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Constraint-Based Metabolic Modeling (FBA/FVA) Training | COBRApy, COBRA Toolbox, OptFlux

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Systems Biology, Network Modeling & Pathway Simulation >> Constraint-Based Metabolic Modeling (FBA/FVA) Training | COBRApy, COBRA Toolbox, OptFlux

Constraint-Based Metabolic Modeling (FBA/FVA) — Hands-on

Build, simulate, and analyze metabolic network models with constraint-based methods. You will learn curation of genome-scale models (GEMs) , objective functions, bounds, and exchange reactions; run FBA/FVA/pFBA; perform gene/reaction knockouts; and generate phenotype predictions and strain designs. Models and reports are packaged with community standards (SBML, COBRA format, MEMOTE) .

Constraint-Based Metabolic Modeling (FBA/FVA)
Help Desk · WhatsApp
Session 1
Fee: Rs 8800
GEM Basics, Media & Model Setup
  • Model anatomy & standards
    • SBML / COBRA format GPR rules BiGG / ModelSEED
  • Media, exchange & biomass objective
    • bounds & uptake limits transport/leakage biomass calibration
  • Toolchain
    • COBRApy / COBRA Toolbox (MATLAB) OptFlux / cameo memote / Escher
Session 2
Fee: Rs 11800
FBA/FVA, pFBA & Pathway Analysis
  • Steady-state & optimality concepts
    • S·v = 0, bounds LP formulation shadow prices
  • Analyses
    • FBA / FVA parsimonious FBA (pFBA) GIMME/iMAT overview
  • Visualization & reporting
    • Escher maps flux distributions pathway summaries
Session 3
Fee: Rs 14800
Knockouts, Design & Data Integration
  • Essentiality & lethality screens
    • single/double gene KO reaction deletions synthetic lethality
  • Strain design & MILP formulations
    • OptKnock/OptGene room/MOMA production envelopes
  • Contextualization & dynamics (overview)
    • transcriptomics: iMAT/GIMME rFBA / dFBA concepts basic validation vs. growth data
Session 4
Fee: Rs 18800
Mini Capstone: From Curation to Simulation
  • Case study: media design, FBA/FVA and KO predictions for a product/growth trade-off
    • Theory + Practical
  • Packaging & QC
    • SBML + JSON model memote summary Escher map exports
  • Deliverables
    • PDF/HTML report .sbml / .mat / .json requirements.txt/environment.yml


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