect2 pVACtools SigProfiler MSIsensor

MCP zerbitzariak

biocontext7 ChEMBL PubMed Paper Intelligence

Adibidea

Profile a tumor from raw reads through prioritized neoantigens.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Omics

Beta

microbiome-os

16S, metagenomics

5 agente · 55 trebetasun · 3 MCP · 2 HITL ate

microbiome-os

Beta

5 agente

55 trebetasun

3 MCP

2 HITL ate

In

16S / shotgun FASTQ · Sample metadata

Out

ASV table · Taxonomy · Function profile

Integratutako tresnak

QIIME 2 Kraken2 HUMAnN MetaPhlAn

MCP zerbitzariak

biocontext7 PubMed Paper Intelligence

Adibidea

Go from raw microbiome reads to differential-abundance figures.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Omics

Beta

proteomics-os

Mass spec

4 agente · 46 trebetasun · 3 MCP · 2 HITL ate

proteomics-os

Beta

4 agente

46 trebetasun

3 MCP

2 HITL ate

In

RAW / mzML · Sample design

Out

Protein matrix · PTM sites · Differential report

Integratutako tresnak

MaxQuant FragPipe DIA-NN MSstats

MCP zerbitzariak

biocontext7 PubMed Paper Intelligence

Adibidea

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

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Omics

Beta

metab-os

Metabolomics

4 agente · 42 trebetasun · 3 MCP · 2 HITL ate

metab-os

Beta

4 agente

42 trebetasun

3 MCP

2 HITL ate

In

LC-MS / NMR · Metadata

Out

Feature table · Annotations · Pathway enrichment

Integratutako tresnak

XCMS MS-DIAL MetaboAnalyst GNPS

MCP zerbitzariak

biocontext7 PubMed Paper Intelligence

Adibidea

Annotate and contextualize untargeted metabolomics features.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Omics

Beta

immuno-os

Immune repertoire

4 agente · 44 trebetasun · 3 MCP · 2 HITL ate

immuno-os

Beta

4 agente

44 trebetasun

3 MCP

2 HITL ate

In

TCR / BCR sequencing · Clonal metadata

Out

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

Integratutako tresnak

MiXCR TRUST4 Immcantation scirpy

MCP zerbitzariak

biocontext7 PubMed Paper Intelligence

Adibidea

Characterize TCR/BCR repertoire dynamics across treatment arms.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Irudia eta egitura

2 produktu

Imaging & Structure

Beta

struct-os

AlphaFold, docking

5 agente · 59 trebetasun · 4 MCP · 2 HITL ate

struct-os

Beta

5 agente

59 trebetasun

4 MCP

2 HITL ate

In

Sequence · Ligand SMILES · Target PDB

Out

Predicted structure · Pocket map · Docked poses

Integratutako tresnak

AlphaFold3 ESMFold Boltz-1 DiffDock

MCP zerbitzariak

biocontext7 PubMed BioRender Knowledge Graph

Adibidea

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

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Imaging & Structure

Beta

bioimage-os

Microscopy

5 agente · 51 trebetasun · 3 MCP · 2 HITL ate

bioimage-os

Beta

5 agente

51 trebetasun

3 MCP

2 HITL ate

In

TIFF / OME-Zarr · Channel metadata

Out

Segmentation · Morphometrics · Tracking

Integratutako tresnak

CellProfiler Cellpose StarDist napari

MCP zerbitzariak

biocontext7 PubMed BioRender

Adibidea

Segment and quantify phenotypes across high-content imaging plates.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Klinikoa eta arautzailea

3 produktu

Clinical & Regulatory

Beta

rare-os

Rare disease, ACMG

5 agente · 57 trebetasun · 3 MCP · 4 HITL ate

rare-os

Beta

5 agente

57 trebetasun

3 MCP

4 HITL ate

In

Proband VCF · HPO phenotypes · Trio (optional)

