Model Sharing, Reproducibility & FAIR Workflows — Hands-on

Turn ad-hoc simulation scripts into well packaged, shareable and reproducible systems biology assets. This module focuses on SBML/SBGN centric model packaging, metadata, version control, environment capture and deposition in public or internal repositories following FAIR (Findable, Accessible, Interoperable, Reusable) principles.

Model Sharing, Reproducibility & FAIR Workflows

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Session Index

Session 1 — Standards, Formats & Model Packaging Session 2 — Reproducible Pipelines & Version Control Session 3 — FAIR Principles, Metadata & Repositories Session 4 — Mini Capstone: Shareable Reproducible Model Bundle

Session 1

Fee: Rs 8800

Standards, Formats & Model Packaging

SBML, SBGN and COMBINE archive basics for sharing

SBML levels and annotations SBGN maps and layouts OMEX / COMBINE archive idea

Coding style and organisation for sharable models

separating model, data and scripts config files and run presets readme and quick start notes

Packaging simulations and figures with the model

reference simulations and outputs linking notebooks to SBML lightweight vs full archives

Session 2

Fee: Rs 11800

Reproducible Pipelines & Version Control

Git based versioning for models and simulations

branching and tagging releases tracking SBML and notebooks changelogs and release notes

Environment capture and dependency management

conda / venv and requirements.txt environment.yml and lock files container basics (Docker idea)

Automating runs and checks for reproducibility

simple makefile / script runners CI style sanity checks hashes and regression checks

Session 3

Fee: Rs 14800

FAIR Principles, Metadata & Repositories

FAIR (Findable, Accessible, Interoperable, Reusable) in practice

persistent identifiers and DOIs licensing and access statements interoperability via standards

Metadata and documentation for reusable models

description of scope and assumptions experimental links and references parameter tables and units

Depositing in public / internal model repositories

Model repositories (concept level) internal registries and catalogs review and curation workflows

Session 4

Fee: Rs 18800

Mini Capstone: Shareable Reproducible Model Bundle

Select an existing systems model and refactor into a package

Theory + Practical

Create SBML / archive, scripts, environment and docs

one command reproducible run minimal environment specification readme and metadata sheet

Deliverables: versioned repo or archive ready to share

Git repo or COMBINE archive example plots and results short FAIR and reproducibility checklist

PDF

Model Sharing, Reproducibility & FAIR Workflows Training | SBML, COMBINE & Versioned Pipelines

Model Sharing, Reproducibility & FAIR Workflows — Hands-on