Primer Design Tool logo

Primer Design Tool

The Primer Design Tool was developed to address a critical bottleneck in standard RT-qPCR laboratory workflows.

By automating the primer design process, the application significantly accelerates experiment planning and eliminates the risk of manual analytical errors, ensuring robust reproducibility across the laboratory.

Key Features

  • Workflow Automation: Replaces manual primer design steps with an automated algorithmic pipeline tailored for complex molecular workflows.
  • Robust Backend: Powered by Python and FastAPI, implementing strict data sanitization and input validation protocols to handle biological sequences.
  • Cross-platform Portability: The entire application infrastructure is containerized using Docker and successfully deployed into a scalable cloud environment.

My Role

I executed the entire software development lifecycle (SDLC) independently, demonstrating total engineering ownership from the initial assessment of user-needs and prototyping, through rigorous testing, and finally to production deployment.

Technologies Used:

Backend

  • Language & Framework: Python 3, FastAPI & uvicorn
  • Data Access & Storage: SQLite with FTS5 full-text search index, managed via aiosqlite and SQLAlchemy 2.0 (async engine)

Background Tasks & Caching:

  • Celery with Redis (supports fallback to eager synchronous mode when Redis is offline)
  • Rate Limiting & Security: JWT authentication (python-jose), password hashing (passlib/bcrypt), and endpoint rate limiting (slowapi)

Bioinformatics Core

  • RNA Structure Prediction: ViennaRNA library (RNAfold wrapper with mock fallback when unavailable on host)
  • Thermodynamic Modeling: Custom Nearest-Neighbor (NN) thermodynamic and hairpin generation algorithms

Frontend

  • Templating: Server-rendered Jinja2 templates
  • Styling & Interactivity: Vanilla CSS, JavaScript / jQuery
  • Visualization: Forna (D3.js-based visualization engine for interactive RNA secondary structure layouts)

Architecture & Testing

  • Pattern: Hexagonal Architecture with abstract interfaces for repositories and services
  • Testing: pytest, pytest-asyncio unit and integration test suite