Model Exchange Standards: SBML, SBOL & OMEX — Hands-on

Standardize and share your systems biology models using SBML, SBOL and OMEX/COMBINE archives. This module focuses on how to encode models, attach metadata, bundle simulations and prepare FAIR, interoperable model packages for collaboration, publication and reuse.

Model Exchange Standards: SBML, SBOL & OMEX

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Session Index

Session 1 — SBML, SBOL & OMEX Landscape Session 2 — Encoding Models in SBML & SBOL Session 3 — COMBINE Archives, OMEX & FAIR Workflows Session 4 — Mini Capstone: Package & Share a Model

Session 1

Fee: Rs 8800

SBML, SBOL & OMEX Landscape

Why standards matter for systems models

reproducibility and interoperability reuse and extension of models FAIR data and model principles

Main standards in the ecosystem

SBML for dynamical models (concept) SBOL for designs and constructs OMEX / COMBINE archives overview

Repositories and community resources (overview)

model repositories idea curation and versioning concepts community guidelines & initiatives

Session 2

Fee: Rs 11800

Encoding Models in SBML & SBOL

SBML structure and concepts (high level)

components, parameters and reactions units and compartments idea annotations and identifiers notion

SBOL basics for synthetic biology designs

components and modules concept sequences and interactions overview linking SBOL to models idea

From informal diagrams to SBML/SBOL encodings

identify species and processes map to components and reactions capture basic metadata and notes

Session 3

Fee: Rs 14800

COMBINE Archives, OMEX & FAIR Workflows

What an OMEX / COMBINE archive contains

models, simulations and metadata linking SBML and SED-ML notion bundling related files together

FAIR and documentation friendly packaging

descriptions, README and manifest provenance and version tags licensing and citation info

Moving models across tools using standards

export and import mental model checking compatibility and warnings simple interoperability checks

Session 4

Fee: Rs 18800

Mini Capstone: Package & Share a Model

Choose a small model or example to standardize

theory plus guided practical

Encode in SBML/SBOL style and create an OMEX package

identify components and annotations add basic metadata and README bundle files in a COMBINE archive

Deliverables: archive, docs and short sharing note

OMEX/zip style archive README and manifest text PDF or HTML summary of contents

PDF

Model Exchange Standards SBML SBOL and OMEX Training | FAIR & Interoperable Systems Models

Model Exchange Standards: SBML, SBOL & OMEX — Hands-on