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

Map biochemical pathways into reaction networks and stoichiometric matrices, enforce mass balances, and prepare models for flux and constraint-based analyses using KEGG/Reactome, SBML, and Python/R workflows.

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Systems Biology, Network Modeling & Pathway Informatics

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 Index

Session 1 — Pathway Maps & Reaction Networks Session 2 — Stoichiometric Matrix Construction Session 3 — Fluxes, Balances & Constraints Session 4 — Mini Capstone: Curate & Analyze a Pathway

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