CodonLab 🧬

CodonLab is a browser-based bioinformatics workspace for sequence analysis, annotation, comparative analysis, primer design, restriction planning, construct planning, validation, and conservation exploration.

BLAST tells you what a sequence resembles. CodonLab is designed to help you understand what you can learn and do with that sequence.

Why I built it

I am a beginner in software development coming from a biotechnology background. I built CodonLab to combine biological knowledge with practical software engineering and explore how bioinformatics workflows can be made more usable for students, researchers, and early-stage HealthTech applications.

Core workflow

Sequence → QC → Annotation → Biological Insight → Comparative Evidence → Design → Validation → Conservation

Features

• DNA / RNA sequence input and FASTA upload
• 600,000-character sequence input limit
• Sequence QC: length, GC%, AT%, discarded characters, and Tm estimate
• DNA, mRNA, protein, reverse-complement and ORF analysis
• Restriction-site scanning and planning
• Pairwise sequence alignment
• SpCas9 sgRNA candidate screening
• Protein molecular weight, pI, GRAVY, aromaticity and extinction coefficient estimates
• NCBI E-utilities integration through a Supabase Edge Function
• GenBank record parsing with feature coordinates and CDS inspection
• Biological Insight workspace with evidence/inference separation
• BLAST comparative analysis with identity, coverage, E-value and ranked hits
• Primer design with candidate ranking and QC signals
• Construct planning with target coordinates and restriction-site conflicts
• Design validation and provenance checks
• Conservation Explorer using available base-by-base alignments
• Report generation and FASTA export

Architecture

┌─────────────────────────────┐
│        CodonLab UI          │
│       HTML / CSS / JS       │
└──────────────┬──────────────┘
               │ HTTPS
               ▼
┌─────────────────────────────┐
│   Supabase Edge Function    │
│        clever-task          │
│  server-side API mediation  │
└──────────────┬──────────────┘
               │
               ▼
┌─────────────────────────────┐
│            NCBI             │
│ E-utilities + BLAST service │
└─────────────────────────────┘

The browser does not contain NCBI private credentials. NCBI credentials, when used, belong in the Edge Function environment.

Security

This repository intentionally contains no real API keys or private credentials.

• config.js is ignored by Git.
• config.example.js contains placeholders only.
• .env.example contains placeholders only.
• NCBI API credentials are read server-side from Supabase Edge Function environment variables.
• Never paste a Supabase secret key into frontend code or GitHub.

If a secret key has ever been exposed publicly, rotate it before publishing the repository.

Run locally

1. Clone the repository

git clone https://github.com/YOUR_USERNAME/CodonLab.git
cd CodonLab

2. Create local frontend configuration

copy config.example.js config.js

Open config.js and add your Supabase Edge Function URL and publishable key.

Do not add a Supabase secret key here.

3. Open the app

For the simplest local test, use a local static server rather than opening the HTML directly with file://.

Example with Python:

python -m http.server 5500

Then open:

http://localhost:5500

Supabase Edge Function

Function source:

supabase/functions/clever-task/index.ts

Function name:

clever-task

Server-side environment variables used by the function:

• NCBI_EMAIL
• NCBI_API_KEY (optional)

Example deployment flow with the Supabase CLI:

supabase login
supabase link --project-ref YOUR_PROJECT_REF
supabase functions deploy clever-task --use-api

Set server-side secrets through Supabase; do not commit them.

Scientific scope and limitations

CodonLab is an educational/research-oriented computational tool. Computational predictions do not replace experimental validation.

Examples:

• sequence similarity does not by itself prove biological function, orthology, phenotype, or clinical significance;
• primer and guide candidates require laboratory validation;
• restriction-site detection identifies recognition sequences and does not guarantee experimental cleavage;
• conservation analysis is only reported when a usable base-by-base alignment is available.

Tech stack

• HTML5
• CSS3
• Vanilla JavaScript
• Supabase Edge Functions
• NCBI E-utilities
• NCBI BLAST
• FASTA / GenBank parsing
• Algorithmic sequence analysis

Resume-ready project description

CodonLab — Bioinformatics Analysis Platform

Independent Project | Biotechnology × Software Engineering

• Built a browser-based bioinformatics workspace for nucleotide sequence QC, ORF/protein analysis, GenBank annotation, comparative analysis, primer design, restriction planning, construct planning, validation, and conservation analysis.
• Integrated NCBI E-utilities and BLAST through a Supabase Edge Function to keep backend credentials out of client-side code.
• Implemented sequence-processing algorithms and biological QC logic in vanilla JavaScript, including ORF detection, reverse complement, restriction scanning, pairwise alignment, primer screening, and conservation statistics.
• Designed an evidence-oriented workflow that separates computational evidence from biological interpretation and explicitly reports limitations.

Portfolio talking points

If you discuss CodonLab in an interview, focus on:

1. Problem: bioinformatics tools can expose raw outputs without guiding the user through interpretation and design.
2. Engineering: built a multi-stage client application and serverless backend instead of a static sequence calculator.
3. Integration: connected NCBI search, GenBank retrieval, and BLAST through an API-mediation layer.
4. Scientific reasoning: avoided presenting similarity or computational predictions as experimental proof.
5. Security: separated frontend configuration from server-side credentials and excluded secrets from version control.
6. Next direction: improve reproducibility, automated testing, domain annotation, richer comparative datasets, and production-grade backend controls.

License

MIT