ModelSEEDTemplates

Reactions in KEGG and MetaCyc have generic versions without electron donors and acceptors defined, which can render energy biosynthesis obviate, and they often include a mixture of lumped and unlumped reactions, which can cause entire pathways to be bypassed during GEM simulation. Our model templates act as “filters” by including only “modeling-ready” reactions in models. Filtering criteria include (1) no abstract compounds such as “acceptor” and “donor” are allowed; (2) reaction must be mass and charged balanced; (3) all reactants must have defined charge and molecular formula (with few explicit exceptions such as biomass and APS); (4) highly lumped reactions should be avoided when unlumped alternatives exist; (5) reactants should be stereochemically explicit; and (6) all metabolites in the model should be standardized to their primary protonated form at pH 7.5.

Repository Structure

This repository is now organized by version to facilitate release management and backward compatibility:

• templates/v6.0/ - Latest templates (current release)
• templates/v5.0/ - Previous stable release
• templates/legacy/ - Archived legacy templates
• ChangeLogs/ - Version-specific change logs
• WS_Specification/ - KBase workspace specifications

June 2025 Release (v6.0)

Release highlights

• Templates coinciding with ModelSEED v2 manuscript submission for publication
• Updated Archaea template (V6)
• Enhanced Core metabolism template (V5.2)
• Updated Gram-negative template (V6)
• Updated Gram-positive template (V6)
• Improved repository organization with versioned structure
• Enhanced biomass formulations with better organism-specific compositions

September 2023 Release (v5.0)

Release highlights

• Templates used to build models in "ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction" pre-print. https://www.biorxiv.org/content/10.1101/2023.10.04.556561v1.abstract
• Introduction of Archaea template.
• Updated core metabolism model template.
• Updated gram-negative template.
• Updated gram-positive template.
• Biomass objective function updated to represent DNA, RNA, and Protein compounds instead of individual metabolites. Corresponding DNA, RNA, and Protein synthesis reactions are added to the templates.
• Reaction drains are now represented in the template.

February 2021 release

Release highlights

• Retiring legacy templates.
• Introduction of core metabolism template.
• Update of RAST functional role mappings to reactions to match RAST's latest release.