CyVerse: Cyberinfrastructure for open science

Tyson L. Swetnam; Parker B. Antin; Ryan Bartelme; Alexander Bucksch; David Camhy; Greg Chism; Illyoung Choi; Amanda M. Cooksey; Michele Cosi; Cindy Cowen; Michael Culshaw-Maurer; Robert Davey; Sean Davey; Upendra Devisetty; Tony Edgin; Andy Edmonds; Dmitry Fedorov; Jeremy Frady; John Fonner; Jeffrey K. Gillan; Iqbal Hossain; Blake Joyce; Konrad Lang; Tina Lee; Shelley Littin; Ian McEwen; Nirav Merchant; David Micklos; Andrew Nelson; Ashley Ramsey; Sarah Roberts; Paul Sarando; Edwin Skidmore; Jawon Song; Mary Margaret Sprinkle; Sriram Srinivasan; Dan Stanzione; Jonathan D. Strootman; Sarah Stryeck; Reetu Tuteja; Matthew Vaughn; Mojib Wali; Mariah Wall; Ramona Walls; Liya Wang; Todd Wickizer; Jason Williams; John Wregglesworth; Eric Lyons

doi:10.1371/journal.pcbi.1011270

CyVerse: Cyberinfrastructure for open science

Tyson L. Swetnam^*, Parker B. Antin, Ryan Bartelme, Alexander Bucksch, David Camhy, Greg Chism, Illyoung Choi, Amanda M. Cooksey, Michele Cosi, Cindy Cowen, Michael Culshaw-Maurer, Robert Davey, Sean Davey, Upendra Devisetty, Tony Edgin, Andy Edmonds, Dmitry Fedorov, Jeremy Frady, John Fonner, Jeffrey K. GillanIqbal Hossain, Blake Joyce, Konrad Lang, Tina Lee, Shelley Littin, Ian McEwen, Nirav Merchant, David Micklos, Andrew Nelson, Ashley Ramsey, Sarah Roberts, Paul Sarando, Edwin Skidmore, Jawon Song, Mary Margaret Sprinkle, Sriram Srinivasan, Dan Stanzione, Jonathan D. Strootman, Sarah Stryeck, Reetu Tuteja, Matthew Vaughn, Mojib Wali, Mariah Wall, Ramona Walls, Liya Wang, Todd Wickizer, Jason Williams, John Wregglesworth, Eric Lyons

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse has enabled access by providing interfaces, Software as a Service (SaaS), and cloud-native Infrastructure as Code (IaC) to leverage new technologies. CyVerse services enable researchers to integrate institutional and private computational resources, custom software, perform analyses, and publish data in accordance with open science principles. Over the past 13 years, CyVerse has registered more than 124,000 verified accounts from 160 countries and was used for over 1,600 peer-reviewed publications. Since 2011, 45,000 students and researchers have been trained to use CyVerse. The platform has been replicated and deployed in three countries outside the US, with additional private deployments on commercial clouds for US government agencies and multinational corporations. In this manuscript, we present a strategic blueprint for creating and managing SaaS cyberinfrastructure and IaC as free and opensource software.

Original language	English
Article number	e1011270
Journal	PLoS Computational Biology
Volume	20
Issue number	2 February
DOIs	https://doi.org/10.1371/journal.pcbi.1011270
Publication status	Published - Feb 2024

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Modelling and Simulation
Ecology
Molecular Biology
Genetics
Cellular and Molecular Neuroscience
Computational Theory and Mathematics

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10.1371/journal.pcbi.1011270Licence: CC BY 4.0

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Swetnam, T. L., Antin, P. B., Bartelme, R., Bucksch, A., Camhy, D., Chism, G., Choi, I., Cooksey, A. M., Cosi, M., Cowen, C., Culshaw-Maurer, M., Davey, R., Davey, S., Devisetty, U., Edgin, T., Edmonds, A., Fedorov, D., Frady, J., Fonner, J., ... Lyons, E. (2024). CyVerse: Cyberinfrastructure for open science. PLoS Computational Biology, 20(2 February), Article e1011270. https://doi.org/10.1371/journal.pcbi.1011270

Swetnam, TL, Antin, PB, Bartelme, R, Bucksch, A, Camhy, D, Chism, G, Choi, I, Cooksey, AM, Cosi, M, Cowen, C, Culshaw-Maurer, M, Davey, R, Davey, S, Devisetty, U, Edgin, T, Edmonds, A, Fedorov, D, Frady, J, Fonner, J, Gillan, JK, Hossain, I, Joyce, B, Lang, K, Lee, T, Littin, S, McEwen, I, Merchant, N, Micklos, D, Nelson, A, Ramsey, A, Roberts, S, Sarando, P, Skidmore, E, Song, J, Sprinkle, MM, Srinivasan, S, Stanzione, D, Strootman, JD, Stryeck, S, Tuteja, R, Vaughn, M, Wali, M, Wall, M, Walls, R, Wang, L, Wickizer, T, Williams, J, Wregglesworth, J & Lyons, E 2024, 'CyVerse: Cyberinfrastructure for open science', PLoS Computational Biology, vol. 20, no. 2 February, e1011270. https://doi.org/10.1371/journal.pcbi.1011270

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abstract = "CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse has enabled access by providing interfaces, Software as a Service (SaaS), and cloud-native Infrastructure as Code (IaC) to leverage new technologies. CyVerse services enable researchers to integrate institutional and private computational resources, custom software, perform analyses, and publish data in accordance with open science principles. Over the past 13 years, CyVerse has registered more than 124,000 verified accounts from 160 countries and was used for over 1,600 peer-reviewed publications. Since 2011, 45,000 students and researchers have been trained to use CyVerse. The platform has been replicated and deployed in three countries outside the US, with additional private deployments on commercial clouds for US government agencies and multinational corporations. In this manuscript, we present a strategic blueprint for creating and managing SaaS cyberinfrastructure and IaC as free and opensource software.",

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AU - Bartelme, Ryan

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AU - Camhy, David

AU - Chism, Greg

AU - Choi, Illyoung

AU - Cooksey, Amanda M.

AU - Cosi, Michele

AU - Cowen, Cindy

AU - Culshaw-Maurer, Michael

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AU - Davey, Sean

AU - Devisetty, Upendra

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AU - Edmonds, Andy

AU - Fedorov, Dmitry

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AU - Fonner, John

AU - Gillan, Jeffrey K.

AU - Hossain, Iqbal

AU - Joyce, Blake

AU - Lang, Konrad

AU - Lee, Tina

AU - Littin, Shelley

AU - McEwen, Ian

AU - Merchant, Nirav

AU - Micklos, David

AU - Nelson, Andrew

AU - Ramsey, Ashley

AU - Roberts, Sarah

AU - Sarando, Paul

AU - Skidmore, Edwin

AU - Song, Jawon

AU - Sprinkle, Mary Margaret

AU - Srinivasan, Sriram

AU - Stanzione, Dan

AU - Strootman, Jonathan D.

AU - Stryeck, Sarah

AU - Tuteja, Reetu

AU - Vaughn, Matthew

AU - Wali, Mojib

AU - Wall, Mariah

AU - Walls, Ramona

AU - Wang, Liya

AU - Wickizer, Todd

AU - Williams, Jason

AU - Wregglesworth, John

AU - Lyons, Eric

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CyVerse: Cyberinfrastructure for open science

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