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 18.13+ and npm (required by Angular 17)
• PostgreSQL 12+ (optional — defaults to an embedded H2 database)

Installation

1. Clone the repository:

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

2. Build the backend: The backend uses Maven for dependency management. Skip tests on the first build since they require a configured database.

   mvn clean install -DskipTests

3. Install frontend dependencies:

   cd src/main/ngapp
   npm install

Configuration

DIVA reads runtime settings from a data directory identified by the DIVA_DATA_HOME environment variable. If unset, it defaults to ~/.DIVAData.

1. Create the config directory and copy the properties template:

   mkdir -p ~/.DIVAData/config
   cp src/main/resources/diva-server.properties.template ~/.DIVAData/config/diva-server.properties

2. Edit ~/.DIVAData/config/diva-server.properties to set the database type and any email / LDAP settings your deployment needs. Supported connectionType values are H2DB (default, zero setup) and POSTGRESQL.

3. PostgreSQL (optional): If you set connectionType=POSTGRESQL, create the database and user first, then fill in connectionUrl, username, password, and dbName in the properties file:

   createuser -P diva            # set password to match diva-server.properties
   createdb -O diva diva_db

Running the Application

Development Mode

1. Start the backend: Run the DevelopmentServer class (in the default package at src/main/java/DevelopmentServer.java) from your IDE. It listens on http://localhost:8081/ with the REST API mounted at /rest/*.

2. Start the frontend:

   cd src/main/ngapp
   npm start

   The UI will be available at http://localhost:4200. Because the Angular dev server and the backend run on different ports, configure a proxy.conf.json that forwards /rest to http://localhost:8081 (or enable CORS on the backend) so the UI can reach the API.

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.