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

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Title: Fedbatchdesigner: A User-Friendly Dashboard for Modeling and Optimizing Growth-Arrested Fed-Batch Processes
Authors: Andrea C. Graf, Julian Libiseller-Egger, Mathias Gotsmy, Jürgen Zanghellini
Publication Year: 2025
Subject Terms: Microbiology, Biotechnology, Inorganic Chemistry, Science Policy, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, supporting rational decision, source code provided, minimal input requirements, microaerobic production stage, maximizing bioprocess efficiency, https :// github, https :// chemnettools, exponential feeding strategies, friendly web tool, batch fermentation strategies, arrested production stage, aid process design, extensive modeling expertise, demonstrate fedbatchdesigner ’, process ’, friendly dashboard, batch processes, arrested fed, saccharomyces cerevisiae, present fedbatchdesigner, optimizing fed, nitrogen starvation, mit license, mathematical modeling
Description: 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.
Document Type: article in journal/newspaper
Language: unknown
DOI: 10.1021/acssynbio.5c00357.s002
Availability: https://doi.org/10.1021/acssynbio.5c00357.s002
https://figshare.com/articles/journal_contribution/Fedbatchdesigner_A_User-Friendly_Dashboard_for_Modeling_and_Optimizing_Growth-Arrested_Fed-Batch_Processes/29614871
Rights: CC BY-NC 4.0
Accession Number: edsbas.44ABC8F
Database: BASE
Description
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.
DOI:10.1021/acssynbio.5c00357.s002