ModelSEED Templates v6.0.0
This release coincides with the ModelSEED v2 manuscript submission and introduces major enhancements to the template collection with improved repository organization.
🚀 New Features
Enhanced Templates
- Archaea Template V6 - Improved metabolic coverage for archaeal organisms
- Core Template V5.2 - Refined reaction set for bacterial core metabolism
- Gram-Negative Template V6 - Enhanced pathway representation
- Gram-Positive Template V6 - Improved organism-specific reactions
Repository Organization
- Versioned Structure - Templates organized by version (
v6.0/,v5.0/,legacy/) - Backward Compatibility - Previous templates preserved and accessible
- Legacy Support - Historical templates archived for reference
- Enhanced Documentation - Comprehensive README and CHANGELOG
📁 Directory Structure
templates/
├── v6.0/ # Latest templates (this release)
├── v5.0/ # Previous stable release
└── legacy/ # Historical templates
🔬 Biomass Formulations
Updated biomass formulations with:
- Better organism-specific compositions
- Enhanced DNA, RNA, and protein representations
- Improved metabolite standardization
📊 Usage
For New Projects
Use templates from templates/v6.0/ for the latest features and improvements.
For Existing Projects
Continue using templates/v5.0/ for consistency, or migrate to v6.0 when ready.
📖 Documentation
- Main README - Updated with new structure and release information
- CHANGELOG - Comprehensive version tracking
- Templates README - Clear usage guidelines for each version
🧬 Scientific Context
These templates are designed as "filters" for KEGG and MetaCyc databases, ensuring:
- No abstract compounds (acceptor/donor)
- Mass and charge balanced reactions
- Defined molecular formulas for all compounds
- Stereochemically explicit metabolites
- Standardized to pH 7.5 protonation states
Full Changelog: https://github.com/ModelSEED/ModelSEEDTemplates/blob/main/CHANGELOG.md