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Machine Learning Takes on Synthetic Biology: Algorithms Can Bioengineer Cells for You

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Tijana Radivojevic (left) and Hector Garcia Martin working on mechanical and statistical modeling, data visualizations, and metabolic maps at the Agile BioFoundry last year. If you've eaten vegan burgers that taste like meat or used synthetic collagen in your beauty routine – both products that are "grown" in the lab – then you've benefited from synthetic biology. It's a field rife with potential, as it allows scientists to design biological systems to specification, such as engineering a microbe to produce a cancer-fighting agent. Yet conventional methods of bioengineering are slow and laborious, with trial and error being the main approach. Now scientists at the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) have developed a new tool that adapts machine learning algorithms to the needs of synthetic biology to guide development systematically.


New AI Speeds Discovery in Synthetic Biology

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Synthetic biology, like artificial intelligence (AI) machine learning, is a relatively modern field that applies emerging technologies to achieve innovation. Now scientists at Lawrence Berkeley National Laboratory (Berkeley Lab) in California merged the two fields by creating a machine learning algorithm for synthetic biology called ART (Automated Recommendation Tool), and published their study a few weeks ago in Nature Communications. Synthetic biology includes the design and formation of novel biological systems or components, and the redesign and production of natural biological systems. Many industries benefit from advances in synthetic biology. Examples include cosmetics, pharmaceutical drugs, vaccines, food and beverage, consumer products, agriculture, delivery plasmids, BioBrick parts, synthetic cells, bioinformatics, DNA synthesis, gene editing, oligonucleotides, chemicals, synthetic genes, and health care.


New Machine Learning Approach Could Accelerate Bioengineering

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A new approach developed by Zak Costello (left) and Hector Garcia Martin brings the the speed and analytic power of machine learning to bioengineering. Scientists from the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) have developed a way to use machine learning to dramatically accelerate the design of microbes that produce biofuel. Their computer algorithm starts with abundant data about the proteins and metabolites in a biofuel-producing microbial pathway, but no information about how the pathway actually works. It then uses data from previous experiments to learn how the pathway will behave. The scientists used the technique to automatically predict the amount of biofuel produced by pathways that have been added to E. coli bacterial cells.


New machine learning approach could accelerate bioengineering

#artificialintelligence

IMAGE: A new approach developed by Zak Costello (left) and Hector Garcia Martin brings the the speed and analytic power of machine learning to bioengineering. Scientists from the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) have developed a way to use machine learning to dramatically accelerate the design of microbes that produce biofuel. Their computer algorithm starts with abundant data about the proteins and metabolites in a biofuel-producing microbial pathway, but no information about how the pathway actually works. It then uses data from previous experiments to learn how the pathway will behave. The scientists used the technique to automatically predict the amount of biofuel produced by pathways that have been added to E. coli bacterial cells.


New machine learning approach could accelerate bioengineering

#artificialintelligence

Their computer algorithm starts with abundant data about the proteins and metabolites in a biofuel-producing microbial pathway, but no information about how the pathway actually works. It then uses data from previous experiments to learn how the pathway will behave. The scientists used the technique to automatically predict the amount of biofuel produced by pathways that have been added to E. coli bacterial cells. The new approach is much faster than the current way to predict the behavior of pathways, and promises to speed up the development of biomolecules for many applications in addition to commercially viable biofuels, such as drugs that fight antibiotic-resistant infections and crops that withstand drought. The research is published May 29 in the journal npj Systems Biology and Applications.