Fedbatchdesigner: A User-Friendly Dashboard for Modeling and Optimizing Growth-Arrested Fed-Batch Processes.

IF 3.7 2区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

ACS Synthetic Biology Pub Date : 2025-07-21 DOI:10.1021/acssynbio.5c00357

Andrea C Graf, Julian Libiseller-Egger, Mathias Gotsmy, Jürgen Zanghellini

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引用次数: 0

Abstract

Optimizing fed-batch fermentation strategies is key to maximizing bioprocess efficiency. While mathematical modeling can aid process design, its complexity often limits accessibility for experimental scientists. We present FedBatchDesigner, a user-friendly web tool for optimizing fed-batch processes with a growth-arrested production stage. With minimal input requirements, FedBatchDesigner enables rapid exploration of a process's titer, rate, and yield (TRY) landscape for constant, linear, and exponential feeding strategies. Interactive visualizations allow users to assess trade-offs between productivity and titer, supporting rational decision-making without the need for extensive modeling expertise. We demonstrate FedBatchDesigner's utility via two case studies: synthesis of (i) l-valine with a microaerobic production stage in Escherichia coli and (ii) ethanol under nitrogen starvation in Saccharomyces cerevisiae. FedBatchDesigner is freely available at https://chemnettools.anc.univie.ac.at/FedBatchDesigner, with the source code provided at https://github.com/julibeg/FedBatchDesigner under the MIT license.

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Fedbatchdesigner：一个用户友好的仪表板，用于建模和优化增长受阻的feed批处理过程。

优化补料分批发酵策略是实现生物工艺效率最大化的关键。虽然数学建模可以帮助过程设计，但其复杂性往往限制了实验科学家的可访问性。我们提出了FedBatchDesigner，一个用户友好的web工具，用于优化饲料批处理过程与增长受阻的生产阶段。通过最小的输入需求，FedBatchDesigner可以快速探索过程的滴度、速率和产量（TRY）景观，以获得恒定、线性和指数馈送策略。交互式可视化允许用户评估生产力和可靠性之间的权衡，支持合理的决策，而不需要广泛的建模专业知识。我们通过两个案例研究证明了FedBatchDesigner的实用性：大肠杆菌在微氧生产阶段合成l-缬氨酸和酿酒酵母在氮饥饿条件下合成乙醇。FedBatchDesigner可以在https://chemnettools.anc.univie.ac.at/FedBatchDesigner上免费获得，源代码在https://github.com/julibeg/FedBatchDesigner上根据MIT许可提供。

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

ACS Synthetic Biology 生物-

CiteScore

8.00

自引率

10.60%

发文量

380

审稿时长

6-12 weeks

期刊介绍： The journal is particularly interested in studies on the design and synthesis of new genetic circuits and gene products; computational methods in the design of systems; and integrative applied approaches to understanding disease and metabolism. Topics may include, but are not limited to: Design and optimization of genetic systems Genetic circuit design and their principles for their organization into programs Computational methods to aid the design of genetic systems Experimental methods to quantify genetic parts, circuits, and metabolic fluxes Genetic parts libraries: their creation, analysis, and ontological representation Protein engineering including computational design Metabolic engineering and cellular manufacturing, including biomass conversion Natural product access, engineering, and production Creative and innovative applications of cellular programming Medical applications, tissue engineering, and the programming of therapeutic cells Minimal cell design and construction Genomics and genome replacement strategies Viral engineering Automated and robotic assembly platforms for synthetic biology DNA synthesis methodologies Metagenomics and synthetic metagenomic analysis Bioinformatics applied to gene discovery, chemoinformatics, and pathway construction Gene optimization Methods for genome-scale measurements of transcription and metabolomics Systems biology and methods to integrate multiple data sources in vitro and cell-free synthetic biology and molecular programming Nucleic acid engineering.