Constraint-Based Modeling — FBA, FVA & Knockout Simulations — Hands-on

Learn how to formulate, solve, and interpret constraint based metabolic models for realistic biological systems. This module focuses on steady state flux formulations, flux balance analysis (FBA) , flux variability analysis (FVA) , and single or multiple knockouts, implemented through practical COBRApy style pipelines on curated metabolic reconstructions.

Constraint-Based Modeling — FBA, FVA & Knockout Simulations

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Session Index

Session 1 — Constraint Based Modeling Foundations Session 2 — Flux Balance Analysis Workflows Session 3 — Flux Variability & Robustness Session 4 — Mini Capstone: Knockouts & Media Scenarios

Session 1

Fee: Rs 8800

Constraint Based Modeling Foundations

Recap of metabolic models and stoichiometric matrices

S matrix structure internal vs exchange reactions compartments and media

Constraint based model formulation

steady state Sv = 0 condition flux bounds and reversibility flags objective functions and growth proxies

Toolchain overview for constraint based models

COBRApy environment LP solvers (GLPK style) SBML / JSON model loading

Session 2

Fee: Rs 11800

Flux Balance Analysis Workflows

Running FBA on curated models

setting objective reactions media constraints and uptake bounds optimal growth and flux vectors

Exploring alternate solutions and shadow prices (concepts)

degeneracy intuition dual variables preview biological interpretation hooks

Implementation toolkit for FBA pipelines

COBRApy FBA functions flux map visualisation helpers tabular result exports (CSV)

Session 3

Fee: Rs 14800

Flux Variability & Robustness

Flux variability analysis concepts and practice

min max flux ranges essential vs flexible reactions network redundancy insight

Robustness and phenotype phase plane style ideas

parameter sweeps of uptake rates growth vs substrate landscapes environmental robustness views

Implementation toolkit for FVA and robustness charts

COBRApy FVA routines Python plotting of flux ranges summary heatmaps and tables

Session 4

Fee: Rs 18800

Mini Capstone: Knockouts & Media Scenarios

Design knockout and media change experiments in silico

Theory + Practical

Run single and double gene or reaction knockouts

essentiality analysis synthetic lethality screens (small scale) growth rescue via media tweaks

Deliverables: scenario notebooks, result tables & report

COBRApy analysis notebook CSV exports of knockout screens PDF/HTML capstone summary

PDF

Constraint-Based Modeling, FBA, FVA & Knockout Simulations Training | Flux Models & In Silico Experiments

Constraint-Based Modeling — FBA, FVA & Knockout Simulations — Hands-on