HERD 1.0z

Project Title: Design and Implementation of a Well-Annotated Database of Putative and Validated Human Enhancers with a Web Application Interface

Project Description: Developed a comprehensive, well-annotated database of putative and validated human enhancers, named HERD (Human Enhancers Relational Database), and an associated web application to facilitate easy access and querying of the database. This project involved processing genomic data, creating a relational database, and developing a user-friendly web interface.

Key Technologies Used:

Data Processing and Analysis:

- Python

- Pandas

- NumPy

- ENCODE Consortium data

Database Development:

- PostgreSQL

- SQLAlchemy (Python SQL toolkit and Object-Relational Mapping)

Web Application Development:

- Flask (Python Web Framework)

- HTML5/CSS3

- JavaScript

- jQuery

- Ajax

- Bootstrap (for responsive design)

Version Control:

- Git (GitHub for repository management)

Key Features and Functionalities:

1. Data Processing and Evaluation:

- Processed genomic data from the ENCODE Consortium to identify putative and validated enhancers.

- Removed redundancies and annotated the merged peaks to provide meaningful context.

- Used DNase I hypersensitive sites to identify regulatory elements indicative of enhancers.

2. HERD Database Development:

- Created a relational database to store and manage the processed enhancer data.

- Designed the conceptual and physical models of the database.

- Implemented the database schema in PostgreSQL.

3. Web Application Development:

- Developed a user-friendly web application using Flask to interface with the HERD database.

- Implemented various functionalities including user registration, authentication, and dynamic data querying.

- Used SQLAlchemy for ORM to handle database interactions.

- Utilized jQuery DataTables for efficient data display and Ajax for dynamic content loading.

- Created wireframes and implemented a responsive design using Bootstrap.

4. Specific Functionalities and Implementations:

- MVC Architecture: Structured the application using the Model-View-Controller pattern for better maintainability.

- Forms and Authentication: Implemented secure user authentication and form handling using Flask-WTF.

- Dynamic Data Loading: Utilized Ajax requests to dynamically load data without refreshing the page.

- Search and Filter: Enabled advanced search and filtering options for querying the HERD database.

- User Account Management: Provided functionalities for users to manage their accounts and view their search history.

5. Testing and Evaluation:

- Conducted unit and functional testing to ensure the reliability and performance of the database and web application.

- Used automated testing tools to streamline the testing process and ensure comprehensive coverage.

Project Outcomes:

- Successfully developed a well-annotated database of human enhancers accessible through an intuitive web application.

- Enhanced the accessibility and usability of genomic data for researchers and scientists.

- Implemented a robust and scalable solution for managing and querying enhancer data.