ModelSEED Templates v6.0.0

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

September 2023 release

The September 2023 release of ModelSEED reconstruction templates.

February 2021 templates

The February 2021 release of the templates