Gen-EpiX 0.0.1

Genomic Epidemiology platform for disease X

Genomic Epidemiology platform for disease X

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Source Code: https://github.com/RIVM-bioinformatics/lsp-api

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Gen-EpiX: Genomic Epidemiology platform for disease X (beta version)

Gen-EpiX is platform for visualizing and analyzing genomic epidemiology data. It has fine-grained access controls for collaboration between multiple organizations.

Key Features

• Visualisation: Visualize cases by time, place, person and also by genome through a phylogenetic tree coupled to the cases.
• Fine-grained access: Give different organizations different access rights per disease, down to individual variables. Organizations can manage access of their own users by themselves.
• Search: Search and filter cases, including on genetic similarity.
• Signal detection: Detect, define and share sets of cases, signals and outbreaks.
• Disease X: Any disease and corresponding analysis variables can be added.
• Data: Adheres to the Medallion data architecture design pattern. The silver layer consists of normalized and standardized patient or subject data compliant with OMOP Common Data Model, and a dedicated database for genetic sequence data and computation of phylogenetic trees. The gold layer consists of case data ready for analysis in the form of a single row of data per case.
• Tech: OpenAPI compliant API, deployable on cloud or on-premise, support for multiple authentication providers. Python/FastAPI backend and default TypeScript/React frontend available from gen-epix-web.

Deliberately not in scope

• Disease-specific knowledge: Every organization has their own variables that are important for analysis, as well as their own bioinformatics to process genetic sequence data. We therefore avoided any disease-specific code both for the generation of these data and for the analysis variables that can be defined. Only the results are stored.
• Collaboration-specific knowledge: Every collaboration or country (e.g. for public health surveillance of diseases) has their own specifics in terms of access rights and any relevant geographic regions. We therefore avoided any country-specific code, both for the type of organizations that have access, and for any geographic data.

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Installation

Below is a streamlined installation guide for various platforms:

1. Install ODBC development headers:

   sudo apt-get update
   sudo apt-get install -y unixodbc-dev
   

2. Create and activate a conda environment:

   conda create --name gen-epix python=3.12
   conda activate gen-epix
   

3. Install dependencies*:

   pip install -r requirements.txt
   pip install --no-binary :all: pyodbc==5.2.*
   

   *Some hardware architectures (especially Apple M1/M2/M3 chips) require pyodbc to be compiled from source for compatibility

4. For development, add testing tools:

   pip install -r dev-requirements.txt
   

SSL Certificate Setup

1. Install mkcert:

   # Linux
   sudo apt install mkcert
   
   # macOS
   brew install mkcert
   

2. Generate certificates:

   mkcert -install
   mkcert -key-file key.pem -cert-file cert.pem localhost 127.0.0.1
   

3. Copy the generated files:

   cp key.pem cert.pem /path/to/project/cert/
   

4. For WSL users: Run the commands in Windows PowerShell and copy files to both the project cert directory and your WSL home directory.

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Usage

Starting the API

1. Activate the conda environment:

conda activate gen-epix

2. Run the application:

python run.py [service] [app_type] [env_name] [idp_config]

• service: The service to run (api, etl)
• app_type: Specific configuration for an app type (casedb, seqdb, omopbd)
• env_name: Name of the environment.
• idp_config: Which authentication setting to use (idps, mock_idps, no_auth, debug, no_ssl)

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Example

conda activate gen-epix
python run.py api casedb local idps

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Dependencies

Gen-EpiX relies on several Python packages to provide its functionality:

Core Dependencies

• fastapi - Modern, high-performance web framework
• sqlalchemy - SQL toolkit and Object-Relational Mapping (ORM) library
• pydantic - Data validation and settings management
• biopython - Tools for computational molecular biology

Database Connectors

• pyodbc - ODBC database adapter

API Server

• uvicorn - ASGI web server

Development Tools

• pytest - Testing framework
• black - Code formatter
• pylint - Static code analyzer
• mypy - Static type checker

For a complete list of dependencies, refer to:

• requirements.txt - Production dependencies
• dev-requirements.txt - Development dependencies

Python Version Gen-EpiX requires Python 3.12 or higher.