Build History
Complete development timeline of the BOL platform — every prompt, feature, and milestone tracked from project inception.
Current Release
v1.0.0Build Timeline
Project Inception & Scaffold
Created project structure, documented existing origin-of-life software, designed 10-prompt build plan, generated initial Python package scaffold with config, world, simulation, and metrics modules.
Primordial Chemistry Engine
Expanded to 27 molecule types and 21 reactions. Added pH/temperature Gaussian modifiers, cell-direct neighbor sampling (O(1) encounters), feedstock injection, ocean loss, and mineral surface catalysis. Validated all 4 scenarios.
Energy Sources & Thermodynamics
Implemented 4 energy sources (thermal, redox, UV Beer-Lambert, stochastic lightning). Added multi-source Gibbs free energy coupling. 5 new energy-driven reactions (26 total). UV photolysis and Miller-Urey synthesis working.
Self-Assembly & Protocells
Micelle formation, vesicle promotion, lipid accretion, membrane permeability, initial encapsulation, vesicle confinement and dissolution. Compartment isolation in chemistry engine. Validated 2+ vesicles in warm_little_pond.
Polymers & Information Chemistry
Amino acid sequences, RNA sequences, ribozyme motif detection, template-directed RNA replication with Watson-Crick pairing and mutations. Peptides to length 15, RNA to length 10, first ribozyme catalyst emerged.
Selection & Variation
Vesicle fitness scoring, osmotic growth, division with content inheritance (gen 3+), semi-permeable monomers, confinement catalysis (2.5× rate), recombination, segment duplication. 10 vesicles, fitness 2.0 in warm_little_pond.
3D Visualization
Vispy 0.16.1 GPU-rendered particle scatter with CPK colours, vent chimney mesh, thermal gradient planes, vesicle shells (fitness-coded), HUD overlay, TurntableCamera, keyboard controls. ~460 lines of rendering code.
Metrics, Sweeps & Testing
Metrics dashboard with Chart.js, parameter sweep engine, scenario JSON system, 56 unit tests (all passing), performance optimizations (cell-direct sampling, dead molecule GC). Completed as part of web dashboard work.
Web Dashboard
Full Splunk-themed Flask web application. Real-time KPI cards, 4 Chart.js time series charts, simulation controls, event log, scenario picker, parameter sweep UI. Dark theme CSS design system (~1,200 lines).
3D Microscope Viewer
Three.js WebGL sprite-based particle renderer. Collapsible documentation panels on all pages. Real-time particle streaming from simulation API. Legend overlay, help panel, camera controls.
Icons & Branding
Multi-resolution favicon (16–256px) and desktop icon generated with Pillow. DNA helix + vesicle motif.
Existing Software Reference
Showcase page documenting 20 real-world origin-of-life tools organized into 5 categories with descriptions, capabilities, and BOL comparison points.
Molecule SVGs
Generated 32 accurate ball-and-stick SVG molecule images. Converted viewer from Points to Sprites. Fixed case normalization, added 7 missing molecule types, removed SVG glow artifacts.
Top Menu Bar, Home Page, Security & Profiles
Replaced sidebar with professional top navigation bar. Created landing home page, security architecture page, user profile system (optional, credential-protected), admin section (documentation, builds, user management).
Dependencies
| Package | Version | Purpose |
|---|---|---|
numpy | Latest | Array operations, spatial math, random sampling |
scipy | Latest | Scientific computing utilities |
matplotlib | Latest | Static plot generation for CLI mode |
flask | Latest | Web server framework |
vispy | 0.16.1 | GPU-accelerated OpenGL desktop visualization |