DIVA: Design Implementation Verification Automation Platform

DIVA is a comprehensive web-based platform designed to facilitate the design, implementation, and verification of biological constructs. It serves as a central hub for managing biological designs, DNA assembly tasks, and project collaboration.

Features

• Biological Design Management: Create, store, and manage complex biological designs.
• DNA Assembly Integration: Built-in support for j5 DNA assembly protocols, including management of master plasmid, oligo, and synthesis lists.
• Project Collaboration: Organize designs into projects with granular permissions and team roles (Administrators, Researchers, DIVA Team).
• Visualization: Integrated visualization tools for DNA sequences and assembly results (using D3.js and Open Vector Editor).
• Automated Tasks: Background task runner for processing complex assembly designs.
• Security & Accounts: Robust user management system with role-based access control, account vetting, and email notifications.

Technology Stack

Backend

• Language: Java 16+
• Framework: Jersey (JAX-RS) for RESTful services
• Persistence: Hibernate ORM with PostgreSQL (production) or H2 (development/embedded) support
• Server: Undertow (embedded for development)
• Build Tool: Maven

Frontend

• Framework: Angular 17
• Styling: Bootstrap 5, Font Awesome
• Visualization: D3.js, ngx-charts, Open Vector Editor
• Build Tool: Angular CLI / npm

Getting Started

Prerequisites

• Java Development Kit (JDK) 16 or higher
• Maven 3.6+
• Node.js and npm (for frontend development)
• PostgreSQL (optional, defaults to H2)

Installation

1. Clone the repository:

   git clone https://github.com/JBEI/diva.git
   cd diva

2. Backend Setup: The backend uses Maven for dependency management.

   mvn clean install

3. Frontend Setup: Navigate to the Angular application directory and install dependencies.

   cd src/main/ngapp
   npm install

Configuration

DIVA looks for a data directory specified by the DIVA_DATA_HOME environment variable. If not set, it defaults to ~/.DIVAData.

Key configuration files (located in $DIVA_DATA_HOME/config):

• diva-server.properties: Database connection details and system settings.
• hibernate.cfg.xml: Hibernate configuration (located in src/main/resources).

Running the Application

Development Mode

1. Start the Backend: You can run the DevelopmentServer class in your IDE or via Maven:

   mvn exec:java -Dexec.mainClass="DevelopmentServer"

   The backend API will be available at http://localhost:8081/rest.

2. Start the Frontend:

   cd src/main/ngapp
   npm start

   The UI will be available at http://localhost:4200.

Production Build

To build the full WAR file for deployment:

mvn clean package

The resulting WAR file will be in the target/ directory.

License

This project is licensed under the BSD 3-Clause License - see the LICENSE file for details.

Acknowledgments

• Developed at the Joint BioEnergy Institute (JBEI).
• Supported by the U.S. Department of Energy.