GeneForgeLang Documentation Index
The Symbolic Language for Biological Reasoning
Welcome to the official documentation for GeneForgeLang (GFL). This index provides easy navigation to all documentation resources.
Getting Started
New to GeneForgeLang? Start here:
- Installation Guide — Install GFL and dependencies
- Quick Start — Your first workflow in 5 minutes
- Comprehensive Tutorial — Step-by-step guide to GFL concepts
User Guides
Practical guides for using GeneForgeLang:
| Guide | Purpose |
|---|---|
| CLI Reference | Command-line interface documentation |
| API Reference | Python API for programmatic access |
| Custom Schemas & IO Contracts | Define data structures and contracts |
Core Features & Capabilities
Learn about GFL's powerful features:
Workflow Components
- Design Block — Generate biological entities
- Optimize Block — Parameter optimization and tuning
- Data Staging — Manage workflow inputs/outputs
- Refine Data — Post-processing and data refinement
Analysis & Reasoning
- Symbolic Reasoning — Bayesian and rule-based reasoning
- Schema Registry — Type definitions and validation
- With Priors Clause — Bayesian prior integration
- IO Contracts — Contract-based data validation
Specialized Features
- Guided Discovery — AI-powered workflow optimization
- Container Execution — Docker container integration
- Spatial Genomic Capabilities — 3D genome analysis
- Locityper Haplotyping — HLA/KIR genotyping
- Epigenetic Editing — CRISPR-based epigenetic modifications
- Capability-Aware Validator — Context-aware validation
Advanced Topics
- Enhancer Module Specification — Regulatory element design
Plugin Ecosystem
Extend GFL with plugins:
Overview & Architecture
- Plugin Ecosystem Overview — Plugin system architecture
- Plugin Ecosystem Documentation — Complete plugin guide
Core Plugins
Available in geneforgelang/plugins/core_plugins/:
- BLAST — Sequence similarity searches
- GATK — Genomic variant analysis
- SAMtools — Sequence manipulation
- And more...
Genesis Plugins
Available in geneforgelang/plugins/genesis_plugins/:
- On-Target Scoring — CRISPR efficiency
- Off-Target Scoring — CRISPR risk
- Evaluator — Combined scoring
- Visualizer — Results visualization
Creating Custom Plugins
- Creating Plugins Guide — Build your own plugins
Development
For developers and contributors:
Architecture & Design
- Organizational Architecture — System organization
- Design Ontology — Core concepts and relationships
- Design History — Evolution of design decisions
Deployment & Operations
- Deployment Guide — Production deployment
Additional Resources
- Examples: See examples/ directory for workflow examples
- Schema: schema/ contains JSON schemas and type definitions
- Source Code: src/ contains the main GeneForgeLang implementation
External Links
- GitHub Repository — Source code
- Security Policy — Security information
- Contributing Guide — How to contribute
- License — MIT License
Document Organization
docs/
├── INDEX.md (this file)
├── guides/
│ ├── user-guides/ # User-facing documentation
│ │ ├── installation.md
│ │ ├── quickstart_user.md
│ │ ├── tutorial.md
│ │ └── custom_schemas_io_contracts.md
│ └── dev-guides/ # Developer documentation
│ ├── creating_plugins.md
│ └── DEPLOYMENT_GUIDE.md
├── geneforgelang/ # App documentation
| ├── features/ # Feature documentation
│ | ├── design_block.md
│ | ├── optimize_block.md
│ | ├── symbolic_reasoning.md
│ | ├── guided_discovery.md
│ | └── ... (15 feature docs total)
│ ├── plugins/ # Plugin documentation
| │ ├── plugins_overview.md
| │ ├── PLUGIN_ECOSYSTEM.md
| │ ├── core_plugins/
| │ └── genesis_plugins/
| ├── api.md
| └── cli.md
└── dev/ # Development resources
├── decisions/ # Architecture decisions
│ ├── organization.md
│ ├── ontology.md
│ └── HISTORY.md
└── reports/
Last updated: April 2026
GeneForgeLang - The Symbolic Language for Biological Reasoning