Constraint Based Modeling COBRA & FBA — Hands-on

Learn how to perform constraint based modeling of metabolism using COBRA style workflows. This module covers the steady state formulation, flux balance analysis, flux variability, knockouts and basic experimental design questions that can be addressed with genome scale metabolic models.

Constraint Based Modeling COBRA & FBA

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Session Index

Session 1 — Foundations of Constraint Based Modeling Session 2 — Flux Balance Analysis with COBRA Session 3 — FVA, Knockouts and Scenario Analysis Session 4 — Mini Capstone: FBA Project on a GSM Model

Session 1

Fee: Rs 8800

Foundations of Constraint Based Modeling

Steady state assumption and S·v = 0 formulation

Stoichiometric matrix S flux vector v mass balance at steady state

Constraints and feasible flux spaces

lower and upper bounds reversibility and directionality thermodynamic and capacity limits

Objective functions and biological meaning

biomass and growth product yield objectives multi objective ideas

Session 2

Fee: Rs 11800

Flux Balance Analysis with COBRA

FBA as a linear programming problem

optimize Z = c·v constraints S·v = 0 bounds on v

Using COBRApy on SBML models

model loading and checks setting objective getting flux distributions

Interpreting FBA outputs

growth predictions exchange fluxes and uptake rates shadow price intuition

Session 3

Fee: Rs 14800

FVA, Knockouts and Scenario Analysis

Flux Variability Analysis (FVA)

minimum and maximum flux ranges alternative optima identifying flexible reactions

Single and double knockouts in silico

gene and reaction deletions essentiality analysis synthetic lethality overview

Medium, diet and environment scenarios

changing uptake bounds carbon and nitrogen sources stress or drug like conditions

Session 4

Fee: Rs 18800

Mini Capstone: FBA Project on a GSM Model

Select a published genome scale model and define questions

Theory plus guided practical

Run FBA, FVA and knockout scenarios

growth vs production tradeoffs candidate engineering targets basic robustness checks

Deliverables: notebook, result tables and short report

Python notebook with COBRApy CSV flux and FVA summaries PDF or HTML project summary

PDF

Constraint Based Modeling COBRA and FBA Training | Flux Balance, FVA and Knockout Analysis

Constraint Based Modeling COBRA & FBA — Hands-on