Fluxomics Modeling from Tracer Data — EMU & COBRA — Hands-on

Learn how to move from stable isotope labeling data to quantitative intracellular flux maps. This module focuses on the EMU framework, 13C metabolic flux analysis workflows, building reaction and atom mapping models, fitting fluxes to tracer data and interpreting flux distributions together with COBRA-style constraint-based models for systems-level insight.

Fluxomics Modeling from Tracer Data — EMU & COBRA

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Session Index

Session 1 — Fluxomics Concepts & EMU Framework Session 2 — Building EMU / Isotopomer Models Session 3 — Fitting Fluxes & Assessing Uncertainty Session 4 — Mini Capstone: Flux Map & Report

Session 1

Fee: Rs 8800

Fluxomics Concepts & EMU Framework

From tracer experiments to fluxomics questions

pool sizes vs fluxes steady state vs non steady state central carbon and beyond

EMU (Elementary Metabolite Unit) framework basics

isotopomers, isotopologues and EMUs atom transitions and mapping why EMUs scale better than full isotopomer models

Inputs, assumptions and data requirements

reaction network and reversibility measured labeling patterns and flux bounds identifiability and experimental design links

Session 2

Fee: Rs 11800

Building EMU / Isotopomer Models

Defining the metabolic network for 13C MFA

choosing reactions and compartments irreversible vs reversible splits linking to genome scale models

Atom mapping and EMU decomposition

carbon atom mapping for key reactions automatic vs manual EMU generation reducing model size without losing identifiability

Software workflows and file formats

model specification tables/spreadsheets exchange with COBRA style models export/import to flux analysis tools

Session 3

Fee: Rs 14800

Fitting Fluxes & Assessing Uncertainty

Objective functions and optimization strategies

least squares cost functions constraints and bounds on fluxes global vs local optimization approaches

Goodness of fit and residual diagnostics

chi square and residual plots detecting model misspecification sensitivity to individual measurements

Confidence intervals and identifiability analysis

profile likelihoods and confidence ranges flux coupling and unidentifiable directions using results to improve experimental design

Session 4

Fee: Rs 18800

Mini Capstone: Flux Map & Report

End to end 13C MFA on a teaching dataset

from labeling data to fitted fluxes

Visualizing and interpreting the flux map

graphical flux diagrams comparing conditions or genotypes linking fluxes to phenotypes and pathways

Deliverables: model files, flux tables & methods text

reaction and atom mapping specification flux estimates with confidence ranges ready to edit methods/results template

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Fluxomics Modeling from Tracer Data — EMU & COBRA Training | 13C MFA & Flux Maps

Fluxomics Modeling from Tracer Data — EMU & COBRA — Hands-on