In Silico Fermentation offers unique capabilities for developing MATLAB applications to standardize and simplify computational modeling workflows. We have unique expertise in app development for metabolic modeling applications involving genome-scale reconstructions and linear programming methods. To date, we have freely released five research apps and two educational apps that provide easily navigated workflows to accelerate the use of metabolic modeling by non-experts. Despite the generality of these free apps, our experience suggests that many biotechnology and biomedical companies have more specialized workflows that can benefit from strategic app development. We can work with industrial partners to conceptualize, design, construct, test and commission apps for a wide range of problems in the domains of microbial metabolic modeling and bioreactor process simulation.
Microbial Metabolic Modeling
We provide established expertise in developing MATLAB apps for implementation of metabolic modeling workflows. These capabilities are demonstrated by our freely released apps for growth medium design and flux balance analysis, computational design of knockout strains for metabolite overproduction, synthetic microbial community simulation, and bacterial microbiome simulation using read data. We can strategically modify any of these apps or develop new apps from scratch to meet the requirements of your organization. Working closely with your scientists and engineers, we can conduct iterative build and test cycles to ensure that the delivered app will satisfy your technical requirements.
Fermentation Process Simulation
We offer unique capabilities for developing apps that integrate genome-scale metabolic reconstructions into bioreactor process simulations. As demonstrated by our freely distributed stirred-tank bioreactor app STBRsim, we combine steady-state models of intracellular metabolism with dynamic mass balance equations of the extracellular environment to allow time-resolved predictions of key fermentation parameters including biomass, nutrient and product concentrations, and intracellular fluxes. We can modify STBRsim to meet your requirements or develop new apps for different processes, such as bubble column bioreactors for gas fermentation. These apps can accelerate the innovation cycle from strain engineering to production scaleup.
Please reach out to discuss your app development needs.
