MultiOmics-Reactome v3.0 - MIMODH-Compliant Pipeline

Production-grade MIMODH-compliant multi-omics harmonization pipeline. Cloud web app (React + FastAPI + AWS) and standalone desktop app (PyQt6). Agamah et al. 2025 - Frontiers in Genetics

Quick Start

Desktop App (offline, no cloud needed)

pip install -r requirements.txt -r desktop/requirements_desktop.txt
python -m desktop.app
# Windows: .\scripts\setup.ps1 -Desktop

Cloud / Docker

docker compose up --build

Bundled Test Data (pipeline-validated)

File	Shape	Note
transcriptomics_test.csv	40x70	HGNC gene symbols, batch effects
proteomics_test.csv	40x24	UniProt accessions
metabolomics_test.csv	40x20	ChEBI IDs
metadata_test.csv	40x14	condition, batch_0/1/2, age, sex...

Click Load Bundled Test Data in the Configure tab to auto-fill paths.

MIMODH Compliance

Tier	Fields	Use case
Tier 1	sample_id, condition, batch, modality, data_path	Minimum
Tier 2	+ age, sex, BMI, platform, tissue_type	Recommended
Tier 3	+ treatment, survival, reference_genome, ethics	Full FAIR

Repository Structure

Path	Lines	Role
backend/multiomics_reactome.py	1,436	Reactome network pipeline (syntax-fixed)
backend/multiomics_pipeline.py	847	Core integration pipeline
backend/app.py	413	FastAPI REST API
desktop/app.py	94	Desktop entry point
desktop/widgets/configure_tab.py	298	Real uploaded widget
desktop/widgets/run_tab.py	179	Real uploaded widget
desktop/widgets/results_tab.py	233	Real uploaded widget
desktop/widgets/about_tab.py	121	Real uploaded widget
desktop/test_data/	-	Pipeline-validated CSVs

References

• Agamah et al. 2025 - Frontiers in Genetics (MIMODH)
• Korsunsky et al. 2019 - Nat. Methods (Harmony)
• Gillespie et al. 2022 - NAR (Reactome v84)