Literature DB >> 33075199

Beyond ecosystem modeling: A roadmap to community cyberinfrastructure for ecological data-model integration.

Istem Fer1, Anthony K Gardella2,3, Alexey N Shiklomanov4, Eleanor E Campbell5, Elizabeth M Cowdery2, Martin G De Kauwe6,7,8, Ankur Desai9, Matthew J Duveneck10, Joshua B Fisher11, Katherine D Haynes12, Forrest M Hoffman13,14, Miriam R Johnston15, Rob Kooper16, David S LeBauer17, Joshua Mantooth18, William J Parton19, Benjamin Poulter4, Tristan Quaife20, Ann Raiho21, Kevin Schaefer22, Shawn P Serbin23, James Simkins24, Kevin R Wilcox25, Toni Viskari1, Michael C Dietze2.   

Abstract

In an era of rapid global change, our ability to understand and predict Earth's natural systems is lagging behind our ability to monitor and measure changes in the biosphere. Bottlenecks to informing models with observations have reduced our capacity to fully exploit the growing volume and variety of available data. Here, we take a critical look at the information infrastructure that connects ecosystem modeling and measurement efforts, and propose a roadmap to community cyberinfrastructure development that can reduce the divisions between empirical research and modeling and accelerate the pace of discovery. A new era of data-model integration requires investment in accessible, scalable, and transparent tools that integrate the expertise of the whole community, including both modelers and empiricists. This roadmap focuses on five key opportunities for community tools: the underlying foundations of community cyberinfrastructure; data ingest; calibration of models to data; model-data benchmarking; and data assimilation and ecological forecasting. This community-driven approach is a key to meeting the pressing needs of science and society in the 21st century.
© 2020 The Authors. Global Change Biology published by John Wiley & Sons Ltd.

Entities:  

Keywords:  accessibility; benchmarking; community cyberinfrastructure; data; data assimilation; ecosystem models; interoperability; reproducibility

Year:  2020        PMID: 33075199      PMCID: PMC7756391          DOI: 10.1111/gcb.15409

Source DB:  PubMed          Journal:  Glob Chang Biol        ISSN: 1354-1013            Impact factor:   10.863


  22 in total

Review 1.  Deep learning and process understanding for data-driven Earth system science.

Authors:  Markus Reichstein; Gustau Camps-Valls; Bjorn Stevens; Martin Jung; Joachim Denzler; Nuno Carvalhais
Journal:  Nature       Date:  2019-02-13       Impact factor: 49.962

2.  Improving data access democratizes and diversifies science.

Authors:  Abhishek Nagaraj; Esther Shears; Mathijs de Vaan
Journal:  Proc Natl Acad Sci U S A       Date:  2020-09-08       Impact factor: 11.205

3.  Our path to better science in less time using open data science tools.

Authors:  Julia S Stewart Lowndes; Benjamin D Best; Courtney Scarborough; Jamie C Afflerbach; Melanie R Frazier; Casey C O'Hara; Ning Jiang; Benjamin S Halpern
Journal:  Nat Ecol Evol       Date:  2017-05-23       Impact factor: 15.460

4.  Does the leaf economic spectrum hold within plant functional types? A Bayesian multivariate trait meta-analysis.

Authors:  Alexey N Shiklomanov; Elizabeth M Cowdery; Michael Bahn; Chaeho Byun; Steven Jansen; Koen Kramer; Vanessa Minden; Ülo Niinemets; Yusuke Onoda; Nadejda A Soudzilovskaia; Michael C Dietze
Journal:  Ecol Appl       Date:  2020-01-30       Impact factor: 4.657

5.  Ten Simple Rules for Digital Data Storage.

Authors:  Edmund M Hart; Pauline Barmby; David LeBauer; François Michonneau; Sarah Mount; Patrick Mulrooney; Timothée Poisot; Kara H Woo; Naupaka B Zimmerman; Jeffrey W Hollister
Journal:  PLoS Comput Biol       Date:  2016-10-20       Impact factor: 4.475

Review 6.  Tools and techniques for computational reproducibility.

Authors:  Stephen R Piccolo; Michael B Frampton
Journal:  Gigascience       Date:  2016-07-11       Impact factor: 6.524

Review 7.  How to measure, report and verify soil carbon change to realize the potential of soil carbon sequestration for atmospheric greenhouse gas removal.

