Víctor Madarnás | Portfolio

GenomIQ

Bioinformatics Platform with AI

Mar 2025 - May 2025

Comprehensive bioinformatics platform combining advanced genomic analysis tools with AI-powered assistance. Features BLAST searches, multiple sequence alignment with WebAssembly, protein structure visualization, functional annotation, and real-time AI chat with streaming responses. Includes OAuth authentication, WebSocket connections, and integration with major biological databases (NCBI, UniProt, Pfam).

Stack

The Problem

Current bioinformatics tools like NCBI BLAST or Clustal Omega have obsolete interfaces from the 2000s, require advanced technical knowledge to interpret results, and lack any kind of intelligent assistance. This creates a significant barrier to entry for students and researchers who are not experts in bioinformatics, limiting access to modern genomic analysis.

The Solution

We designed an all-in-one platform integrating BLAST search, multiple sequence alignment (MSA), functional annotation, and 3D visualization of molecular structures. The key differentiator is the execution of MSA algorithms (MAFFT, MUSCLE, Kalign) directly in the browser via WebAssembly, eliminating network latency and reducing server load by over 60%. Additionally, a specialized AI chatbot explains results and suggests analyses, making bioinformatics accessible to non-expert users.

Architecture

Wireframe

Frontend

The frontend is built with Next.js, React, and TypeScript, providing a modern and responsive interface where users can perform BLAST searches, execute multiple alignments with WebAssembly, visualize 3D structures with NGL.js, and explore interactive phylogenetic trees. Global state is managed with Zustand, data fetching with SWR and React Query, and styling with TailwindCSS. It supports full internationalization (Spanish/English) with i18next.

Wireframe

Backend & External Services

The backend, developed with FastAPI and Python, serves as the central API. It handles JWT and OAuth2 (Google) authentication, an AI usage quota system, and integration with the NCBI API for BLAST searches. It uses WebSockets for real-time job status communication, SQLAlchemy 2.0 with PostgreSQL for persistence, and Redis for caching and queues. GenomIQ integrates with multiple external APIs: NCBI API, OpenRouter (GPT-4, Claude), Hugging Face, plus DeepInfra and Cohere with automatic fallback.

WebAssembly

Multiple Sequence Alignment algorithms run directly in the browser via WebAssembly modules (MAFFT, MUSCLE, Kalign), processing sequences up to 10,000 amino acids locally with zero network latency and without overwhelming the server. Modules load on demand and computation is completely client-side.

AI Integration

An intelligent assistant is integrated directly into the analysis pipeline. It can provide recommendations, interpret complex results, and suggest the right tools based on the user's specific goals.

Deployment & CI/CD

Docker + Docker Compose on a VPS. GitLab pipeline: builds frontend (multi-stage) and backend (Poetry), runs tests (pytest + ESLint), pushes images to GitLab Registry, deploys via a .sh script (pull + restart). Automatic HTTPS with Certbot, health checks on all services, and daily PostgreSQL backups.

Screenshots

Homepage

Comprehensive bioinformatics platform with BLAST searches, sequence alignment, and AI assistance.

Log In

Secure login page to access personalized bioinformatics workspaces and saved analyses.

Register

Account creation interface to start managing sequence alignments and functional annotations.

Dashboard

User dashboard displaying recent analyses, saved results, and quick access tools.

Bioinformatics Tools

Suite of tools available for genomic and proteomic sequence analysis.

BLAST Search

Interface for finding regions of similarity between biological sequences using NCBI APIs.

Multiple Sequence Alignment

Interactive MSA visualization and analysis via WebAssembly integration.

Sequence Annotation

Detailed visualization of sequence features and functional regions using UniProt data.

Sequence Translation

Tool to translate nucleotide sequences to proteins and analyze open reading frames.

3D Protein Visualization

Interactive Three.js viewer for analyzing protein structures and molecular configurations.

AI Assistant

Real-time AI chat integrated within tools to guide analysis and interpret results.

Chat Interface

Dedicated AI chat view for continuous bioinformatic support and querying.

Accessibility & Localization

Full support for Dark/Light mode viewing and seamless bilingual switching (English/Spanish).