NVIDIA Corporation, Redmond, WA 98052, United States.
Department of Mathematics, University of Washington, Seattle, WA 98195, United States.
Bioinformatics. 2023 Dec 1;39(12). doi: 10.1093/bioinformatics/btad753.
Developing biochemical models in systems biology is a complex, knowledge-intensive activity. Some modelers (especially novices) benefit from model development tools with a graphical user interface. However, as with the development of complex software, text-based representations of models provide many benefits for advanced model development. At present, the tools for text-based model development are limited, typically just a textual editor that provides features such as copy, paste, find, and replace. Since these tools are not "model aware," they do not provide features for: (i) model building such as autocompletion of species names; (ii) model analysis such as hover messages that provide information about chemical species; and (iii) model translation to convert between model representations. We refer to these as BAT features.
We present VSCode-Antimony, a tool for building, analyzing, and translating models written in the Antimony modeling language, a human readable representation of Systems Biology Markup Language (SBML) models. VSCode-Antimony is a source editor, a tool with language-aware features. For example, there is autocompletion of variable names to assist with model building, hover messages that aid in model analysis, and translation between XML and Antimony representations of SBML models. These features result from making VSCode-Antimony model-aware by incorporating several sophisticated capabilities: analysis of the Antimony grammar (e.g. to identify model symbols and their types); a query system for accessing knowledge sources for chemical species and reactions; and automatic conversion between different model representations (e.g. between Antimony and SBML).
VSCode-Antimony is available as an open source extension in the VSCode Marketplace https://marketplace.visualstudio.com/items?itemName=stevem.vscode-antimony. Source code can be found at https://github.com/sys-bio/vscode-antimony.
在系统生物学中开发生化模型是一项复杂的、知识密集型的活动。一些建模者（尤其是新手）受益于具有图形用户界面的模型开发工具。然而，与复杂软件的开发一样，基于文本的模型表示形式为高级模型开发提供了许多好处。目前，基于文本的模型开发工具较为有限，通常只是一个提供复制、粘贴、查找和替换等功能的文本编辑器。由于这些工具不是“模型感知”的，因此它们不提供以下功能：（i）模型构建，例如物种名称的自动补全；（ii）模型分析，例如提供有关化学物质信息的悬停消息；以及（iii）模型翻译，以在模型表示之间进行转换。我们将这些功能称为 BAT 功能。
我们介绍了 VSCode-Antimony，这是一个用于构建、分析和转换 Antimony 建模语言编写的模型的工具，Antimony 是系统生物学标记语言（SBML）模型的一种人类可读表示形式。VSCode-Antimony 是一个源编辑器，是一个具有语言感知功能的工具。例如，有变量名自动补全功能可辅助模型构建，有悬停消息可辅助模型分析，以及 SBML 模型的 XML 和 Antimony 表示之间的转换。这些功能是通过使 VSCode-Antimony 成为模型感知工具来实现的，具体方法是结合几种复杂的功能：Antimony 语法的分析（例如，识别模型符号及其类型）；用于访问化学物质和反应知识库的查询系统；以及不同模型表示之间的自动转换（例如，Antimony 和 SBML 之间）。
VSCode-Antimony 作为开放源代码扩展在 VSCode 市场中可用，网址为 https://marketplace.visualstudio.com/items?itemName=stevem.vscode-antimony。源代码可在 https://github.com/sys-bio/vscode-antimony 找到。
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