KATALOGOA

Domeinu Sistema Eragileak. 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.

CRISPRos Esploratu Domeinu guztiak ikusi

DomainOS produktuak arrazoibide plugin partekatuen eta MCP datu-geruza partekatu 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.

7 kategoria, 24 sistema eragile biltegiarekin, 6 aurreikusita. Egin klik txartel batean integratutako tresnak, sarrerak eta irteerak eta adibide bat ikusteko.

Genomika eta aldaerak

9 produktu

Genomics & Variants

Beta

BIOos

Alignment, QC, RNA-seq

3 MCP · HITL ate

BIOos

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Genomics & Variants

Beta

GWASos

Association, fine-mapping

3 MCP · HITL ate

Ireki →

GWASos

Beta

3 MCP

HITL ate

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

Dokumentazioa ireki →

Genomics & Variants

Beta

varfx-os

Variant annotation

3 MCP · HITL ate

varfx-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Genomics & Variants

Beta

finemap-os

Statistical fine-mapping

3 MCP · HITL ate

finemap-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Genomics & Variants

Beta

prs-os

Polygenic risk scores

3 MCP · HITL ate

prs-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Genomics & Variants

Beta

mendel-os

Mendelian genetics

3 MCP · HITL ate

mendel-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Genomics & Variants

Beta

clinvar-os

ClinVar interpretation

3 MCP · HITL ate

clinvar-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Genomics & Variants

Beta

longread-os

ONT, PacBio

3 MCP · HITL ate

longread-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Genomics & Variants

Beta

reg-os

Enhancers, TF binding, chromatin

2 MCP · HITL ate

reg-os

Beta

2 MCP

HITL ate

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

Out

Consensus peaks · Motif enrichment · Enhancer-gene links

Integratutako tresnak

MACS2 HOMER TOBIAS chromVAR ENCODE Cistrome DB

MCP zerbitzariak

PubMed Knowledge Graph

Adibidea

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

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

Sarbidea eskatu →

Zelula eta molekularra

5 produktu

Cell & Molecular

Beta

CRISPRos

Guide design, knockouts

3 MCP · HITL ate

Ireki →

CRISPRos

Beta

3 MCP

HITL ate

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

Dokumentazioa ireki →

Cell & Molecular

Beta

screen-os

CRISPR screens, MAGeCK

3 MCP · HITL ate

screen-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Cell & Molecular

Beta

cell-os

Cell biology analysis

3 MCP · HITL ate

cell-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Cell & Molecular

Beta

spatial-os

Spatial transcriptomics

3 MCP · HITL ate

spatial-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Cell & Molecular

Beta

atlas-os

Cell atlas construction

2 MCP · HITL ate

atlas-os

Beta

2 MCP

HITL ate

Single-cell counts · Reference atlas · Study metadata

Out

Integrated atlas · Reference mapping · Annotation report

Integratutako tresnak

Scanpy scvi-tools CellTypist scArches CELLxGENE scIB

MCP zerbitzariak

Knowledge Graph PubMed

Adibidea

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

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

Sarbidea eskatu →

Omikak

6 produktu

Omics

Beta

onco-os

Somatic, neoantigen

4 MCP · HITL ate

onco-os

Beta

4 MCP

HITL ate

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

Sarbidea eskatu →

Omics

Beta

microbiome-os

16S, metagenomics

3 MCP · HITL ate

microbiome-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Omics

Beta

proteomics-os

Mass spec

3 MCP · HITL ate

proteomics-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Omics

Beta

metab-os

Metabolomics

3 MCP · HITL ate

metab-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Omics

Beta

immuno-os

Immune repertoire

3 MCP · HITL ate

immuno-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Omics

Beta

multi-os

Multi-omics integration

2 MCP · HITL ate

multi-os

Beta

2 MCP

HITL ate

Transcriptomics · Proteomics · Metabolomics

Out

Shared factors · Integrated model · Interpretation report

Integratutako tresnak

MOFA mixOmics scikit-learn networkx

MCP zerbitzariak

Knowledge Graph PubMed

Adibidea

Find shared latent factors across transcriptome, proteome and metabolome.

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

Sarbidea eskatu →

Irudia eta egitura

2 produktu

Imaging & Structure

Beta

struct-os

AlphaFold, docking

4 MCP · HITL ate

struct-os

Beta

4 MCP

HITL ate

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

Sarbidea eskatu →

Imaging & Structure

Beta

bioimage-os

Microscopy

3 MCP · HITL ate

bioimage-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Klinikoa eta arautzailea

2 produktu

Clinical & Regulatory

Beta

rare-os

Rare disease, ACMG

3 MCP · HITL ate

rare-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Clinical & Regulatory

Aurreikusita

clinical-os

EHR and cohort analysis

Oraindik biltegirik gabe: ez dago atzealdean zer erakutsi.

Farmako-aurkikuntza

3 produktu

Drug Discovery

Beta

chem-os

Cheminformatics

3 MCP · HITL ate

chem-os

Beta

3 MCP

HITL ate

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

Sarbidea eskatu →

Drug Discovery

Aurreikusita

admet-os

ADMET prediction

Oraindik biltegirik gabe: ez dago atzealdean zer erakutsi.

Drug Discovery

Aurreikusita

virtual-screen-os

Virtual screening

Oraindik biltegirik gabe: ez dago atzealdean zer erakutsi.

Sistemak eta sareak

3 produktu

Systems & Networks

Aurreikusita

systems-os

Systems biology

Oraindik biltegirik gabe: ez dago atzealdean zer erakutsi.

Systems & Networks

Aurreikusita

pathway-os

Pathway analysis

Oraindik biltegirik gabe: ez dago atzealdean zer erakutsi.

Systems & Networks

Aurreikusita

grn-os

Gene regulatory networks

Oraindik biltegirik gabe: ez dago atzealdean zer erakutsi.

24 Domeinu Sistema Eragile biltegiarekin, 6 aurreikusita · Biltegi honetako erregistrotik zenbatuta · 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.

4 Trebetasun nagusiak · 5 Agenteak · 3 MCP

co-writer

Compiles scientific writing

Beta

4 Trebetasun nagusiak

5 Agenteak

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.

4 Trebetasun nagusiak · 7 Agenteak · 4 MCP

co-scientist

Generates and critiques hypotheses

Beta

4 Trebetasun nagusiak

7 Agenteak

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.

4 Trebetasun nagusiak · 9 Agenteak · 2 MCP

sophia-claudette

Audits scientific reasoning

Beta

4 Trebetasun nagusiak

9 Agenteak

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. Every claim carries the source it came from.

4 Trebetasun nagusiak · 3 Agenteak · 4 MCP

paper-intelligence

Extracts and tracks claims

Beta

4 Trebetasun nagusiak

3 Agenteak

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.

4 Trebetasun nagusiak · 1 Agenteak · 4 MCP

knowledge-graph

Unifies biomedical knowledge

Beta

4 Trebetasun nagusiak

1 Agenteak

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/research-knowledge-graph

Ikusi nola konposatzen diren geruzak

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.

Harremanetan Jarri Arkitektura irakurri