Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes
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Kinetic metabolic models provide invaluable insights into cellular metabolism, supporting applications in synthetic biology, metabolic engineering, and systems biology. However, reproducibility and utility of these models hinge on clear and rigorous documentation, standardized annotation, and accessible visualization. This paper presents a workflow for building, annotating, visualizing, and sharing kinetic metabolic models. Our method integrates community standards and open-source tools to ensure reproducibility, interoperability, and user accessibility. This procedure enables researchers to produce reusable and well-documented kinetic models, advancing their role as powerful tools in metabolic research.
An overarching goal of the Department of Energy mission is the efficient deployment and engineering of microbial and plant systems to enable biomass conversion in pursuit of high energy density liquid biofuels. This has spurred the pace at which new organisms are sequenced and annotated. This torrent of genomic information has opened the door to understanding metabolism in not just skeletal pathways and a handful of microorganisms but for truly genome-scale reconstructions derived for hundreds of microbes and plants. Understanding and redirecting metabolism is crucial because metabolic fluxes are unique descriptors of cellular physiology that directly assess the current cellular state and quantify the effect of genetic engineering interventions. At the same time, however, trying to keep pace with the rate of genomic data generation has ushered in a number of modeling and computational challenges related to (i) the automated assembly, testing and correction of genome-scale metabolic models, (ii) metabolic flux elucidation using labeled isotopes, and (iii) comprehensive identification of engineering interventions leading to the desired metabolism redirection.
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The health and well-being of the Nation’s men and women who have served in uniform is the highest priority for the U.S. Department of Veterans Affairs (VA). VA is committed to providing timely access to high-quality, recovery-oriented, evidence-based mental health care that anticipates and responds to Veterans’ needs and supports the reintegration of returning Service members into their communities. VA is working to eliminate suicide among all Veterans by developing and implementing innovative suicide prevention approaches and resources.
The health and well-being of the Nation’s men and women who have served in uniform is the highest priority for the U.S. Department of Veterans Affairs (VA). VA is committed to providing timely access to high-quality, recovery-oriented, evidence-based mental health care that anticipates and responds to Veterans’ needs and supports the reintegration of returning Service members into their communities. VA is working to eliminate suicide among all Veterans by developing and implementing innovative suicide prevention approaches and resources.
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In FY20, the Savannah River National Laboratory (SRNL) was funded by the National Nuclear Security Administration’s Office of Defense Nuclear Non-Proliferation Research and Development (NA-22) to build a machine learning based modeling pipeline that could extract proliferation events of interest from open text-based data sources. As a test case, the research team targeted the identification/fusion of events and indicators that fissile core fabrication would be executed at the Savannah River Site prior to its official announcement in May of 2018. The demonstration prototype proved successful by applying natural language processing and graph theoretical techniques to identify contextual shifts in key words and phrases that acted as indicators that pit production would be carried out at the Savannah River Site up to two years prior to the official announcement.
The health and well-being of the Nation’s men and women who have served in uniform is the highest priority for the U.S. Department of Veterans Affairs (VA). VA is committed to providing timely access to high-quality, recovery-oriented, evidence-based mental health care that anticipates and responds to Veterans’ needs and supports the reintegration of returning Service members into their communities. VA is working to eliminate suicide among all Veterans by developing and implementing innovative suicide prevention approaches and resources.
The U.S. Department of Veterans Affairs (VA) places the health and well-being of our nation’s veterans as its top priority. VA is dedicated to offering timely access to high-quality, evidence-based mental health care that meets the needs of veterans and supports their reintegration into society. One of our core missions is to prevent suicide among veterans through innovative approaches and resources. Health outcomes, including suicide, are typically influenced by both genetics and environmental factors, such as air quality, transportation access, food availability, homelessness, and more. Mental health outcomes are associated with various stressors across socioeconomic, economic, and physical environments. Analyzing the connections between these stressors, covariates, and health outcomes relies on standardized data, which can be integrated into models like the VA’s Recovery Engagement and Coordination for Health, Veterans Enhanced Treatment (REACH VET). The World Health Organization (WHO) defines Environmental Determinants of Health (EDH) as factors like clean air, stable climate, water and sanitation, chemical safety, radiation protection, safe workplaces, sustainable agriculture, healthy urban environments, and nature preservation, all of which are crucial for good health.
