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Stoudt S, Jernite Y, Marshall B, Marwick B, Sharan M, Whitaker K, Danchev V. Ten simple rules for building and maintaining a responsible data science workflow. PLoS Comput Biol 2024; 20:e1012232. [PMID: 39024267 PMCID: PMC11257324 DOI: 10.1371/journal.pcbi.1012232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024] Open
Affiliation(s)
- Sara Stoudt
- Department of Mathematics, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Yacine Jernite
- Hugging Face, Inc., New York, New York, United States of America
| | | | - Ben Marwick
- Department of Anthropology, University of Washington, Seattle, Washington, United States of America
| | | | | | - Valentin Danchev
- School of Business and Management, Queen Mary University of London, London, United Kingdom
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Lowndes JS, Holder AM, Markowitz EH, Clatterbuck C, Bradford AL, Doering K, Stevens MH, Butland S, Burke D, Kross S, Hollister JW, Stawitz C, Siple MC, Rios A, Welch JN, Li B, Nojavan F, Davis A, Steiner E, London JM, Fenwick I, Hunzinger A, Verstaen J, Holmes E, Virdi M, Barrett AP, Robinson E. Shifting institutional culture to develop climate solutions with Open Science. Ecol Evol 2024; 14:e11341. [PMID: 38826171 PMCID: PMC11143379 DOI: 10.1002/ece3.11341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/24/2024] [Accepted: 04/01/2024] [Indexed: 06/04/2024] Open
Abstract
To address our climate emergency, "we must rapidly, radically reshape society"-Johnson & Wilkinson, All We Can Save. In science, reshaping requires formidable technical (cloud, coding, reproducibility) and cultural shifts (mindsets, hybrid collaboration, inclusion). We are a group of cross-government and academic scientists that are exploring better ways of working and not being too entrenched in our bureaucracies to do better science, support colleagues, and change the culture at our organizations. We share much-needed success stories and action for what we can all do to reshape science as part of the Open Science movement and 2023 Year of Open Science.
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Affiliation(s)
| | - Anna M. Holder
- California Environmental Protection AgencySacramentoCaliforniaUSA
| | | | | | - Amanda L. Bradford
- NOAA Fisheries Pacific Islands Fisheries Science CenterHonoluluHawaiiUSA
| | - Kathryn Doering
- ECS Federal LLC in support of NOAA Fisheries Office of Science and TechnologySeattleWashingtonUSA
| | - Molly H. Stevens
- NOAA Fisheries Southeast Fisheries Science CenterMiamiFloridaUSA
| | | | - Devan Burke
- California Environmental Protection AgencySacramentoCaliforniaUSA
| | - Sean Kross
- Fred Hutch Cancer CenterSeattleWashingtonUSA
| | | | - Christine Stawitz
- ECS Federal LLC in support of NOAA Fisheries Office of Science and TechnologySeattleWashingtonUSA
| | | | - Adyan Rios
- NOAA Fisheries Southeast Fisheries Science CenterMiamiFloridaUSA
| | | | - Bai Li
- ECS Federal LLC in support of NOAA Fisheries Office of Science and TechnologySeattleWashingtonUSA
| | - Farnaz Nojavan
- United States Environmental Protection AgencyWashingtonDCUSA
| | - Alexandra Davis
- University of California, Los AngelesLos AngelesCaliforniaUSA
| | - Erin Steiner
- NOAA Fisheries Northwest Fisheries Science CenterSeattleWashingtonUSA
| | - Josh M. London
- NOAA Fisheries Alaska Fisheries Science CenterSeattleWashingtonUSA
| | - Ileana Fenwick
- The University of North Carolina at Chapel HillChapel HillNorth CarolinUSA
| | - Alexis Hunzinger
- Adnet Systems, Inc. / NASA Goddard Earth Sciences Data and Information Services CenterGreenbeltMDUSA
| | - Juliette Verstaen
- NOAA Fisheries Pacific Islands Fisheries Science CenterHonoluluHawaiiUSA
- Cooperative Institute for Marine and Atmospheric Research, University of HawaiiHonoluluHawaiiUSA
| | - Elizabeth Holmes
- NOAA Fisheries Northwest Fisheries Science CenterSeattleWashingtonUSA
| | - Makhan Virdi
- NASA Atmospheric Science Data CenterWashingtonDCUSA
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Savonen C, Wright C, Hoffman A, Humphries E, Cox K, Tan F, Leek J. Motivation, inclusivity, and realism should drive data science education. F1000Res 2024; 12:1240. [PMID: 38764793 PMCID: PMC11101914 DOI: 10.12688/f1000research.134655.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/06/2024] [Indexed: 05/21/2024] Open
Abstract
Data science education provides tremendous opportunities but remains inaccessible to many communities. Increasing the accessibility of data science to these communities not only benefits the individuals entering data science, but also increases the field's innovation and potential impact as a whole. Education is the most scalable solution to meet these needs, but many data science educators lack formal training in education. Our group has led education efforts for a variety of audiences: from professional scientists to high school students to lay audiences. These experiences have helped form our teaching philosophy which we have summarized into three main ideals: 1) motivation, 2) inclusivity, and 3) realism. 20 we also aim to iteratively update our teaching approaches and curriculum as we find ways to better reach these ideals. In this manuscript we discuss these ideals as well practical ideas for how to implement these philosophies in the classroom.
