Model Standards — SBML, SBGN & COMBINE Archive — Hands-on

Learn how to make your systems biology models FAIR, interoperable and shareable using community standards. This module covers SBML for model encoding, SBGN for pathway diagrams, and COMBINE archives for packaging models, data and metadata together. You will practice working with these standards in tools such as COPASI, tellurium, libSBML based scripts and SBGN editors, and produce publication and repository ready model packages.

Model Standards — SBML, SBGN & COMBINE Archive

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Session Index

Session 1 — Standards Ecosystem & SBML Basics Session 2 — SBML Models: Structure, Tools & Annotations Session 3 — SBGN Diagrams & COMBINE Archives Session 4 — Mini Capstone: Standardizing & Packaging a Model

Session 1

Fee: Rs 8800

Standards Ecosystem & SBML Basics

Why standards for systems biology models

reproducibility & interoperability FAIR principles community resources & repositories

Overview of SBML, SBGN & COMBINE

roles of SBML, SBGN and COMBINE how they connect in workflows model, diagram & archive layers

SBML basics & level overview

SBML core concepts (species, reactions, parameters) levels & packages (high level) simple SBML example walkthrough

Session 2

Fee: Rs 11800

SBML Models: Structure, Tools & Annotations

Inside an SBML model file

components: compartments, species, reactions parameters, rules & events (overview) units & consistency checks

Tools for working with SBML

COPASI & tellurium libSBML based scripts (Python/R) model import/export across tools

Annotations & metadata for SBML

MIRIAM style annotations (high level) linking to ontologies and databases good practices for FAIR models

Session 3

Fee: Rs 14800

SBGN Diagrams & COMBINE Archives

SBGN languages & pathway diagrams

SBGN Process Description, Activity Flow (overview) core glyphs & visual conventions linking SBGN diagrams to models

Tools for SBGN & layouts

CellDesigner / SBGN-ED / Newt (overview) layout & style considerations export for figures & sharing

COMBINE archives for packaging models

what a COMBINE archive contains models, diagrams, data & metadata together basic archive creation workflows

Session 4

Fee: Rs 18800

Mini Capstone: Standardizing & Packaging a Model

End to end standardization of a small model

Theory + Practical

From raw model to SBML, SBGN & COMBINE archive

encoding or cleaning the SBML model creating a matching SBGN diagram packing into a COMBINE archive with metadata

Validation, sharing & repository submission (concept level)

running basic validators preparing for BioModels or similar repositories PDF/HTML documentation & archive description

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Model Standards — SBML, SBGN & COMBINE Archive Training | FAIR & Interoperable Systems Models

Model Standards — SBML, SBGN & COMBINE Archive — Hands-on