Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress

Mikaela Cashman; Verónica G.Melesse Vergara; John Lagergren; Matthew Lane; Jean Merlet; Mikaela Atkinson; Jared Streich; Christopher Bradburne; Raina Plowright; Wayne Joubert; Daniel Jacobson

doi:10.1145/3592979.3593402

Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress

Mikaela Cashman, Verónica G.Melesse Vergara, John Lagergren, Matthew Lane, Jean Merlet, Mikaela Atkinson, Jared Streich, Christopher Bradburne, Raina Plowright, Wayne Joubert, Daniel Jacobson

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

In this work we identify changes in high-resolution zones across the globe linked by environmental similarity that have implications for agriculture, bioenergy, and zoonosis. We refine exhaustive vector comparison methods with improved similarity metrics as well as provide multiple methods of amalgamation across 744 months of climatic data. The results of the vector comparison are captured as networks which are analyzed using static and longitudinal comparison methods to reveal locations around the globe experiencing dramatic changes in abiotic stress. Specifically we (i) incorporate updated similarity scores and provide a comparison between similarity metrics, (ii) implement a new feature for resource optimization, (iii) compare an agglomerative view to a longitudinal view, (iv) compare across 2-way and 3-way vector comparisons, (v) implement a new form of analysis, and (vi) demonstrate biological applications and discuss implications across a diverse set of species distributions by detecting changes that affect their habitats. Species of interest are related to agriculture (e.g., coffee, wine, chocolate), bioenergy (e.g., poplar, switchgrass, pennycress), as well as those living in zones of concern for zoonotic spillover that may lead to pandemics (e.g., eucalyptus, flying foxes).

Original language	English
Title of host publication	Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2023
Publisher	Association for Computing Machinery, Inc
ISBN (Electronic)	9798400701900
DOIs	https://doi.org/10.1145/3592979.3593402
State	Published - Jun 26 2023
Event	2023 Platform for Advanced Scientific Computing Conference, PASC 2023 - Davos, Switzerland Duration: Jun 26 2023 → Jun 28 2023

Publication series

Name	Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2023

Conference

Conference	2023 Platform for Advanced Scientific Computing Conference, PASC 2023
Country/Territory	Switzerland
City	Davos
Period	06/26/23 → 06/28/23

Funding

This research used resources of the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC05-00OR22725. Funding was also provided by the Integrated Pennycress Resilience Project (IPReP), the Center for Bioenergy Innovation (CBI), and the DOE Systems Biology Knowledgebase (KBase), all of which are supported by the Genomic Sciences Program of Office of Biological and Environmental Research in the DOE Office of Science. KBase is funded under Award Numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886. The authors would also like to acknowledge funding from the U.S. National Science Foundation (EF-2133763). This manuscript has been co-authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government This research used resources of the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC05-00OR22725. Funding was also provided by the Integrated Pennycress Resilience Project (IPReP), the Center for Bioenergy Innovation (CBI), and the DOE Systems Biology Knowledgebase (KBase), all of which are supported by the Genomic Sciences Program of Office of Biological and Environmental Research in the DOE Office of Science. KBase is funded under Award Numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DEAC05- 00OR22725, and DE-AC02-98CH10886. The authors would also like to acknowledge funding from the U.S. National Science Foundation (EF-2133763). This manuscript has been co-authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).

Keywords

climate analysis
high performance computing

Access to Document

10.1145/3592979.3593402

Cite this

Cashman, M., Vergara, V. G. M., Lagergren, J., Lane, M., Merlet, J., Atkinson, M., Streich, J., Bradburne, C., Plowright, R., Joubert, W., & Jacobson, D. (2023). Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress. In Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2023 (Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2023). Association for Computing Machinery, Inc. https://doi.org/10.1145/3592979.3593402

Cashman, Mikaela ; Vergara, Verónica G.Melesse ; Lagergren, John et al. / Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress. Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2023. Association for Computing Machinery, Inc, 2023. (Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2023).

