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MakeSBML: a tool for converting between Antimony and SBML.

Bartholomew E Jardine1, Lucian P Smith1, Herbert M Sauro1

  • 1Department of Bioengineering, University of Washington, Box 355061, Seattle, 98195, WA, USA.

Journal of Integrative Bioinformatics
|June 11, 2024
PubMed
Summary
This summary is machine-generated.

MakeSBML is a free, web-based tool for creating and editing systems biology models in System Biology Markup Language (SBML). It simplifies model creation using the human-readable Antimony language, enhancing accessibility for researchers.

Keywords:
AntimonySBMLmodelingreaction networkssoftwaresystems biology

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Bioinformatics

Background:

  • System Biology Markup Language (SBML) is crucial for describing biochemical networks but is computer-readable, not human-readable.
  • Creating and editing SBML models can be complex, hindering reproducibility and accessibility in systems biology research.

Purpose of the Study:

  • To introduce MakeSBML, an installation-free, web-based application for creating, editing, and searching SBML models.
  • To facilitate the use of SBML in systems biology by enabling translation between human-readable Antimony and SBML.

Main Methods:

  • Developed a client-based web application, MakeSBML, accessible via a GitHub page.
  • Implemented translation functionality between the Antimony language and SBML.
  • Designed for installation-free use, requiring no active server maintenance.

Main Results:

  • MakeSBML provides a user-friendly interface for generating and modifying SBML-compliant models.
  • The tool supports bidirectional conversion between Antimony and SBML formats.
  • The web-based, client-side architecture simplifies deployment and reduces maintenance overhead.

Conclusions:

  • MakeSBML enhances the accessibility and usability of SBML modeling in systems biology.
  • The tool promotes model reproducibility and collaboration by simplifying the creation and editing of complex biological models.
  • Its installation-free, web-based nature makes it a readily available resource for the systems biology community.