Snapshot of STBRsim for determining optimal time for aerobic-to-anaerobic switch to maximize the production of R-1,2-propanediol production in engineered Escherichia coli.
STBRsim was released by In Silico Fermentation in August 2024. Please continue reading this page to learn more about the application and to download this free software.
An emerging application of genome-scale metabolic reconstructions is the development of rigorous dynamic simulations of stirred tank bioreactors (STBRs). By exploiting dynamic flux balance analysis (DFBA) methods, the same metabolic model can be used as a common platform for medium design, metabolic engineering and bioreactor simulation. While the research literature contains numerous DFBA computational methods, effective utilization of these approaches requires significant experience with high-level programming languages such as MATLAB. As a result, available modeling tools are largely inaccessible to industrial practitioners who typically wish to perform bioreactor simulations with minimal coding effort.
STBRsim is a MATLAB application that streamlines the development of dynamic metabolic models for bioreactor simulation. Given a genome-scale metabolic reconstruction of the target strain, the GUI tool generates dynamic predictions of extracellular variables including biomass, substrate and product concentrations and liquid/gas phase volumes for user-specified reactor conditions and liquid/gas feeding strategies. The workflow allows the definition of the growth medium (compatible with MediumFBA), growth-limiting substrates and secreted products along with their Michaelis-Menten uptake kinetics, bioreactor operating conditions such as multiple stages for different liquid/gas feeding policies, dissolution and mass transfer parameters for dissolved gases, and initial conditions for the extracellular variables. Dynamic simulations can be performed for different combinations of the user-defined model parameters and stored for plotting and comparison using the included visualization App.
The following PDF file provides an overview of how STBRsim can be used to determine the optimal time for aerobic-to-anaerobic switch to maximize the production of R-1,2-propanediol production in engineered Escherichia coli. The genome-scale metabolic reconstruction iML1515 available in the BIGG repository was used for this example.
STBRsim has the following requirements:
- Version 2021a or newer version of MATLAB.
- Installed COBRA toolbox for MATLAB.
- A linear program (LP) solver compatible with COBRA. A list of compatible LP solvers is available here.
- Genome-scale metabolic reconstructions compatible with COBRA. STBRsim has been tested with selected reconstructions from the BIGG repository and the Virtual Metabolic Human resource (i.e., AGORA1 models).
STBRsim can be freely downloaded using the link below. The software is distributed under The GNU General Public License v3.0. Based on user feedback, Version 1.1 of STBRsim offers the following improvements over the initial release:
- Fixed coding bug that caused App error when the result list menu value was changed.
- Improved data structures to substantially reduce the size of stored simulation result cases and improve code speed.
STBRsim is a MATLAB application that performs dynamic bioreactor simulations based on genome-scale metabolic reconstructions.
The Zip file should be processed as follows:
- Download and unzip the file using Zip archive software.
- The unzipped file will contain the following files: (1) the main application, STBRsim_ver_1_1.mlappinstall; (2) InSilicoKO designed genome-scale metabolic reconstructions for a R-1,2-propanediol production strain derived from the BIGG model iML1515 and for a propionate production strain derived from the AGORA1 model Bacteroides_thetaiotaomicron_VPI_5482; and (3) saved App states for dynamic simulations of different aerobic-to-anaerobic switch times for R-1,2-propanediol production and for different batch-to-continuous switch strategies for propionate production.
- Save the files in the desired working directory.
- To install the STBRsim application, go to the Apps tab on the main Matlab page and click “Install App”. Select the saved STBRsim_ver_1_1.mlappinstall. The STBRsim application will appear as a new icon in the Apps tab.
- Launch the application by clicking on the icon.
Please contact me by email if you have any questions or feedback about STBRsim.
