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Template library

The Templates workspace opens on the Template Library: every template GEMs MAP knows, built-in and your own, grouped by section.

The Template Library: a search box, Import template and New template buttons, a BiGG data notice, the GEM currently in the Map Builder, and two sections of template cards — Central carbon (Global central carbon metabolism, Glycolysis, TCA cycle, Pentose phosphate (oxidative), Amino acid biosynthesis overview) and KEGG-derived templates (map00010, map00020, map00030, map00250) — each with a preview, description, size, scope, completeness, author and version, and buttons Open, Duplicate, Export and Apply to GEM.

The Template Library. AI-generated templates carry an orange "needs review" label until a person reviews them.

Each card shows a preview, the pathway, the number of drawn metabolites and reactions (side compounds such as ATP are not counted), the organism scope, completeness, the author and the template version. Open shows it in Template Design Mode; Duplicate makes your own editable copy; Export writes the file; Apply to GEM maps it onto the model in the Map Builder; Delete removes your own templates. A banner tells whether the BiGG tables are installed and which GEM is currently in the Map Builder. Drop a .gemsmap-template.json file on the window to import it.

Built-in templates

Central carbon

These four were drawn and curated by hand. Their identities are confirmed in the GEMs MAP library, and their equations are complete (cofactors included) and checked for heavy-atom balance, with KEGG reaction IDs checked against the KEGG equations.

Template Drawn Reactions Compartments Notes
Glycolysis glucose → G6P → F6P → FBP → DHAP / GAP → 1,3-BPG → 3PG → 2PG → PEP → pyruvate, plus lactate and acetyl-CoA HEX, PGI, PFK, FBA, TPI, GAPD, PGK, PGM, ENO, PYK, LDH (optional branch), PDH Cytosol; acetyl-CoA in the mitochondrion (cytosol as fallback) Drawn vertically. Links to the PPP (from G6P) and to the TCA cycle (from acetyl-CoA).
TCA cycle acetyl-CoA, citrate, isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, L-malate, oxaloacetate CS, ACONT, ICDH, AKGDH, SUCOAS, SDH, FUM, MDH Mitochondrion, with the cytosol as fallback Drawn as a circle.
Pentose phosphate (oxidative) G6P, 6-phosphogluconolactone, 6-phosphogluconate, ribulose 5-P, ribose 5-P, xylulose 5-P G6PDH, PGL, GND, RPI, RPE Cytosol Oxidative branch only.
Global central carbon metabolism The three above, composed (26 drawn metabolites) 25 Cytosol + mitochondrion Used in the examples of these pages.

Compartments are expectations, not requirements. The TCA cycle prefers the mitochondrion, because it is mitochondrial in eukaryotes. In a model without mitochondria, such as the bacterium E. coli, the matcher falls back to the cytosol and says so in the review dialog. A template is therefore adapted to each model; it is not assumed to be universally correct. A eukaryotic model with a cytosolic acetyl-CoA pool, or a bacterium with an incomplete TCA cycle, will show open or low-confidence slots that need a person to decide.

How they map. On iML1515 the global template maps 25 of its 26 slots with high confidence and one with medium confidence: D-ribose 5-phosphate, which iML1515 names as the α-anomer (see Identity and matching). Coverage on iML1515 is 25/25 core metabolites and 23/23 core reactions. The automated tests map the built-ins on E. coli core, iJO1366, a ModelSEED-namespace copy and an annotation-free copy of E. coli core, and check that the results do not change.

Amino acid biosynthesis (overview) and KEGG-derived templates

Template Section Reference Drawn
Amino acid biosynthesis (overview) Central carbon KEGG map01230 32 metabolites, 31 arrows, 20 of them pathway summaries
Glycolysis / Gluconeogenesis KEGG-derived templates KEGG map00010 23 metabolites, 31 reactions
Citrate cycle (TCA cycle) KEGG-derived templates KEGG map00020 12 metabolites, 13 reactions
Pentose phosphate pathway KEGG-derived templates KEGG map00030 31 metabolites, 34 reactions
Alanine, aspartate and glutamate metabolism KEGG-derived templates KEGG map00250 27 metabolites, 36 reactions

AI-generated — needs review These templates were curated and drawn offline by an AI curator with a reproducible pipeline (see AI-assisted templates), and remain marked AI-generated — needs review until a person reviews them. KEGG is used as the biological and topological reference only; every drawing is GEMs MAP's own and is not an official KEGG map. Every KEGG compound and reaction of each map is drawn, folded (anomers, lumped complexes, cofactor variants) or omitted with a written reason. Per-map generation reports, identity and reaction tables, layout QC and previews are in the repository under docs/templates/kegg/<map>/, for example the map00010 report.

Next: how a template finds its way into a model: Identity and matching.