DOE News
    Doe Science news source
    The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
    • 2018-05-29 17:05:12
    • Article ID: 695268

    New Machine Learning Approach Could Accelerate Bioengineering

    Scientists use technique to automatically predict the amount of biofuel produced by microbes

    • Credit: Marilyn Chung , Berkeley Lab

      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.

    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 Nature Systems Biology and Applications.

    In biology, a pathway is a series of chemical reactions in a cell that produce a specific compound. Researchers are exploring ways to re-engineer pathways, and import them from one microbe to another, to harness nature’s toolkit to improve medicine, energy, manufacturing, and agriculture. And thanks to new synthetic biology capabilities, such as the gene-editing tool CRISPR-Cas9, scientists can conduct this research at a precision like never before.

    “But there’s a significant bottleneck in the development process,” said Hector Garcia Martin, group lead at the DOE Agile BioFoundry and director of Quantitative Metabolic Modeling at the Joint BioEnergy Institute (JBEI), a DOE Bioenergy Research Center funded by DOE’s Office of Science and led by Berkeley Lab. The research was performed by Zak Costello (also with the Agile BioFoundry and JBEI) under the direction of Garcia Martin. Both researchers are also in Berkeley Lab’s Biological Systems and Engineering Division.

    “It’s very difficult to predict how a pathway will behave when it’s re-engineered. Trouble-shooting takes up 99% of our time. Our approach could significantly shorten this step and become a new way to guide bioengineering efforts,” Garcia Martin added.

    The current way to predict a pathway’s dynamics requires a maze of differential equations that describe how the components in the system change over time. Subject-area experts develop these “kinetic models” over several months, and the resulting predictions don’t always match experimental results. 

    Machine learning, however, uses data to train a computer algorithm to make predictions. The algorithm learns a system’s behavior by analyzing data from related systems. This allows scientists to quickly predict the function of a pathway even if its mechanisms are poorly understood — as long as there are enough data to work with.

    The scientists tested their technique on pathways added to E. coli cells. One pathway is designed to produce a bio-based jet fuel called limonene; the other produces a gasoline replacement called isopentenol. Previous experiments at JBEI yielded a trove of data related to how different versions of the pathways function in various E. coli strains. Some of the strains have a pathway that produces small amounts of either limonene or isopentenol, while other strains have a version that produces large amounts of the biofuels.

    The researchers fed this data into their algorithm. Then machine learning took over: The algorithm taught itself how the concentrations of metabolites in these pathways change over time, and how much biofuel the pathways produce. It learned these dynamics by analyzing data from the two experimentally known pathways that produce small and large amounts of biofuels. 

    The algorithm used this knowledge to predict the behavior of a third set of “mystery” pathways the algorithm had never seen before. It accurately predicted the biofuel-production profiles for the mystery pathways, including that the pathways produce a medium amount of fuel. In addition, the machine learning-derived prediction outperformed kinetic models.   

    “And the more data we added, the more accurate the predictions became,” said Garcia Martin. “This approach could expedite the time it takes to design new biomolecules. A project that today takes ten years and a team of experts could someday be handled by a summer student.”

    The work was part of the DOE Agile BioFoundry, supported by DOE’s Office of Energy Efficiency and Renewable Energy, and the Joint BioEnergy Institute, supported by DOE’s Office of Science. 


    • other-fb
    • other-tw
    X
    X
    X
    • Filters

    • × Clear Filters
    Do Alpha Particle Condensates Exist in Oxygen Nuclei?

    Do Alpha Particle Condensates Exist in Oxygen Nuclei?

    Yes. Such condensates, analogous to those in carbon-12, in heavier nuclei could change how we describe certain elements.

    Not All Ions in Tokamaks Go with the Flow

    Not All Ions in Tokamaks Go with the Flow

    Spectroscopic measurements reveal that main ions flow much faster than impurities at the edge of fusion-relevant plasmas.

    Researchers watch molecules in a light-triggered catalyst ring 'like an ensemble of bells'

    Researchers watch molecules in a light-triggered catalyst ring 'like an ensemble of bells'

    An international team has used an X-ray laser at the Department of Energy's SLAC National Accelerator Laboratory to get an incredibly detailed look at what happens to the structure of a model photocatalyst when it absorbs light.

    Measuring the Impossible: X-ray Photoelectron Spectroscopy of Hydrogen and Helium

    Measuring the Impossible: X-ray Photoelectron Spectroscopy of Hydrogen and Helium

    The two most abundant elements in the universe, hydrogen and helium, were previously thought to be impossible to measure by X-ray photoelectron spectroscopy.