Authors:  Pete Smith; Jean-Francois Soussana; Denis Angers; Louis Schipper; Claire Chenu; Daniel P Rasse; Niels H Batjes; Fenny van Egmond; Stephen McNeill; Matthias Kuhnert; Cristina Arias-Navarro; Jorgen E Olesen; Ngonidzashe Chirinda; Dario Fornara; Eva Wollenberg; Jorge Álvaro-Fuentes; Alberto Sanz-Cobena; Katja Klumpp
Journal:  Glob Chang Biol       Date:  2019-10-06       Impact factor: 10.863

8.  Beyond ecosystem modeling: A roadmap to community cyberinfrastructure for ecological data-model integration.

Authors:  Istem Fer; Anthony K Gardella; Alexey N Shiklomanov; Eleanor E Campbell; Elizabeth M Cowdery; Martin G De Kauwe; Ankur Desai; Matthew J Duveneck; Joshua B Fisher; Katherine D Haynes; Forrest M Hoffman; Miriam R Johnston; Rob Kooper; David S LeBauer; Joshua Mantooth; William J Parton; Benjamin Poulter; Tristan Quaife; Ann Raiho; Kevin Schaefer; Shawn P Serbin; James Simkins; Kevin R Wilcox; Toni Viskari; Michael C Dietze
Journal:  Glob Chang Biol       Date:  2020-11-06       Impact factor: 10.863

9.  To Model or not to Model, That is no Longer the Question for Ecologists.

Authors:  Rupert Seidl
Journal:  Ecosystems       Date:  2017-03       Impact factor: 4.217

10.  Beyond Static Benchmarking: Using Experimental Manipulations to Evaluate Land Model Assumptions.

Authors:  William R Wieder; David M Lawrence; Rosie A Fisher; Gordon B Bonan; Susan J Cheng; Christine L Goodale; A Stuart Grandy; Charles D Koven; Danica L Lombardozzi; Keith W Oleson; R Quinn Thomas
Journal:  Global Biogeochem Cycles       Date:  2019-10-28       Impact factor: 5.703

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  5 in total

1.  Increasing the spatial and temporal impact of ecological research: A roadmap for integrating a novel terrestrial process into an Earth system model.

Authors:  Emily Kyker-Snowman; Danica L Lombardozzi; Gordon B Bonan; Susan J Cheng; Jeffrey S Dukes; Serita D Frey; Elin M Jacobs; Risa McNellis; Joshua M Rady; Nicholas G Smith; R Quinn Thomas; William R Wieder; A Stuart Grandy
Journal:  Glob Chang Biol       Date:  2021-10-14       Impact factor: 13.211

2.  The Terrestrial Biosphere Model Farm.

Authors:  Joshua B Fisher; Munish Sikka; Gary L Block; Christopher R Schwalm; Nicholas C Parazoo; Hannah R Kolus; Malen Sok; Audrey Wang; Anna Gagne-Landmann; Shakirudeen Lawal; Alexandre Guillaume; Alyssa Poletti; Kevin M Schaefer; Bassil El Masri; Peter E Levy; Yaxing Wei; Michael C Dietze; Deborah N Huntzinger
Journal:  J Adv Model Earth Syst       Date:  2022-02-16       Impact factor: 8.469

3.  Beyond ecosystem modeling: A roadmap to community cyberinfrastructure for ecological data-model integration.

Authors:  Istem Fer; Anthony K Gardella; Alexey N Shiklomanov; Eleanor E Campbell; Elizabeth M Cowdery; Martin G De Kauwe; Ankur Desai; Matthew J Duveneck; Joshua B Fisher; Katherine D Haynes; Forrest M Hoffman; Miriam R Johnston; Rob Kooper; David S LeBauer; Joshua Mantooth; William J Parton; Benjamin Poulter; Tristan Quaife; Ann Raiho; Kevin Schaefer; Shawn P Serbin; James Simkins; Kevin R Wilcox; Toni Viskari; Michael C Dietze
Journal:  Glob Chang Biol       Date:  2020-11-06       Impact factor: 10.863

4.  Bridging implementation gaps to connect large ecological datasets and complex models.

Authors:  Ann M Raiho; E Fleur Nicklen; Adrianna C Foster; Carl A Roland; Mevin B Hooten
Journal:  Ecol Evol       Date:  2021-12-14       Impact factor: 2.912

5.  PERFICT: A Re-imagined foundation for predictive ecology.

Authors:  Eliot J B McIntire; Alex M Chubaty; Steven G Cumming; Dave Andison; Ceres Barros; Céline Boisvenue; Samuel Haché; Yong Luo; Tatiane Micheletti; Frances E C Stewart
Journal:  Ecol Lett       Date:  2022-03-22       Impact factor: 11.274

  5 in total

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