MakeSBML: a tool for converting between Antimony and SBML.

IF 1.5 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Journal of Integrative Bioinformatics Pub Date : 2024-06-11 eCollection Date: 2024-03-01 DOI:10.1515/jib-2024-0002

Bartholomew E Jardine, Lucian P Smith, Herbert M Sauro

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引用次数: 0

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.

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MakeSBML：在 Antimony 和 SBML 之间进行转换的工具。

我们描述了一个基于网络的工具 MakeSBML (https://sys-bio.github.io/makesbml/)，它提供了一个免安装的应用程序，用于创建、编辑和搜索生物模型库中基于 SBML 的模型。MakeSBML 是一个基于客户端的网络应用程序，可将以人类可读的锑表示的模型转换为系统生物学标记语言（SBML），反之亦然。由于 MakeSBML 是基于网络的应用程序，用户无需安装。目前，MakeSBML 托管在 GitHub 页面上，基于客户端的设计使其可以轻松转移到其他主机上。这种软件部署模式还能降低维护成本，因为不需要活动服务器。SBML 建模语言常用于系统生物学研究，用于描述复杂的生化网络，使模型的复制更加容易。然而，SBML 的设计是计算机可读的，而不是人类可读的。因此，我们采用了人类可读的锑语言，使创建和编辑 SBML 模型变得更加容易。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Integrative Bioinformatics Medicine-Medicine (all)

CiteScore

3.10

自引率

5.30%

发文量

审稿时长

12 weeks