Genome-Scale Metabolic Models: Reconstruction & Curation (GEMs) — Hands-on

Learn the practical workflow to reconstruct, curate and quality control genome-scale metabolic models (GEMs) for microbes, cell lines and other organisms. Starting from genome annotation and pathway databases, you will generate draft networks, perform gap-filling, check mass and charge balance, ensure thermodynamic and structural consistency, and benchmark with MEMOTE and experimental data. The final output is a reusable, publication-grade GEM in SBML/COBRA format with full provenance.

Genome-Scale Metabolic Models: Reconstruction & Curation (GEMs)

Help Desk · WhatsApp

Session Index

Session 1 — Inputs, Annotation & Draft GEM Generation Session 2 — Gap-Filling, Balancing & Thermodynamic Checks Session 3 — Validation, Contextualization & Versioning Session 4 — Mini Capstone: End-to-End GEM Reconstruction

Session 1

Fee: Rs 8800

Inputs, Annotation & Draft GEM Generation

Data & reference resources

genome annotation (Prokka, RAST) BiGG / KEGG / MetaCyc ModelSEED & KBase

Draft model generation workflows

ModelSEED pipeline CarveMe / AuReMe template-based reconstructions

Model structure & bookkeeping

compartments & transporters GPR associations naming & identifiers

Session 2

Fee: Rs 11800

Gap-Filling, Balancing & Thermodynamic Checks

Gap analysis & gap-filling strategies

blocked reactions & dead-end metabolites topology-based gap-filling condition specific gap-filling

Mass, charge & stoichiometric consistency

formula and charge checks leaks & energy generating cycles thermodynamic directions

Toolchain for curation

RAVEN / COBRA Toolbox COBRApy diagnostics MEMOTE scores

Session 3

Fee: Rs 14800

Validation, Contextualization & Versioning

Model validation against experiments

growth phenotypes substrate utilization panels gene essentiality screens

Context specific GEMs (overview)

tissue and environment specific models expression constrained networks basic integration workflows

Documentation, provenance & version control

metadata & changelogs Git/GitHub for models FAIR sharing practices

Session 4

Fee: Rs 18800

Mini Capstone: End-to-End GEM Reconstruction

Case study: reconstruct, curate & benchmark a GEM for a chosen organism

Theory + Practical

Quality control & packaging

final MEMOTE report SBML/JSON/Matlab exports Escher map and README

Deliverables

PDF/HTML report .sbml / .json / .mat requirements.txt/environment.yml

PDF

Genome-Scale Metabolic Models (GEMs) Reconstruction & Curation Training | Drafts, Gap-Filling, MEMOTE QC

Genome-Scale Metabolic Models: Reconstruction & Curation (GEMs) — Hands-on