Developer Documentation

This section contains documentation for developers working on or extending siRNAforge.

• siRNAforge Architecture
  • Short version (TL;DR)
  • Overview
  • System Architecture Flow
  • Package Structure
  • Architectural Layers
  • Design Principles
  • Data Flow
  • Extension Points
  • Performance Considerations
  • Testing Architecture
  • Deployment Architecture
  • Future Architecture Considerations
• Development Guide
  • Development Environment Setup
  • Make Commands Reference
  • Development Workflow
  • Branching & Release Strategy
  • Code Style and Standards
  • Testing Best Practices
  • Contribution Guidelines
  • Advanced Development
  • Debugging
  • Release Process
  • Getting Help
• Testing Guide
  • Quick Commands
  • Local Development Testing
  • Docker Testing (Comprehensive Validation)
  • Best Practices
  • ZFN Manual Validation
  • miRNA default-backend rollout validation
  • Quick Health Checks
• Comprehensive Review: Chemical Modification Handling in siRNAforge
  • Executive Summary
  • Current Infrastructure
  • Integration Opportunities
  • Recommended Integration Strategy
  • Implementation Patterns
  • Modification Pattern Library
  • Testing Strategy
  • Recommendations Summary
  • Conclusion
  • Appendix: Common Modification Types
• ZFN Backend Tuning Summary
  • Question Answered
  • Benchmark Surfaces Used
  • Decision
  • Why pyahocorasick Won
  • Why fm_index Is the Alternate
  • Why exhaustive_python Did Not Stay First
  • Resulting Runtime Policy
  • Durable Artifacts
  • Manual Validation Scope
• ZFN Nextflow Bridge: Sanity Validation
  • Scope
  • uv invocation guidance
  • Fixtures
  • Results
  • Unit verification
  • Notes for maintainers
• ZFN Hg38 Primary Validation Commands
  • Annotation URL
  • Recommended output root
  • Measured Backend Order
  • Real Run on hg38 Primary with pyahocorasick
  • Real Run on hg38 Primary with exhaustive_python
  • Expected Artifacts
  • Quick Checks

Quick Links

• Architecture Overview: System design and data flow

• Development Setup: Environment setup and contribution guidelines

• Testing Guide: Test categories, Docker testing, and running tests

• Chemical Modifications: Review of modification implementation

• ZFN Backend Tuning: Why pyahocorasick is first choice and where fm_index fits

• ZFN Nextflow Bridge Validation: Internal bridge behavior and sanity checks

• ZFN hg38 Primary Commands: Manual real-genome validation commands