Monthly Archives: August 2018

Techno-Economic Analysis

Overview:  Techno-economic analysis (TEA) is a powerful tool that quantifies the impact that research and development have on the economics of an integrated process. TEAs are performed to evaluate the potential economic viability of a process. Additionally, TEAs can be used to 1) identify cost drivers of an integrated design and help set specific targets/metrics […]

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Life-Cycle Analysis – GREET® model -Greenhouse gases, Regulated Emissions, and Energy use in Transportation

Overview:  The GREET model is used to evaluate environmental impacts of advanced vehicle technologies, alternative transportation fuels, and new bio-derived chemicals.  With GREET, one can estimate 1) energy consumption including total energy (energy in non-renewable and renewable sources) and fossil fuels (petroleum, natural gas, and coal), 2) water consumption, 3) greenhouse gases (GHG) emissions, and […]

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Multiscale Bioreactor Cultivation

Overview:  The ABF has multiple scales of integrated bioreactor cultivation equipment ranging from the microscale BioLector Pro systems (2 mL cultivation volumes), more than 30 0.5-L fully controlled bioreactors, multiple 2 L, 5 L, and 10 L scales, up to 100, 1,000, and 9,000 L reactors in the Integrated Biorefinery Refinery Facility that opérate on […]

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Fermentation Scale-up Recovery and Purification

Overview:  Fermentation in bioreactors offer environments that are substantially different from shake flask environments. Strains that are optimized through the design-build-test-learn cycle will be subjected to these unexpected environments and thereby, most often, lead to unanticipated results. At the ABPDU, we have been resolving this disparity between lab-scale and a commercially relevant scale of biomanufacturing. […]

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Regulatory Modeling

Overview: Bacteria are not simply passive consumers of nutrients or merely steady-state systems. Rather bacteria are active participants in their environments, collecting information from their surroundings, processing and using that information to adapt their behavior and optimize survival. The bacterial regulome is the set of physical interactions that link environmental information to the expression of […]

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Pan Genome Analysis

Overview:  Pan-genomic analysis leverages recent advances in the ability to routinely sequence and annotate whole genomes. No longer restricted to considering one genome at a time, the capability now exists to study multiple genomes from the same taxonomic grouping and observe how genomes change with evolutionary time and with adaptations to new environmental niches. It […]

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Metabolic Flux Analysis

Overview: Building and employing models for learning form integrated systems biology data is an important capability within the ABF. Pathway genome databases are developed for host strains and used in the building of metabolic models for quantitative analysis of in vivo carbon fluxes in metabolic networks, i.e. intracellular activities of enzymes and pathways. 13C Metabolic […]

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Mechanistic Models of Metabolic Flux

Overview:  Two-scale 13C Metabolic Flux Analysis (TS-13C MFA) measures intracellular metabolic fluxes by using data obtained from 13C substrate labeling experiments and genome-scale models. Metabolic fluxes map how carbon and electrons flow through metabolism to enable cell function and provide the best available insights to guide metabolic engineering. This is the only 13C labeling technique that has been […]

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Machine Learning

Overview:  Often we do not know all the biological mechanisms required to predict the behavior of a bioengineered system through mechanistic modeling (e.g. how does induction time or amount affect flux through a pathway). In those cases, a data-intensive, statistics-based approach can still predict bioengineered systems to the degree required to drive metabolic engineering efforts. […]

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Deep Learning

Overview: The amount of information that can be collected by a multi-omics analysis of fermentation (e.g. combined metabolomics, transcriptomics, and proteomics experiments) or the information that can be collected from sensors in an industrial bioprocess can easily amount to terabytes of data.  Accommodating this massive outpouring of information is one of the defining challenges for […]

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