    New Model Sheds Light on Key Physics of Magnetic Islands that Can Halt Fusion Reactions

    New Model Sheds Light on Key Physics of Magnetic Islands that Can Halt Fusion Reactions

    Surprisingly, a magnetic island does not necessarily perturb the plasma current in a dangerous way and destroy fusion performance.

    Correlated Nucleons May Solve 35-Year-Old Mystery

    Correlated Nucleons May Solve 35-Year-Old Mystery

    A careful re-analysis of data taken at the Department of Energy's Thomas Jefferson National Accelerator Facility has revealed a possible link between correlated protons and neutrons in the nucleus and a 35-year-old mystery. The data have led to the extraction of a universal function that describes the EMC Effect, the once-shocking discovery that quarks inside nuclei have lower average momenta than predicted, and supports an explanation for the effect. The study has been published in the journal Nature.

    Early "Fossils" Formed by Tectonics, not Life

    Early "Fossils" Formed by Tectonics, not Life

    The 3.7-billion-year-old structures were considered the first evidence for life on the planet; new evidence suggests differently.

    High-Energy X-Ray Bursts from Low-Energy Plasma

    High-Energy X-Ray Bursts from Low-Energy Plasma

    Scientists discover why solar flares produce X-rays; a few electrons avoid collisions and accelerate to produce a microsecond burst.

    Taking Diamond Qubits for a Spin

    Taking Diamond Qubits for a Spin

    Scientists use implanted silicon ions and electricity to increase the spin time of quantum bits, moving closer to the tech needed for quantum networks.

    Story Tips From the Department of Energy's Oak Ridge National Laboratory, February 18, 2019

    Story Tips From the Department of Energy's Oak Ridge National Laboratory, February 18, 2019

    ORNL neutrons investigate novel carbon capture crystals; gleaning valuable Twitter data to quickly map power outages; ORNL's lightweight, heat-shielding graphite foam test yields positive results in fusion reactors; open source software scales up analysis of motor designs to run on supercomputers


    • Filters

    • × Clear Filters
    DOE launches its first lithium-ion battery recycling R&D center: ReCell

    DOE launches its first lithium-ion battery recycling R&D center: ReCell

    The launch of the Energy Department's first lithium-ion battery recycling center, called the ReCell Center, will help the United States grow a globally competitive recycling industry and reduce our reliance on foreign sources of battery materials.

    James Wishart Awarded Maria Skłodowska-Curie Medal

    James Wishart Awarded Maria Skłodowska-Curie Medal

    James Wishart, a chemist at the U.S. Department of Energy's (DOE) Brookhaven National Laboratory, has been awarded the Maria Skłodowska-Curie Medal by the Polish Radiation Research Society (PRRS). The award recognizes his distinguished achievements in the field of radiation chemistry and his long-lasting and productive interactions with Polish scientists.

    Lynbrook High wins 2019 SLAC Regional Science Bowl competition

    Lynbrook High wins 2019 SLAC Regional Science Bowl competition

    Twenty-eight teams from 17 Bay Area high schools faced off Feb. 9 in the SLAC Regional DOE Science Bowl, a series of fast-paced question-and-answer matches that test knowledge in biology, chemistry, physics, earth and space sciences, energy and math. The competition is hosted annually by the Department of Energy's SLAC National Accelerator Laboratory.

    UNLV Among 11 Teams Worldwide To Compete in 2020 Solar Decathlon

    UNLV Among 11 Teams Worldwide To Compete in 2020 Solar Decathlon

    Students to build sustainable home of healing for military veterans for U.S. Department of Energy contest; UNLV competed in 2013 and 2017.

    Three Brookhaven Scientists Named Highly Cited Researchers

    Three Brookhaven Scientists Named Highly Cited Researchers

    Three scientists from the U.S. Department of Energy's (DOE) Brookhaven National Laboratory have been named to the 2018 Highly Cited Researchers List, which recognizes influential researchers whose work ranks in the top one percent of the world's most-cited scientific papers. Brookhaven's Radoslav Adzic, Mark Hybertsen, and Xiao-Qing Yang are among only 4,000 researchers from around the world whom achieved the distinction in 2018.

    New tools in transportation

    New tools in transportation

    A new version of the AFLEET Tool from the U.S. Department of Energy's (DOE) Argonne National Laboratory calculates and compares the costs and environmental benefits of a broad range of alternative fuel technologies. Covering 18 fuel/vehicle technologies, AFLEET Online offers an easy-to-use web-based platform.

    Remote-Control Plasma Physics Experiment is Named One of Top Webcams of 2018

    Remote-Control Plasma Physics Experiment is Named One of Top Webcams of 2018

    EarthCam names remote-control experiment at PPPL one of 25 most interesting Webcams of 2018.

