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Biochemical Pathways & Stoichiometric Modeling Training | Stoichiometric Matrices, Fluxes, Constraints

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Systems Biology, Network Modeling & Pathway Informatics >> Biochemical Pathways & Stoichiometric Modeling Training | Stoichiometric Matrices, Fluxes, Constraints

Biochemical Pathways & Stoichiometric Modeling — Hands-on

Learn how to convert biochemical pathway diagrams into mathematically consistent models using stoichiometric representations. You will construct reaction networks, build stoichiometric matrices, apply mass balance constraints, and prepare models in standard formats suitable for downstream flux balance and systems biology simulations.

Biochemical Pathways & Stoichiometric Modeling
Help Desk · WhatsApp
Session 1
Fee: Rs 8800
Pathway Maps & Reaction Networks
  • From pathway diagrams to reaction lists
    • KEGG / Reactome navigation BioCyc & MetaCyc views metabolites & compartments
  • Reaction network structure & notation
    • irreversible vs reversible exchange & transport reactions boundary conditions
  • Toolchain for pathway handling
    • KEGG Mapper Escher / Cytoscape Python / R parsing scripts
Session 2
Fee: Rs 11800
Stoichiometric Matrix Construction
  • Stoichiometric coefficients & reaction balancing
    • mass & charge balance elemental composition simplifying assumptions
  • Building the stoichiometric matrix (S)
    • metabolites as rows reactions as columns sparse representation
  • Implementation toolkit
    • Python / pandas / numpy R / Matrix objects SBML model export
Session 3
Fee: Rs 14800
Fluxes, Balances & Constraints
  • Flux vectors and steady-state condition S·v = 0
    • internal vs exchange fluxes uptake & secretion bounds null space intuition
  • Constraint specification & model sanity checks
    • reaction reversibility flags infeasibility detection mass leakage checks
  • Toolchain preview for constraint-based modeling
    • COBRApy basics linear programming backends model I/O (SBML / JSON)
Session 4
Fee: Rs 18800
Mini Capstone: Curate & Analyze a Pathway
  • Select a KEGG/Reactome pathway and build its S matrix
    • Theory + Practical
  • Check mass balance, define flux bounds & constraints
    • diagnostic scripts sanity reports pre-FBA readiness
  • Deliverables: curated model files & documentation
    • SBML / JSON model S matrix (CSV/TSV) PDF/HTML pathway report


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