Out

ACMG classification · Candidate list · Report draft

Integratutako tresnak

Exomiser InterVar VarSome Franklin

MCP zerbitzariak

ClinicalTrials PubMed Knowledge Graph

Adibidea

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

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Clinical & Regulatory

Beta

clinical-os

EHR, PyHealth

4 agente · 49 trebetasun · 3 MCP · 3 HITL ate

clinical-os

Beta

4 agente

49 trebetasun

3 MCP

3 HITL ate

In

FHIR / OMOP CDM · Cohort criteria

Out

Cohort table · Endpoint schedule · Audit log

Integratutako tresnak

PyHealth OHDSI CEDAR Synthea

MCP zerbitzariak

ClinicalTrials PubMed Synapse

Adibidea

Build an OMOP cohort with endpoints that survive regulatory audit.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Clinical & Regulatory

Beta

reg-os

ISO 13485, FDA QMSR

4 agente · 41 trebetasun · 3 MCP · 4 HITL ate

reg-os

Beta

4 agente

41 trebetasun

3 MCP

4 HITL ate

In

Requirements · Test records · Change log

Out

DHF package · Traceability matrix · Submission draft

Integratutako tresnak

ISO 13485 FDA QMSR IEC 62304

MCP zerbitzariak

ClinicalTrials PubMed Synapse

Adibidea

Compile a design-history file with claim-to-evidence traceability.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Farmako-aurkikuntza

3 produktu

Drug Discovery

Beta

chem-os

Cheminformatics

5 agente · 50 trebetasun · 3 MCP · 2 HITL ate

chem-os

Beta

5 agente

50 trebetasun

3 MCP

2 HITL ate

In

SMILES · Assay readouts

Out

Property table · Scaffold map · SAR summary

Integratutako tresnak

RDKit ChEMBL DataWarrior Reaxys

MCP zerbitzariak

ChEMBL PubMed Paper Intelligence

Adibidea

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

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Drug Discovery

Beta

admet-os

ADMET prediction

4 agente · 45 trebetasun · 3 MCP · 3 HITL ate

admet-os

Beta

4 agente

45 trebetasun

3 MCP

3 HITL ate

In

SMILES · Reference compounds

Out

ADMET profile · Alert flags · Confidence bands

Integratutako tresnak

ADMET-AI SwissADME TDC DeepPurpose

MCP zerbitzariak

ChEMBL PubMed Paper Intelligence

Adibidea

Profile ADMET liabilities with calibrated uncertainty, not point estimates.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Drug Discovery

Beta

virtual-screen-os

Virtual screening

4 agente · 48 trebetasun · 3 MCP · 2 HITL ate

virtual-screen-os

Beta

4 agente

48 trebetasun

3 MCP

2 HITL ate

In

Target structure · Compound library

Out

Ranked hits · Pose library · Enrichment report

Integratutako tresnak

AutoDock Vina GNINA DiffDock DeepDock

MCP zerbitzariak

ChEMBL PubMed Knowledge Graph

Adibidea

Dock a million compounds and surface high-confidence candidates.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Sistemak eta sareak

3 produktu

Systems & Networks

Beta

systems-os

Systems biology

4 agente · 43 trebetasun · 3 MCP · 2 HITL ate

systems-os

Beta

4 agente

43 trebetasun

3 MCP

2 HITL ate

In

Expression matrix · Perturbation data

Out

Causal graph · Intervention plan · Model fit

Integratutako tresnak

CellOracle COBRA Tellurium GeneFormer

MCP zerbitzariak

Knowledge Graph PubMed Paper Intelligence

Adibidea

Build a causal systems model that predicts perturbation response.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Systems & Networks

Beta

pathway-os

Pathway analysis

4 agente · 40 trebetasun · 3 MCP · 2 HITL ate

pathway-os

Beta

4 agente

40 trebetasun

3 MCP

2 HITL ate

In

Gene lists · Expression data

Out

Enriched pathways · Network figure · Citation trail

Integratutako tresnak

Reactome GSEA enrichR WebGestalt

MCP zerbitzariak

Knowledge Graph PubMed Paper Intelligence

Adibidea

Convert a gene hit list into a pathway narrative grounded in citations.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

Systems & Networks

Beta

grn-os

Gene regulatory networks

4 agente · 46 trebetasun · 3 MCP · 2 HITL ate

grn-os

Beta

4 agente

46 trebetasun

3 MCP

2 HITL ate

In

scRNA + ATAC · TF motif database

Out

Regulon set · TF targets · Perturbation predictions

Integratutako tresnak

SCENIC+ Pando GRNBoost2 CellOracle

MCP zerbitzariak

Knowledge Graph PubMed Paper Intelligence

Adibidea

Infer TF regulons from multiomic data and simulate knockouts.

