Chapter 8

Lecture Videos #

A Massive Open Online Course on Computational Systems Biology, which is in part, a basis for this book, is also available, through the Indian educational platforms, NPTEL (National Programme on Technology Enhanced Learning) and SWAYAM.

The lectures (including hands-on lab sessions), totalling over 30 hours of content, are also available on YouTube.

Chapter 8: Introduction to constraint-based modelling #

Constraint-based Modelling of Metabolic Networks (22:53)

  • Introduction
  • Constraints on Biological Systems
  • Stoichiometric Matrix

Flux Balance Analysis (21:21)

  • Steady-state Mass Balance
  • Constraints
  • Optimisation (LP)

Flux Balance Analysis (21:39)

  • The Objective Function
  • Illustration of FBA

Flux Balance Analysis (17:58)

  • Choice of Objective Function
  • Alternate Optima in FBA

Lab: FBA using MATLAB (24:19)

  • Understanding and Solving FBA using \texttt{linprog}
  • COBRA Model Structure
  • FBA using COBRA Toolbox

Lab: COBRA Toolbox (46:28)

  • \texttt{optimizeCbModel}
  • Exchange Reactions
  • Varying Glucose Uptake Rates

Understanding FBA (15:08)

  • Gaps
  • Dead-end Metabolites
  • Blocked Reactions

Understanding FBA (16:34)

  • Troubleshooting FBA
  • ATP Maintenance Flux
  • Flux Variability Analysis