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Systems Biology Foundations & Modeling Paradigms Training | ODE/Stochastic, SBML, COPASI

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Systems Biology, Network Modeling & Pathway Simulation >> Systems Biology Foundations & Modeling Paradigms Training | ODE/Stochastic, SBML, COPASI

Systems Biology Foundations & Modeling Paradigms — Hands-on

Kickstart your journey into computational systems biology. Learn the core modeling paradigms (deterministic ODEs, stochastic SSA, rule-based) , biochemical kinetics (mass-action, Hill) , parameterization and basic verification & reporting with community standards (SBML/SBGN/COMBINE) . You will implement small yet realistic pathway/GRN models using COPASI, CellDesigner and Python (Tellurium) .

Systems Biology Foundations & Modeling Paradigms
Help Desk · WhatsApp
Session 1
Fee: Rs 8800
Systems Thinking & Math Foundations
  • Systems biology principles & modeling workflow
    • problem framing scope & assumptions model diagramming
  • Math preliminaries
    • linear algebra (vectors/matrices) calculus & ODE basics phase portraits
  • Toolchain & standards
    • COPASI CellDesigner SBML / SBGN Python (Tellurium)
Session 2
Fee: Rs 11800
Deterministic Modeling (ODE) & Kinetics
  • Writing ODE models from reaction networks
    • mass-action Hill/Michaelis–Menten inhibition/activation
  • Simulation & analysis
    • time-course / steady state stability & Jacobian nondimensionalization
  • Practice
    • COPASI tasks deSolve/Tellurium sensitivity scans
Session 3
Fee: Rs 14800
Stochastic & Rule-Based Modeling
  • When to use stochastic models
    • intrinsic noise low copy numbers heterogeneity
  • Algorithms & tools
    • Gillespie SSA tau-leaping BioNetGen / Kappa
  • Basic parameter estimation & goodness-of-fit
    • least squares likelihood ideas profile scans
Session 4
Fee: Rs 18800
Mini Capstone: Build & Share a Model
  • From diagram to simulation: a small signaling/GRN model
    • Theory + Practical
  • Packaging & verification
    • export SBML/SBGN basic tests & sanity checks COMBINE-like bundle
  • Deliverables: notebook/report & model files
    • PDF/HTML .xml (SBML) / .sedml .cdml (CellDesigner) / .bngl


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