domains / families / science / metabolic-modeling-pipeline

metabolic-modeling-pipeline

separate

Orchestrates genome-scale metabolic modeling from a protein FASTA to flux predictions, chaining CarveMe/gapseq reconstruction, memote QC, gap-filling, media-constrained FBA/FVA, gene essentiality, and context-specific models. Use when committing the reconstruction tool (which locks the identifier NAMESPACE forever - BiGG vs ModelSEED vs KEGG, no automatic translation), setting the medium BEFORE FBA (the exchange bounds ARE the medium; essentiality and gap-fill are computed relative to it), curating iteratively (stoichiometric-consistency first, then mass/charge, then directionality, then GPR) with energy-generating-cycle removal, and reading a MEMOTE score as well-formedness NOT correctness. Hands mechanism to the systems-biology component skills; not a re-teach of any single step.

When to use

• genome-scale metabolic modeling
• CarveMe/gapseq reconstruction
• memote QC
• gap-filling
• media-constrained FBA/FVA
• gene essentiality
• context-specific models

When not to use

• re-teach of any single step
• automatic namespace translation

Skill page

Source