The U.S. Department of Veterans Affairs (VA) places the health and well-being of our nation’s veterans as its top priority. VA is dedicated to offering timely access to high-quality, evidence-based mental health care that meets the needs of veterans and supports their reintegration into society. One of our core missions is to prevent suicide among veterans through innovative approaches and resources. Health outcomes, including suicide, are typically influenced by both genetics and environmental factors, such as air quality, transportation access, food availability, homelessness, and more. Mental health outcomes are associated with various stressors across socioeconomic, economic, and physical environments. Analyzing the connections between these stressors, covariates, and health outcomes relies on standardized data, which can be integrated into models like the VA’s Recovery Engagement and Coordination for Health, Veterans Enhanced Treatment (REACH VET). The World Health Organization (WHO) defines Environmental Determinants of Health (EDH) as factors like clean air, stable climate, water and sanitation, chemical safety, radiation protection, safe workplaces, sustainable agriculture, healthy urban environments, and nature preservation, all of which are crucial for good health.
The U.S. Department of Veterans Affairs (VA) places the health and well-being of our nation’s veterans as its top priority. VA is dedicated to offering timely access to high-quality, evidence-based mental health care that meets the needs of veterans and supports their reintegration into society. One of our core missions is to prevent suicide among veterans through innovative approaches and resources. Health outcomes, including suicide, are typically influenced by both genetics and environmental factors, such as air quality, transportation access, food availability, homelessness, and more. Mental health outcomes are associated with various stressors across socioeconomic, economic, and physical environments. Analyzing the connections between these stressors, covariates, and health outcomes relies on standardized data, which can be integrated into models like the VA’s Recovery Engagement and Coordination for Health, Veterans Enhanced Treatment (REACH VET). The World Health Organization (WHO) defines Environmental Determinants of Health (EDH) as factors like clean air, stable climate, water and sanitation, chemical safety, radiation protection, safe workplaces, sustainable agriculture, healthy urban environments, and nature preservation, all of which are crucial for good health.
The specialized ontology for the Carbon Storage Open Database will enable more rapid assignment of appropriate symbology standards for visualization improvements, optimize topical and spatial tagging within keywords, and improve flexibility for utilization in existing data repositories such as EDX. This effort also aims to establish a foundation for utilization of ontologies for organization of other data related to geologic carbon storage in the future.
The U.S. Department of Veterans Affairs (VA) places the health and well-being of our nation’s veterans as its top priority. VA is dedicated to offering timely access to high-quality, evidence-based mental health care that meets the needs of veterans and supports their reintegration into society. One of our core missions is to prevent suicide among veterans through innovative approaches and resources. Health outcomes, including suicide, are typically influenced by both genetics and environmental factors, such as air quality, transportation access, food availability, homelessness, and more. Mental health outcomes are associated with various stressors across socioeconomic, economic, and physical environments. Analyzing the connections between these stressors, covariates, and health outcomes relies on standardized data, which can be integrated into models like the VA’s Recovery Engagement and Coordination for Health, Veterans Enhanced Treatment (REACH VET). The World Health Organization (WHO) defines Environmental Determinants of Health (EDH) as factors like clean air, stable climate, water and sanitation, chemical safety, radiation protection, safe workplaces, sustainable agriculture, healthy urban environments, and nature preservation, all of which are crucial for good health.
Explore the source record for details and available documents.
Explore the source record for details and available documents.
The U.S. Department of Veterans Affairs (VA) places the health and well-being of our nation’s veterans as its top priority. VA is dedicated to offering timely access to high-quality, evidence-based mental health care that meets the needs of veterans and supports their reintegration into society. One of our core missions is to prevent suicide among veterans through innovative approaches and resources.
Explore the source record for details and available documents.