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Core Concepts

Simulation Foundations
Simulation philosophy, guiding principles, success metrics.
System Architecture
High-level diagrams, core services, data flow, and deployment topology.
Technology Stack
Languages, frameworks, tooling, dependencies, and versioning policy.
Evolution Dynamics
Digital evolution principles, troubleshooting guide, and configuration best practices.

Simulation Mechanics

World Model
Spatial/temporal resolution, environmental layers, resource systems, and global rules.
Entity Lifecycle
Creation, reproduction, death, and persistence rules for entities.
Interaction Models
How entities interact (competition, cooperation, communication) and conflict resolution.
Event Processing
Tick/update loop, scheduling, randomness, and determinism controls.
Ai Behavior
Decision-making algorithms, behavior trees, reinforcement learning policies, tuning knobs.
Opcode Reference
Full instruction set listing, opcode families, and alias mapping.
Seed Bank
Seed retention policy, taxonomy metadata, reserve guarantees, and checkpoint audits.

Taxonomy & Biology

Taxonomy Overview
Classification scheme, terminology, and naming conventions.
Species Profiles
Individual Markdown files per species describing traits, abilities, habitats, and evolution paths.
Traits And Mutations
Trait definitions, mutation rules, heritability, and balancing notes.
Ecosystem Dynamics
Food webs, population dynamics, resource regeneration, and disequilibrium scenarios.

Data & Analytics

Data Pipelines
Logging strategy, telemetry, ETL jobs, storage formats, and retention policy.
Metrics And Observability
Key performance indicators, dashboards, alerting, and health checks.
Experiment Playbooks
How to design, run, and evaluate simulation experiments.
Scripts
CLI utilities, dashboards, and analysis tooling built atop the core simulator.

Architecture & Infrastructure

Distributed Architecture
Worker/server payloads, aggregation, and distributed metrics schema.
Hybrid Tuning
Discovery, authority, policies, and operational playbooks for the hybrid tuning subsystem.

User Interface & APIs

Ui Ux Overview
Interface patterns, wireframes, and accessibility considerations.
Ui Components
UI system architecture, components, and integration with distributed server.
Web Styling Guide
Comprehensive design system and styling conventions for the web interface.
Icon System
Procedural icon generation system for organism visualization.
Memory Map
Real-time soup memory visualization system.
Api Reference
Public APIs, endpoints, authentication, rate limits, and sample requests.
Scenario Authoring
How to author custom scenarios, scripts, or mods.

Operations & Maintenance

Deployment Guide
Environment setup, CI/CD pipelines, release process, rollback strategy.
Worker Build Process
Worker binary build process, SSL/TLS configuration, and distribution.
Runtime Operations
Monitoring, scaling, backups, SLAs, incident response.
Security And Compliance
Threat model, access controls, auditing, and compliance requirements.
Testing
Comprehensive testing guide including unit tests, integration tests, and User Acceptance Tests (UAT).
Environment
Complete reference for all environment variables used throughout the system.
Configuration Tuning
Parameter tuning guide for simulation stability and evolution dynamics.
Checkpointing
Checkpointing operations, state restoration, and troubleshooting guide.
Distributed Quickstart
Step-by-step server/worker smoke test for contributors.

Planned upgrades

Auto Upgrade
Worker distribution roadmap and packaging-first rollout plan.
Worker Self Update
Staged rollout plan for automated worker updates.

Project Management

Working Agreements
Team norms, code review expectations, decision-making process.
Roadmap
Near-term milestones, long-term vision, and dependency tracking.
Change Log
Summary of major simulation changes and historical context.
References
External research papers, datasets, and inspiration sources.

Quick Reference

Glossary
Canonical definitions for domain-specific terms.
Faq
Common questions from devs, scientists, and stakeholders.

Entity Lifecycle

Entity Lifecycle¶

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ByteBiota tracks every organism from ancestor seeding through execution, reproduction, and eventual reaping. This page summarizes the state transitions and data structures coordinating those phases so lifecycle changes remain consistent.

Lifecycle Stages {#lifecycle-stages}¶

Each organism progresses from creation (ancestor load or seed-bank spawn) into scheduled execution, reproduction attempts, and termination via reaper policies. Update this section when new lifecycle hooks, age/error metrics, or energy gating rules are introduced.

Organism Model {#organism-model}¶

Organism and OrganismFactory (src/bytebiota/organism.py) encapsulate CPU registers, reproduction bookkeeping, energy budgets, and write-access control. Document field additions, serialization changes, or energy-sharing adjustments here.

Ancestor Programs {#ancestor-programs}¶

Ancestor assembly tooling (src/bytebiota/ancestor.py) seeds the soup with the minimal self-replicator and provides assembler helpers. Capture updates to the ancestor genome, assembly syntax, or seeding workflows in this section.