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Updated: Jun 25, 2026

3D Printing of Biomolecular Models for Research and Pedagogy

3D Printing of Biomolecular Models for Research and Pedagogy

Published on: March 13, 2017

Curating models from BioModels: Developing a workflow for creating OMEX files.

Jin Xu¹, Lucian Smith¹

¹Department of Bioengineering, University of Washington, Seattle, WA, USA.

Biorxiv : the Preprint Server for Biology

|April 1, 2024

Summary

This summary is machine-generated.

Reproducing computational biology models is crucial. This study validated 50 models, creating standardized files (SBML, SED-ML, OMEX) to enhance future model curation and verification.

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Area of Science:

Computational Biology
Systems Biology
Bioinformatics

Background:

Reproducibility in computational biology is essential for scientific progress.
Public repositories like BioModels Database are vital for sharing models.
Ensuring model accuracy and reusability requires robust validation and standardization.

Purpose of the Study:

To assess and improve the reproducibility of 50 computational biology models from the BioModels Database.
To develop a manual workflow for model validation and correction.
To identify limitations and areas for enhancement in current model curation and verification tools.

Main Methods:

Utilized Tellurium to reproduce published results for 50 selected models.
Manually created standardized files using Systems Biology Markup Language (SBML) for model information.
Generated Simulation Experiment Description Markup Language (SED-ML) files for simulation instructions.
Bundled SBML, SED-ML, and simulation data into Open Modeling Exchange (OMEX) archives for cross-simulator compatibility.

Main Results:

Successfully reproduced results for the examined computational biology models.
Developed a manual workflow that serves as a foundation for an automated model curation platform.
Identified limitations in existing curation tools and proposed enhancements for model verification.

Conclusions:

The manual workflow developed aids in validating and correcting computational biology models.
Standardized formats (SBML, SED-ML, OMEX) facilitate model reproducibility across different simulators.
Findings will inform the development of automated tools to improve model curation and verification in systems biology.