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title = "Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress",

abstract = "In this work we identify changes in high-resolution zones across the globe linked by environmental similarity that have implications for agriculture, bioenergy, and zoonosis. We refine exhaustive vector comparison methods with improved similarity metrics as well as provide multiple methods of amalgamation across 744 months of climatic data. The results of the vector comparison are captured as networks which are analyzed using static and longitudinal comparison methods to reveal locations around the globe experiencing dramatic changes in abiotic stress. Specifically we (i) incorporate updated similarity scores and provide a comparison between similarity metrics, (ii) implement a new feature for resource optimization, (iii) compare an agglomerative view to a longitudinal view, (iv) compare across 2-way and 3-way vector comparisons, (v) implement a new form of analysis, and (vi) demonstrate biological applications and discuss implications across a diverse set of species distributions by detecting changes that affect their habitats. Species of interest are related to agriculture (e.g., coffee, wine, chocolate), bioenergy (e.g., poplar, switchgrass, pennycress), as well as those living in zones of concern for zoonotic spillover that may lead to pandemics (e.g., eucalyptus, flying foxes).",

keywords = "climate analysis, high performance computing",

author = "Mikaela Cashman and Vergara, {Ver{\'o}nica G.Melesse} and John Lagergren and Matthew Lane and Jean Merlet and Mikaela Atkinson and Jared Streich and Christopher Bradburne and Raina Plowright and Wayne Joubert and Daniel Jacobson",

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doi = "10.1145/3592979.3593402",

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Cashman, M, Vergara, VGM, Lagergren, J, Lane, M, Merlet, J, Atkinson, M, Streich, J, Bradburne, C, Plowright, R, Joubert, W & Jacobson, D 2023, Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress. in Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2023. Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2023, Association for Computing Machinery, Inc, 2023 Platform for Advanced Scientific Computing Conference, PASC 2023, Davos, Switzerland, 06/26/23. https://doi.org/10.1145/3592979.3593402

Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress. / Cashman, Mikaela; Vergara, Verónica G.Melesse; Lagergren, John et al.
Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2023. Association for Computing Machinery, Inc, 2023. (Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2023).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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T1 - Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress

AU - Cashman, Mikaela

AU - Vergara, Verónica G.Melesse

AU - Lagergren, John

AU - Lane, Matthew

AU - Merlet, Jean

AU - Atkinson, Mikaela

AU - Streich, Jared

AU - Bradburne, Christopher

AU - Plowright, Raina

AU - Joubert, Wayne

AU - Jacobson, Daniel

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N2 - In this work we identify changes in high-resolution zones across the globe linked by environmental similarity that have implications for agriculture, bioenergy, and zoonosis. We refine exhaustive vector comparison methods with improved similarity metrics as well as provide multiple methods of amalgamation across 744 months of climatic data. The results of the vector comparison are captured as networks which are analyzed using static and longitudinal comparison methods to reveal locations around the globe experiencing dramatic changes in abiotic stress. Specifically we (i) incorporate updated similarity scores and provide a comparison between similarity metrics, (ii) implement a new feature for resource optimization, (iii) compare an agglomerative view to a longitudinal view, (iv) compare across 2-way and 3-way vector comparisons, (v) implement a new form of analysis, and (vi) demonstrate biological applications and discuss implications across a diverse set of species distributions by detecting changes that affect their habitats. Species of interest are related to agriculture (e.g., coffee, wine, chocolate), bioenergy (e.g., poplar, switchgrass, pennycress), as well as those living in zones of concern for zoonotic spillover that may lead to pandemics (e.g., eucalyptus, flying foxes).

AB - In this work we identify changes in high-resolution zones across the globe linked by environmental similarity that have implications for agriculture, bioenergy, and zoonosis. We refine exhaustive vector comparison methods with improved similarity metrics as well as provide multiple methods of amalgamation across 744 months of climatic data. The results of the vector comparison are captured as networks which are analyzed using static and longitudinal comparison methods to reveal locations around the globe experiencing dramatic changes in abiotic stress. Specifically we (i) incorporate updated similarity scores and provide a comparison between similarity metrics, (ii) implement a new feature for resource optimization, (iii) compare an agglomerative view to a longitudinal view, (iv) compare across 2-way and 3-way vector comparisons, (v) implement a new form of analysis, and (vi) demonstrate biological applications and discuss implications across a diverse set of species distributions by detecting changes that affect their habitats. Species of interest are related to agriculture (e.g., coffee, wine, chocolate), bioenergy (e.g., poplar, switchgrass, pennycress), as well as those living in zones of concern for zoonotic spillover that may lead to pandemics (e.g., eucalyptus, flying foxes).

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M3 - Conference contribution

AN - SCOPUS:85166199052

T3 - Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2023

BT - Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2023

PB - Association for Computing Machinery, Inc

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Cashman M, Vergara VGM, Lagergren J, Lane M, Merlet J, Atkinson M et al. Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress. In Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2023. Association for Computing Machinery, Inc. 2023. (Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2023). doi: 10.1145/3592979.3593402

Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress

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