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Award Abstract # 1928315
EarthCube Data Capabilities: Collaborative Research: Integration of Reproducible Methods into Community Cyberinfrastructure

NSF Org: RISE
Integrative and Collaborative Education and Research (ICER)
Recipient: RECTOR & VISITORS OF THE UNIVERSITY OF VIRGINIA
Initial Amendment Date: August 26, 2019
Latest Amendment Date: August 26, 2019
Award Number: 1928315
Award Instrument: Standard Grant
Program Manager: Eva Zanzerkia
RISE
 Integrative and Collaborative Education and Research (ICER)
GEO
 Directorate for Geosciences
Start Date: September 1, 2019
End Date: August 31, 2023 (Estimated)
Total Intended Award Amount: $276,662.00
Total Awarded Amount to Date: $276,662.00
Funds Obligated to Date: FY 2019 = $276,662.00
History of Investigator:
  • Jonathan Goodall (Principal Investigator)
    goodall@virginia.edu
Recipient Sponsored Research Office: University of Virginia Main Campus
1001 EMMET ST N
CHARLOTTESVILLE
VA  US  22903-4833
(434)924-4270
Sponsor Congressional District: 05
Primary Place of Performance: University of Virginia
151 Engineer's Way, Olsson Hall
Charlottesville
VA  US  22904-4259
Primary Place of Performance
Congressional District:
05
Unique Entity Identifier (UEI): JJG6HU8PA4S5
Parent UEI:
NSF Program(s): EarthCube
Primary Program Source: 01001920DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 7433
Program Element Code(s): 807400
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.050

ABSTRACT

For science to reliably support new discoveries, its results must be reproducible. This has proven to be a challenge in many fields including, most notably, fields that rely on computational studies as a means for supporting new discoveries. Reproducibility in these studies is particularly difficult because they require open sharing of data and models and careful control by the original researcher. This is to ensure that products can be run on later generations of hardware and software and produce consistent results. This project will develop software that helps support computational reproducibility and makes it easier and more efficient for geoscientists to preserve, share, repeat and replicate scientific computations. The Broader Impacts of this project include a collaboration between computer scientists, hydrologists and the Consortium of Universities for the Advancement of Hydrologic Science Inc. (CUAHSI) for the hydrology research community. With over 3500 users, and holding over 8000 model and data resources, this collaboration will bring improved tools and best practices to a broad and diverse community of geoscientists. Beyond hydrology, the methods and tools developed as part of this project have the potential to be extended to the solid Earth and space science geoscience domains. They also have the potential to inform the reproducibility evaluation process as currently undertaken by journals and publishers. The projct will also conduct workshops to train researchers and be used in the classroom at Utah Sate Universtiy, DePaul University and the University of Virginia.

Emphasis on the importance of research reproducibility is steadily rising, however many studies still continue to not be reproducible. Reproducibility in computational studies is particularly difficult because of the challenges involved in completely documenting the data, models and procedures used together with the underlying hardware and software dependencies. The reproducibility workbench software (ReproBench) developed in this project will address reproducibility questions by establishing a container-based reproducible workflow that will make it easy and efficient for geoscientists to verify scientific results. Automation and documentation are two key methods for improving verification and, in general, the conduct of reproducible science. This project will build-from past investments: (I) automated containerization methods, through the Sciunit project, and (II) well-documented, community-adopted interfaces, through HydroShare, and bring these investments together to establish a novel, robust, and reproducible workflow. By applying this workflow to water-related science use cases, this project will demonstrate how to preserve, share, repeat, and replicate scientific results. The interfaces can become an exemplar for other community cyberinfrastructure that, akin to Hydrology, aims to share data and models at a large scale. In establishing this workflow, the ReproBench project team combines expertise in cyberinfrastructure, domain science, and reproducible computational data science. By leveraging Sciunit, ReproBench brings formal methods for the conduct of reproducible computational science into the geosciences.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Choi, Young-Don and Goodall, Jonathan L. and Sadler, Jeffrey M. and Castronova, Anthony M. and Bennett, Andrew and Li, Zhiyu and Nijssen, Bart and Wang, Shaowen and Clark, Martyn P. and Ames, Daniel P. and Horsburgh, Jeffery S. and Yi, Hong and Bandaragod "Toward open and reproducible environmental modeling by integrating online data repositories, computational environments, and model Application Programming Interfaces" Environmental Modelling & Software , v.135 , 2021 https://doi.org/10.1016/j.envsoft.2020.104888 Citation Details
Choi, Young-Don and Roy, Binata and Nguyen, Jared and Ahmad, Raza and Maghami, Iman and Nassar, Ayman and Li, Zhiyu and Castronova, Anthony M. and Malik, Tanu and Wang, Shaowen and Goodall, Jonathan L. "Comparing containerization-based approaches for reproducible computational modeling of environmental systems" Environmental Modelling & Software , v.167 , 2023 https://doi.org/10.1016/j.envsoft.2023.105760 Citation Details
Essawy, Bakinam T. and Goodall, Jonathan L. and Voce, Daniel and Morsy, Mohamed M. and Sadler, Jeffrey M. and Choi, Young Don and Tarboton, David G. and Malik, Tanu "A taxonomy for reproducible and replicable research in environmental modelling" Environmental Modelling & Software , 2020 https://doi.org/10.1016/j.envsoft.2020.104753 Citation Details
Maghami, Iman and Van Beusekom, Ashley and Hay, Lauren and Li, Zhiyu and Bennett, Andrew and Choi, YoungDon and Nijssen, Bart and Wang, Shaowen and Tarboton, David and Goodall, Jonathan L. "Building cyberinfrastructure for the reuse and reproducibility of complex hydrologic modeling studies" Environmental Modelling & Software , v.164 , 2023 https://doi.org/10.1016/j.envsoft.2023.105689 Citation Details

PROJECT OUTCOMES REPORT

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

The goal of this project was to advance computational reproducibility and make it easier and more efficient for geoscientists to preserve, share, repeat and replicate scientific computations. Reproducibility is a core principle of scientific research. As computational studies become increasingly important across scientific disciplines, including geosciences, it is necessary to create methods and tools that support computational scientists in making their research easier for others to reproduce. The complexity of computational models and the computer environments needed to run geoscience models makes achieving reproducibility challenging.  

The first objective of this research was to advance the use of Sciunit as a software tool to support reproducibility of computational modeling studies in the geosciences. Sciunit allows scientists to encapsulate application dependencies composed of system binaries, code, data, environment and application provenance so that the resulting computational research object can be shared and re-executed on different platforms. As a result, scientists can more easily capture the exact computational environment used to complete a modeling experiment in a way that can be ported to other computing platforms. Achieving portability of the computer environment is a major step toward creating reproducible computational modeling experiments.  

The second objective of this research was to deploy Sciunit within the HydroShare JupyterHub platform operated by the Consortium of Universities for the Advancement of Hydrologic Science Inc. (CUAHSI). This deployment provides an avenue for hydrologists to take advantage of Sciunit and the reproducibility enabled by Sciunit within a software system tailored for the hydrologic science community. It illustrates how Sciunit can be embedded within a discipline-specific computational environment that can be followed by other subdisciplines of the geosciences, and scientific disciplines beyond the geosciences as well. The result of the deployment provides a prototype of a software approach for the hydrology research community. The research also resulted in studies to demonstrate how to preserve, share, repeat and replicate scientific results from the field of hydrologic modeling using Sciunit and other software tools for fostering computational reproducibility. 


Last Modified: 01/01/2024
Modified by: Jonathan L Goodall

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