Biodesign Center, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.
Nucleic Acids Res. 2023 Jul 5;51(W1):W70-W77. doi: 10.1093/nar/gkad360.
Flux balance analysis (FBA) is an important method for calculating optimal pathways to produce industrially important chemicals in genome-scale metabolic models (GEMs). However, for biologists, the requirement of coding skills poses a significant obstacle to using FBA for pathway analysis and engineering target identification. Additionally, a time-consuming manual drawing process is often needed to illustrate the mass flow in an FBA-calculated pathway, making it challenging to detect errors or discover interesting metabolic features. To solve this problem, we developed CAVE, a cloud-based platform for the integrated calculation, visualization, examination and correction of metabolic pathways. CAVE can analyze and visualize pathways for over 100 published GEMs or user-uploaded GEMs, allowing for quicker examination and identification of special metabolic features in a particular GEM. Additionally, CAVE offers model modification functions, such as gene/reaction removal or addition, making it easy for users to correct errors found in pathway analysis and obtain more reliable pathways. With a focus on the design and analysis of optimal pathways for biochemicals, CAVE complements existing visualization tools based on manually drawn global maps and can be applied to a broader range of organisms for rational metabolic engineering. CAVE is available at https://cave.biodesign.ac.cn/.
通量平衡分析（FBA）是一种在基因组尺度代谢模型（GEMs）中计算生产工业上重要化学品的最优途径的重要方法。然而，对于生物学家来说，编码技能的要求成为了使用 FBA 进行途径分析和工程目标识别的重大障碍。此外，通常需要耗时的手动绘图过程来说明 FBA 计算途径中的质量流，这使得检测错误或发现有趣的代谢特征变得具有挑战性。为了解决这个问题，我们开发了 CAVE，这是一个基于云的代谢途径综合计算、可视化、检查和校正平台。CAVE 可以分析和可视化超过 100 个已发布的 GEM 或用户上传的 GEM 的途径，从而能够更快地检查和识别特定 GEM 中的特殊代谢特征。此外，CAVE 提供模型修改功能，例如基因/反应的删除或添加，使用户能够纠正途径分析中发现的错误，并获得更可靠的途径。CAVE 专注于设计和分析生物化学的最优途径，补充了基于手动绘制全局图谱的现有可视化工具，并且可以应用于更广泛的生物体，以进行合理的代谢工程。CAVE 可在 https://cave.biodesign.ac.cn/ 上获得。
