RNA-Bee — exploring RNA folding and evolution
RNA-Bee is an open-source experimental platform for exploring RNA structure, mutation and computational evolution.
The project combines established scientific RNA software with a modern web platform to create an environment where sequences can be analysed, mutated, compared and eventually evolved through reproducible simulations.
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What is RNA?
RNA, or ribonucleic acid, is one of the fundamental molecules of life. It carries biological information, participates in the production of proteins and can also perform regulatory and catalytic functions.
Unlike the familiar double-stranded structure of DNA, RNA is commonly single-stranded. Parts of the molecule can pair with each other, causing the sequence to fold into characteristic structures.
This relationship between sequence and structure makes RNA particularly interesting computationally. A small mutation in the sequence can preserve a structure, slightly modify it or produce a completely different folding pattern.
Sequence determines folding, folding influences behaviour, and mutation creates new possibilities.
What RNA-Bee explores
RNA-Bee turns these relationships into a computational playground. Instead of studying only a single sequence, the long-term goal is to create experiments in which populations of RNA sequences can change over many generations.
- RNA structure prediction — calculate predicted secondary structures from nucleotide sequences.
- Mutation — create variants and observe how sequence changes affect predicted folding.
- Comparison — compare sequences, structures and calculated properties.
- Fitness and selection — evaluate sequences according to configurable objectives.
- Evolution — repeatedly combine mutation, evaluation and selection across generations.
- Visualization — expose computational experiments through an interactive web interface.
Sequence → mutation → folding → evaluation → selection → next generation.
Why build RNA-Bee?
RNA-Bee is both a software project and an experiment in computational biology. The aim is not to replace established scientific tools, but to build an accessible environment around them where different ideas can be implemented, combined and tested.
The evolutionary aspect is particularly interesting: instead of manually designing every sequence, a simulation can create variation, evaluate the resulting candidates and repeatedly select sequences that better satisfy a chosen objective.
This makes RNA-Bee a useful playground for studying how simple computational rules can produce increasingly complex populations and structures over time.
Built on open science
RNA-Bee does not attempt to reinvent RNA folding algorithms. Instead, the project is designed to integrate established open-source scientific software and expose it through a reproducible simulation environment.
ViennaRNA
The ViennaRNA ecosystem provides widely used algorithms and libraries for analysing and predicting RNA secondary structures.
RNAstructure
RNAstructure provides another established collection of tools for RNA structure prediction and analysis and gives RNA-Bee room to compare or extend computational approaches later.
RNA-Bee focuses on the layer around these scientific engines: experiment definition, mutation, fitness models, evolutionary workflows, persistence, reproducibility and visualization.
A web platform around scientific computation
RNA-Bee is built as a containerized full-stack application. The public website and interactive interface are separated from the Python computation layer so that each part of the project has a clear responsibility.
- WordPress provides the public-facing website and block-based user interface.
- Django REST Framework provides the application API and Python backend.
- PostgreSQL stores application and simulation data.
- Redis and Celery provide the foundation for asynchronous computational jobs.
- Docker Compose keeps the different services isolated and makes the environment reproducible.
The complete system architecture, service boundaries and technical decisions are documented separately in the next RNA-Bee article.
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Open source by design
RNA-Bee is developed as an open-source project. The source code and technical documentation are public so that the system can be inspected, reproduced and extended.
The project is intended to remain modular: scientific engines can be exchanged or extended, new simulation strategies can be introduced, and the web interface can evolve independently from the computational core.
- Study the implementation
- Reproduce the application environment
- Experiment with RNA simulations
- Extend the simulation engine
- Develop additional interfaces and visualization tools
Current status
RNA-Bee is under active development. The initial application infrastructure is already running, including the containerized WordPress and Django services, PostgreSQL, Redis, Celery and the public HTTPS routing.
The next development phase moves from infrastructure toward the scientific core of the project: RNA folding integration, experiment models, mutation strategies, fitness functions, evolutionary simulations and interactive visualization.
- Available: Docker-based application environment
- Available: WordPress frontend
- Available: Django REST API foundation
- Available: PostgreSQL, Redis and Celery infrastructure
- Next: scientific RNA folding integration
- Next: mutation and fitness models
- Next: evolutionary simulation engine
- Next: interactive WordPress simulation interface
The RNA-Bee series
This introduction is the first part of a series documenting the project from both the scientific and software-engineering perspectives.
- Introducing RNA-Bee — the project, RNA folding, evolution and its goals
- RNA-Bee Architecture — system architecture and technical decisions
- Building the RNA Simulation Engine — folding, mutation, fitness and evolution
- Building the RNA-Bee Web Platform — Docker, Django, Celery, Redis and WordPress integration
Follow the experiment
RNA-Bee will evolve alongside the experiments it runs. The live application provides the project environment, while GitHub contains the source code and technical documentation.
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