    Jefferson Lab Scientist Awarded Distinguished Lectureship

    Jefferson Lab Scientist Awarded Distinguished Lectureship

    Cynthia Keppel, leader of Jefferson Lab's Halls A&C, has been honored with the APS 2019 Distinguished Lectureship Award on the Applications of Physics.

    Journal Special Issues Honor Chemists Radoslav Adzic and Jan Hrbek

    Journal Special Issues Honor Chemists Radoslav Adzic and Jan Hrbek

    The Journal of the Electrochemical Society and Surface Science recognized the contributions of Brookhaven Lab chemists Radoslav Adzic and Jan Hrbek to electrocatalysis and catalysis.

    Argonne scientist elected as SAE Fellow

    Argonne scientist elected as SAE Fellow

    Scientist Michael Wang from the U.S. Department of Energy's (DOE) Argonne National Laboratory was recently inducted as a Fellow of the professional engineering organization SAE (Society of Automotive Engineers). The organization reserves this prestigious grade of membership for thosewho have made significant contributions to mobility technology and have demonstrated leadership in their field.


    • Filters

    • × Clear Filters
    Do Alpha Particle Condensates Exist in Oxygen Nuclei?

    Do Alpha Particle Condensates Exist in Oxygen Nuclei?

    Yes. Such condensates, analogous to those in carbon-12, in heavier nuclei could change how we describe certain elements.

    Not All Ions in Tokamaks Go with the Flow

    Not All Ions in Tokamaks Go with the Flow

    Spectroscopic measurements reveal that main ions flow much faster than impurities at the edge of fusion-relevant plasmas.

    Measuring the Impossible: X-ray Photoelectron Spectroscopy of Hydrogen and Helium

    Measuring the Impossible: X-ray Photoelectron Spectroscopy of Hydrogen and Helium

    The two most abundant elements in the universe, hydrogen and helium, were previously thought to be impossible to measure by X-ray photoelectron spectroscopy.

    New Model Sheds Light on Key Physics of Magnetic Islands that Can Halt Fusion Reactions

    New Model Sheds Light on Key Physics of Magnetic Islands that Can Halt Fusion Reactions

    Surprisingly, a magnetic island does not necessarily perturb the plasma current in a dangerous way and destroy fusion performance.

    Early "Fossils" Formed by Tectonics, not Life

    Early "Fossils" Formed by Tectonics, not Life

    The 3.7-billion-year-old structures were considered the first evidence for life on the planet; new evidence suggests differently.

    High-Energy X-Ray Bursts from Low-Energy Plasma

    High-Energy X-Ray Bursts from Low-Energy Plasma

    Scientists discover why solar flares produce X-rays; a few electrons avoid collisions and accelerate to produce a microsecond burst.

    Taking Diamond Qubits for a Spin

    Taking Diamond Qubits for a Spin

    Scientists use implanted silicon ions and electricity to increase the spin time of quantum bits, moving closer to the tech needed for quantum networks.

    Newly Discovered Design Rules Lead to Better Fuel Cell Catalyst

    Newly Discovered Design Rules Lead to Better Fuel Cell Catalyst

    Optimized oxides made from common metals use less energy and show the potential of new design approach.

    Too Close for Comfort: Nanoparticles Need Some Space to Transfer Energy

    Too Close for Comfort: Nanoparticles Need Some Space to Transfer Energy

    Particle crowding interferes with moving energy efficiently along promising molecular chains.

    Atomic Snapshots of Photosynthesis

    Atomic Snapshots of Photosynthesis

    Scientists catch details with atomic resolution, potentially helping design systems to use sunlight and water to produce fuels.


    Spotlight

    Lynbrook High wins 2019 SLAC Regional Science Bowl competition
    Wednesday February 13, 2019, 02:05 PM

    Lynbrook High wins 2019 SLAC Regional Science Bowl competition

    SLAC National Accelerator Laboratory

    Equipping the next generation for a technological revolution
    Thursday January 24, 2019, 01:05 PM

    Equipping the next generation for a technological revolution

    Argonne National Laboratory

    Chemistry intern inspired by Argonne's real-world science
    Friday January 18, 2019, 05:05 PM

    Chemistry intern inspired by Argonne's real-world science

    Argonne National Laboratory

    Chasing a supernova
    Friday January 18, 2019, 04:05 PM

    Chasing a supernova

    Argonne National Laboratory

    Argonne intern streamlines the beamline
    Tuesday January 08, 2019, 02:05 PM

    Argonne intern streamlines the beamline

    Argonne National Laboratory

    Research on Light-Matter Interaction Could Lead to Improved Electronic and Optoelectronic Devices
    Thursday October 11, 2018, 04:00 PM