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Affiliation(s)
| | - Carrie Wright
- Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Ava Hoffman
- Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | | | - Katherine Cox
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | | | - Jeffrey Leek
- Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
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Fredston AL, Lowndes JSS. Welcoming More Participation in Open Data Science for the Oceans. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:537-549. [PMID: 37418835 DOI: 10.1146/annurev-marine-041723-094741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Open science is a global movement happening across all research fields. Enabled by technology and the open web, it builds on years of efforts by individuals, grassroots organizations, institutions, and agencies. The goal is to share knowledge and broaden participation in science, from early ideation to making research outputs openly accessible to all (open access). With an emphasis on transparency and collaboration, the open science movement dovetails with efforts to increase diversity, equity, inclusion, and belonging in science and society. The US Biden-Harris Administration and many other US government agencies have declared 2023 the Year of Open Science, providing a great opportunity to boost participation in open science for the oceans. For researchers day-to-day, open science is a critical piece of modern analytical workflows with increasing amounts of data. Therefore, we focus this article on open data science-the tooling and people enabling reproducible, transparent, inclusive practices for data-intensive research-and its intersection with the marine sciences. We discuss the state of various dimensions of open science and argue that technical advancements have outpaced our field's culture change to incorporate them. Increasing inclusivity and technical skill building are interlinked and must be prioritized within the marine science community to find collaborative solutions for responding to climate change and other threats to marine biodiversity and society.
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Affiliation(s)
- Alexa L Fredston
- Department of Ocean Sciences, University of California, Santa Cruz, California, USA;
| | - Julia S Stewart Lowndes
- National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara, California, USA
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Dillon EM, Dunne EM, Womack TM, Kouvari M, Larina E, Claytor JR, Ivkić A, Juhn M, Carmona PSM, Robson SV, Saha A, Villafaña JA, Zill ME. Challenges and directions in analytical paleobiology. PALEOBIOLOGY 2023; 49:377-393. [PMID: 37809321 PMCID: PMC7615171 DOI: 10.1017/pab.2023.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite-or even spurred by-this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.
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Affiliation(s)
- Erin M. Dillon
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, U.S.A.; Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - Emma M. Dunne
- GeoZentrum Nordbayern, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Tom M. Womack
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Miranta Kouvari
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom; Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Ekaterina Larina
- Jackson School of Geosciences, University of Texas, Austin, Texas 78712, U.S.A
| | - Jordan Ray Claytor
- Department of Biology, University of Washington, Seattle, Washington 98195, U.S.A; Burke Museum of Natural History and Culture, Seattle, Washington 98195, U.S.A
| | - Angelina Ivkić
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2,1090 Vienna, Austria
| | - Mark Juhn
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California 90095, U.S.A
| | - Pablo S. Milla Carmona
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ciencias Geológicas, Buenos Aires C1428EGA, Argentina; Instituto de Estudios Andinos “Don Pablo Groeber” (IDEAN, UBA-CONICET), Buenos Aires C1428EGA, Argentina
| | - Selina Viktor Robson
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Anwesha Saha
- Institute of Palaeobiology, Polish Academy of Sciences, ul. Twarda 51/55, 00-818 Warsaw, Poland; Laboratory of Paleogenetics and Conservation Genetics, Centre of New Technologies (CeNT), University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Jaime A. Villafaña
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria; Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O ‘Higgins, Santiago 8370993, Chile
| | - Michelle E. Zill
- Department of Earth and Planetary Sciences, University of California Riverside, Riverside, California 92521, U.S.A
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