Lisa-sudo872/TBGenSurv

TB Genomic Surveillance System — University of Zimbabwe BIBE Department # TBGenSurv — Zimbabwe TB Genomic Surveillance System **Developer:** Lisa Rutendo Mhlanga **Institution:** Department of Biomedical Informatics & Biomedical Engineering, University of Zimbabwe **Supervisor:** Dr. T. Simbini | Dr. Zulu ## Overview TBGenSurv is a six-module integrated TB genomic surveillance platform combining whole-genome sequencing, machine learning resistance prediction, geospatial mapping, and clinical decision support — built for the Zimbabwe National Microbiology Reference Laboratory (NMRL) context. ## Modules | Module | Description | Stack | |--------|-------------|-------| | 1 — Clinic & Sample Tracking | Android/web app for clinic-to-NMRL sample registration and 7-day transit monitoring | React Native + Expo | | 2 — NMRL Lab Interface | Lab technician dashboard for GeneXpert/DST result capture, FHIR R4 output, DHIS2 export | React | | 3 — WGS Bioinformatics Pipeline | Pipeline management for FastQC → BWA-MEM → GATK → WHO annotation → lineage typing | React | | 4 — ML Resistance Prediction | k-mer feature extraction + XGBoost/RF models for 8-drug resistance prediction. Extended from HIV-1 NRTI pipeline. | React | | 5 — Geospatial & Phylogenetics | Province-level TB mapping, Getis-Ord Gi* hotspot analysis, transmission cluster phylogenetics | React | | 6 — National Dashboard | Coming soon | React | ## Running Locally Each module is an independent React app (Modules 2–5) or React Native app (Module 1): ```bash cd module2-nmrl-lab npm install npm start ``` ## Related Work - HIV-1 Drug Resistance Prediction using ML (predecessor project) - NMRL Zimbabwe data request in progress ## Live Demos - Module 2 NMRL Lab: tbgensurv-module2.vercel.app - Module 3 Pipeline: tbgensurv-module3.vercel.app - Module 4 ML Engine: tbgensurv-module4.vercel.app - Module 5 Geospatial: tbgensurv-module5.vercel.app