Sortzen du: manifest.json · SHA-256 artefaktu bakoitzeko

28 Domeinu Sistema Eragile · Q2 2026ko zenbaketak · Egin klik edozein txarteletan integrazio eta adibideak ikusteko

ARRAZOIBIDE GERUZA

Bost plugin Claudek exekuzio bakoitzean konposatzen dituenak.

DomainOS produktuak arrazoibide geruza partekatu batera bidaltzen dira: Claudek exekuzio bakoitzean konposatzen dituen bost plugin. Bakoitzak arazo zientifiko zail bat ondo ebazten du.

Arrazoibide plugina

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.

34 trebetasun · 5 agente · 3 MCP

co-writer

Compiles scientific writing

Beta

34 trebetasun

5 agente

3 MCP

Trebetasun nagusiak

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

Agenteak

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

MCP zerbitzariak

PubMed Paper Intelligence bioRxiv

Adibidea

Compile an R01 renewal from lab data, prior papers, and aims — every sentence cited to a source artifact.

Sortzen du: claim-to-evidence map + manifest.json

plugin/co-writer

Arrazoibide plugina

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.

8 trebetasun · 7 agente · 4 MCP

co-scientist

Generates and critiques hypotheses

Beta

8 trebetasun

7 agente

4 MCP

Trebetasun nagusiak

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

Agenteak

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

MCP zerbitzariak

PubMed bioRxiv Paper Intelligence Knowledge Graph

Adibidea

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

Sortzen du: HypothesisIR + DebateRecord + Elo ranking

plugin/co-scientist

Arrazoibide plugina

Beta

sophia-claudette

Audits 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 trebetasun · 9 agente · 2 MCP

sophia-claudette

Audits scientific reasoning

Beta

7 trebetasun

9 agente

2 MCP

Trebetasun nagusiak

uncertainty-calibration causal-skepticism drift-audit decision-audit

Agenteak

socratic-facilitator epistemic-diagnostician evidence-curator causal-skeptic experimental-designer uncertainty-calibrator decision-auditor +2

MCP zerbitzariak

Paper Intelligence PubMed

Adibidea

Flag correlation-vs-causation drift in a mid-flight manuscript before it ships to peer review.

Sortzen du: epistemic card + drift log

plugin/sophia-claudette

Arrazoibide plugina

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. Provenance is never fabricated.

12 trebetasun · 3 agente · 4 MCP

paper-intelligence

Extracts and tracks claims

Beta

12 trebetasun

3 agente

4 MCP

Trebetasun nagusiak

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

Agenteak

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

MCP zerbitzariak

PubMed bioRxiv Paper Intelligence Knowledge Graph

Adibidea

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

Sortzen du: claim graph + provenance chain per claim

plugin/paper-intelligence

Arrazoibide plugina

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.

5 trebetasun · 1 agente · 4 MCP

knowledge-graph

Unifies biomedical knowledge

Beta

5 trebetasun

1 agente

4 MCP

Trebetasun nagusiak

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

Agenteak

graph-builder

MCP zerbitzariak

Knowledge Graph PubMed ChEMBL Paper Intelligence

Adibidea

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

Sortzen du: Biolink-schema graph + citation edges

plugin/hordago-knowledge-graph

Ekarri ebidentzian oinarritutako AA zure laborategira.

Ikerketa laborategiekin, bioteknologia enpresekin, gobernu programekin eta zientzia industrialeko taldeekin lan egiten dugu. Esaguzu domeinua; guk egokia den DomainOS-a, motorrak eta giza ateak mapatuko ditugu.