    Research on Light-Matter Interaction Could Lead to Improved Electronic and Optoelectronic Devices

    Rensselaer Polytechnic Institute (RPI)

    Innovating Our Energy Future
    Wednesday October 03, 2018, 07:05 PM

    Innovating Our Energy Future

    Oregon State University, College of Engineering

    Physics graduate student takes her thesis research to a Department of Energy national lab
    Tuesday October 02, 2018, 03:05 PM

    Physics graduate student takes her thesis research to a Department of Energy national lab

    University of Alabama at Birmingham

    Friday September 21, 2018, 01:05 PM

    "Model" students enjoy Argonne campus life

    Argonne National Laboratory

    Writing Code for a More Skilled and Diverse STEM Workforce
    Thursday September 06, 2018, 01:05 PM

    Writing Code for a More Skilled and Diverse STEM Workforce

    Brookhaven National Laboratory

    New graduate student summer school launches at Princeton Plasma Physics Laboratory
    Tuesday September 04, 2018, 11:30 AM

    New graduate student summer school launches at Princeton Plasma Physics Laboratory

    Princeton Plasma Physics Laboratory

    The Gridlock State
    Friday August 31, 2018, 06:05 PM

    The Gridlock State

    California State University (CSU) Chancellor's Office

    Meet Jasmine Hatcher and Trishelle Copeland-Johnson
    Friday August 31, 2018, 02:05 PM

    Meet Jasmine Hatcher and Trishelle Copeland-Johnson

    Brookhaven National Laboratory

    Argonne hosts Modeling, Experimentation and Validation Summer School
    Friday August 24, 2018, 11:05 AM

    Argonne hosts Modeling, Experimentation and Validation Summer School

    Argonne National Laboratory

    Students affected by Hurricane Maria bring their research to SLAC
    Wednesday August 22, 2018, 01:05 PM

    Students affected by Hurricane Maria bring their research to SLAC

    SLAC National Accelerator Laboratory

    Brookhaven Lab Pays Tribute to 2018 Summer Interns
    Wednesday August 22, 2018, 10:05 AM

    Brookhaven Lab Pays Tribute to 2018 Summer Interns

    Brookhaven National Laboratory

    Changing How Buildings Are Made
    Monday August 20, 2018, 12:05 PM

    Changing How Buildings Are Made

    Washington University in St. Louis

    CSUMB Selected to Host Architecture at Zero Competition in 2019
    Thursday August 16, 2018, 12:05 PM

    CSUMB Selected to Host Architecture at Zero Competition in 2019

    California State University, Monterey Bay

    Department of Energy Invests $64 Million in Advanced Nuclear Technology
    Friday July 20, 2018, 03:00 PM

    Department of Energy Invests $64 Million in Advanced Nuclear Technology

    Rensselaer Polytechnic Institute (RPI)

    Professor Miao Yu Named the Priti and Mukesh Chatter '82 Career Development Professor
    Thursday July 19, 2018, 05:00 PM

    Professor Miao Yu Named the Priti and Mukesh Chatter '82 Career Development Professor

    Rensselaer Polytechnic Institute (RPI)

    2018 RHIC & AGS Annual Users' Meeting: 'Illuminating the QCD Landscape'
    Tuesday July 03, 2018, 11:05 AM

    2018 RHIC & AGS Annual Users' Meeting: 'Illuminating the QCD Landscape'

    Brookhaven National Laboratory

    Argonne welcomes <em>The Martian</em> author Andy Weir
    Friday June 29, 2018, 06:05 PM

    Argonne welcomes The Martian author Andy Weir

    Argonne National Laboratory

    Creating STEM Knowledge and Innovations to Solve Global Issues Like Water, Food, and Energy
    Monday June 18, 2018, 09:55 AM

    Creating STEM Knowledge and Innovations to Solve Global Issues Like Water, Food, and Energy

    Illinois Mathematics and Science Academy (IMSA)

    Professor Emily Liu Receives $1.8 Million DoE Award for Solar Power Systems Research
    Friday June 15, 2018, 10:00 AM

    Professor Emily Liu Receives $1.8 Million DoE Award for Solar Power Systems Research

    Rensselaer Polytechnic Institute (RPI)

    Celebrating 40 years of empowerment in science
    Thursday June 07, 2018, 03:05 PM

    Celebrating 40 years of empowerment in science

    Argonne National Laboratory

    Introducing Graduate Students Across the Globe to Photon Science
    Monday May 07, 2018, 10:30 AM

