Systems Biology Foundations & Standards — Hands-on

Build a rigorous foundation in systems biology and community standards for executable models. This module connects conceptual modeling paradigms with SBML, SBGN and COMBINE Archives so that your pathway and network models are reusable, shareable and compliant with FAIR principles.

Systems Biology Foundations & Standards

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Session Index

Session 1 — Systems Biology Concepts & Modeling Paradigms Session 2 — SBML, SBGN & Model Encodings Session 3 — Repositories, Tools & Workflows Session 4 — Mini Capstone: Pathway to Executable Model

Session 1

Fee: Rs 8800

Systems Biology Concepts & Modeling Paradigms

From pathways to systems level behavior

feedback and feedforward loops homeostasis and oscillations emergent properties

Modeling formalisms and assumptions

ODE and deterministic models stochastic and Gillespie view logical and constraint based

States, parameters and observables

species and compartments rate laws and units linking data to models

Session 2

Fee: Rs 11800

SBML, SBGN & Model Encodings

SBML structure and common patterns

species and reactions parameters and rules events and initialisation

SBGN diagrams and pathway communication

process description maps entity relationship views activity flow schematics

FAIR friendly metadata and archives

annotations and ontologies COMBINE Archive basics MIRIAM style reporting

Session 3

Fee: Rs 14800

Repositories, Tools & Workflows

Model repositories and discovery

BioModels and CellML JWS Online and VCell community curated models

Simulation and analysis toolchain

COPASI and tellurium Python based workflows parameter scans and basic sensitivity

Reproducible configurations

environment capture version control of models notebooks and reports

Session 4

Fee: Rs 18800

Mini Capstone: Pathway to Executable Model

From pathway diagram to SBML and SBGN

Theory + Practical

Basic simulations and scenario analysis

time course runs parameter changes qualitative sensitivity

Packaging and documentation

COMBINE Archive metadata and README FAIR oriented deliverables

PDF

Systems Biology Foundations & Standards Training | SBML, SBGN & Reproducible Pathway Modeling

Systems Biology Foundations & Standards — Hands-on