SBMLtoOdin和menelmacar:为专家和非专家观众提供系统生物学模型的交互可视化
Leonie J Lorenz1, Antoine Andréoletti1,2,3, Tung V N Nguyen1
1European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
Bioinformatics (Oxford, England)
|September 2, 2025
概括
通过SBMLtoOdin和Menelmacar提高了生物模型的可访问性. 这些工具将计算模型转化为可执行代码, 并提供交互式可视化, 赋予研究人员无需编程专业知识的权力.
科学领域:
- 计算生物学
- 系统生物学
- 生物信息学
背景情况:
- 计算模型对于理解生物系统和做出预测至关重要.
- 由于复杂的实施要求,这些模型的可访问性和可重复使用性往往仅限于专家.
- 目前的方法需要专门的编程和数学技能,阻碍了更广泛的科学采用.
研究的目的:
- 提高计算生物模型的可访问性和可重复使用性.
- 使研究人员,包括非专家,能够轻松模拟和研究生物模型.
- 弥合复杂的数学符号和实际模型应用之间的差距.
主要方法:
- 使用"odin"包将系统生物学标记语言 (SBML) 模型转换为可执行的R代码.
- 创建一个基于Web的应用程序Menelmacar,用于直接在浏览器中对这些模型进行交互可视化和模拟.
- 利用生物模型数据库对各种微分方程模型进行分析.
主要成果:
- 通过SBMLtoOdin成功将SBML模型转换为可重复使用的R代码,从而促进模型集成和分析.
- 对于非程序员来说,Menelmacar提供了一个直观的界面,可以与复杂的生物模型进行交互和探索.
- 开发的工具大大降低了在生物研究中使用计算模型的入门障碍.
结论:
- 通过SBMLtoOdin和Menelmacar提高了生物学的计算模型的实用性和可访问性.
- 这些工具使更广泛的研究人员能够利用先进的建模技术进行科学调查.
- 促进模型的重复使用和交互式探索加速了生物学发现和理解.
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