MakeSBML: a tool for converting between Antimony and SBML
Author:
Jardine Bartholomew E.1ORCID, Smith Lucian P.1, Sauro Herbert M.1
Affiliation:
1. Department of Bioengineering , University of Washington , Box 355061 , Seattle , 98195 , WA , USA
Abstract
Abstract
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.
Funder
National Institute of General Medical Sciences National Institute of Biomedical Imaging and Bioengineering
Publisher
Walter de Gruyter GmbH
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