2023/09/06 by Bartholomew Jardine, Jardine, Bartholomew E., Lucian P. Smith +3
Biochemistry, Genetics and Molecular Biology · #Bioinformatics and Genomic Networks #FOS: Biological sciences #Gene Regulatory Network Analysis #Microbial Metabolic Engineering and Bioproduction #Molecular Networks (q-bio.MN) #Quantitative Methods (q-bio.QM)
paper · pdf · doi:10.48550/arxiv.2309.03344
openalex publication_date 2023/09/06 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
We describe a web-based tool, MakeSBML (https://sys-bio.github.io/makesbml/), that provides an installation-free application for creating, editing, and searching the Biomodels repository for SBML-based models. MakeSBML is a client-based web application that translates models expressed in human-readable Antimony to the System Biology Markup Language (SBML) and vice-versa. Since MakeSBML is a web-based application it requires no installation on the user's part. Currently, MakeSBML is hosted on a GitHub page where the client-based design makes it trivial to move to other hosts. This model for software deployment also reduces maintenance costs since an active server is not required. The SBML modeling language is often used in systems biology research to describe complex biochemical networks and makes reproducing models much easier. However, SBML is designed to be computer-readable, not human-readable. We therefore employ the human-readable Antimony language to make it easy to create and edit SBML models.