domains / families / science / metabolic-reconstruction

metabolic-reconstruction

separate

Builds draft genome-scale metabolic models from an annotated genome using CarveMe (top-down carving of a BiGG universal model) or gapseq (bottom-up pathway-evidence reconstruction), then loads and sanity-checks the draft in COBRApy. Use when creating a model for an organism without one, choosing between CarveMe and gapseq, gap-filling to a target medium, understanding why a draft that grows is still only a hypothesis, handling BiGG-vs-ModelSEED namespace mismatch, or preparing a draft for curation and community modeling.

When to use

• creating a model for an organism without one
• choosing between CarveMe and gapseq
• gap-filling to a target medium
• understanding why a draft that grows is still only a hypothesis
• handling BiGG-vs-ModelSEED namespace mismatch
• preparing a draft for curation and community modeling

When not to use

• finished model curation
• community metabolic modeling

Skill page

Source