    Introducing Graduate Students Across the Globe to Photon Science

    Brookhaven National Laboratory

    Students from Massachusetts and Washington Win DOE's 28th National Science Bowl(r)
    Wednesday May 02, 2018, 04:05 PM

    Students from Massachusetts and Washington Win DOE's 28th National Science Bowl(r)

    Department of Energy, Office of Science

    The Race for Young Scientific Minds
    Thursday April 12, 2018, 07:05 PM

    The Race for Young Scientific Minds

    Argonne National Laboratory

    Q&A: Al Ashley Reflects on His Efforts to Diversify SLAC and Beyond
    Wednesday March 14, 2018, 02:05 PM

    Q&A: Al Ashley Reflects on His Efforts to Diversify SLAC and Beyond

    SLAC National Accelerator Laboratory

    Insights on Innovation in Energy, Humanitarian Aid Highlight UVA Darden's Net Impact Week
    Thursday February 15, 2018, 12:05 PM

    Insights on Innovation in Energy, Humanitarian Aid Highlight UVA Darden's Net Impact Week

    University of Virginia Darden School of Business

    Ivy League Graduate, Writer and Activist with Dyslexia Visits CSUCI to Reframe the Concept of Learning Disabilities
    Friday February 09, 2018, 11:05 AM

    Ivy League Graduate, Writer and Activist with Dyslexia Visits CSUCI to Reframe the Concept of Learning Disabilities

    California State University, Channel Islands

    Photographer Adam Nadel Selected as Fermilab's New Artist-in-Residence for 2018
    Wednesday January 17, 2018, 12:05 PM

    Photographer Adam Nadel Selected as Fermilab's New Artist-in-Residence for 2018

    Fermi National Accelerator Laboratory (Fermilab)

    Fermilab Computing Partners with Argonne, Local Schools for Hour of Code
    Wednesday January 17, 2018, 12:05 PM

    Fermilab Computing Partners with Argonne, Local Schools for Hour of Code

    Fermi National Accelerator Laboratory (Fermilab)

    Q&A: Sam Webb Teaches X-Ray Science from a Remote Classroom
    Wednesday December 20, 2017, 01:05 PM

    Q&A: Sam Webb Teaches X-Ray Science from a Remote Classroom

    SLAC National Accelerator Laboratory

    The Future of Today's Electric Power Systems
    Monday December 18, 2017, 01:05 PM

    The Future of Today's Electric Power Systems

    Rensselaer Polytechnic Institute (RPI)

    Supporting the Development of Offshore Wind Power Plants
    Monday December 18, 2017, 12:05 PM

    Supporting the Development of Offshore Wind Power Plants

    Rensselaer Polytechnic Institute (RPI)

    Stairway to Science
    Tuesday October 03, 2017, 01:05 PM

    Stairway to Science

    Argonne National Laboratory

    After-School Energy Rush
    Thursday September 28, 2017, 12:05 PM

    After-School Energy Rush

    Argonne National Laboratory

    Bringing Diversity Into Computational Science Through Student Outreach
    Thursday September 28, 2017, 10:05 AM

    Bringing Diversity Into Computational Science Through Student Outreach

    Brookhaven National Laboratory

    From Science to Finance: SLAC Summer Interns Forge New Paths in STEM
    Thursday September 21, 2017, 03:05 PM

    From Science to Finance: SLAC Summer Interns Forge New Paths in STEM

    SLAC National Accelerator Laboratory

    Students Discuss 'Cosmic Opportunities' at 45th Annual SLAC Summer Institute
    Thursday September 07, 2017, 02:05 PM

    Students Discuss 'Cosmic Opportunities' at 45th Annual SLAC Summer Institute

    SLAC National Accelerator Laboratory

    Binghamton University Opens $70 Million Smart Energy Building
    Thursday August 31, 2017, 05:05 PM

    Binghamton University Opens $70 Million Smart Energy Building

    Binghamton University, State University of New York

    Widening Horizons for High Schoolers with Code
    Wednesday August 23, 2017, 05:05 PM

    Widening Horizons for High Schoolers with Code

    Argonne National Laboratory

    Rensselaer Polytechnic Institute Graduates Urged to Embrace Change at 211th Commencement
    Saturday May 20, 2017, 12:05 PM

    Rensselaer Polytechnic Institute Graduates Urged to Embrace Change at 211th Commencement

    Rensselaer Polytechnic Institute (RPI)

    ORNL, University of Tennessee Launch New Doctoral Program in Data Science
    Monday May 15, 2017, 01:05 PM

    ORNL, University of Tennessee Launch New Doctoral Program in Data Science

    Oak Ridge National Laboratory





    Showing results

    0-4 Of 2215