VSCode-Antimony: a source editor for building, analyzing, and translating antimony models.
VSCode-Antimony: a source editor for building, analyzing, and translating antimony models.
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DOI：
10.1093/bioinformatics/btad753
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发表时间：
2023-12-01
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在系统生物学中开发生物化学模型是一项复杂的知识密集型活动。一些建模者（特别是新手）受益于带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为高级模型开发提供了许多好处。目前，用于基于文本的模型开发的工具是有限的，通常只是一个文本编辑器，提供诸如复制、粘贴、查找和替换之类的功能。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完成;（ii）模型分析，例如提供有关化学物种的信息的悬停消息;以及（iii）模型转换，以在模型表示之间进行转换。我们将这些称为BAT特征。 我们提出了VSCode-Antimony，一个用于构建，分析和翻译用Antimony建模语言编写的模型的工具，该语言是系统生物学标记语言（SBML）模型的人类可读表示。VSCode-Antimony是一个源代码编辑器，一个具有语言感知功能的工具。例如，变量名的自动完成可以帮助模型构建，悬停消息可以帮助模型分析，以及SBML模型的XML和Antimony表示之间的转换。这些功能是通过整合几个复杂的功能使VSCode-Antimony模型感知的结果：Antimony语法分析（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源的查询系统;以及不同模型表示之间的自动转换（例如Antimony和SBML之间）。VSCode-Antimony作为开源扩展在VSCode Marketplace https://marketplace.visualstudio.com/items?上提供itemName=stevem.vscode-antimony.源代码可以在https://github.com/sys-bio/vscode-antimony上找到。
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.
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DOI：
10.1016/j.biosystems.2018.07.006
发表时间：
2018-09
期刊：
Bio Systems
影响因子：
--
作者：
Choi K;Medley JK;König M;Stocking K;Smith L;Gu S;Sauro HM
通讯作者：
Sauro HM
影响因子：
5.8
作者：
Gevorgyan, Albert;Poolman, Mark G.;Fell, David A.
通讯作者：
Fell, David A.
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J
影响因子：
3.3
作者：
BRAY, D;BOURRET, RB
通讯作者：
BOURRET, RB
影响因子：
4.3
作者：
Haiman ZB;Zielinski DC;Koike Y;Yurkovich JT;Palsson BO
通讯作者：
Palsson BO