@article{e264926688d6415dbd8632494e2680df,
title = "Toward open and reproducible environmental modeling by integrating online data repositories, computational environments, and model Application Programming Interfaces",
abstract = "Cyberinfrastructure needs to be advanced to enable open and reproducible environmental modeling research. Recent efforts toward this goal have focused on advancing online repositories for data and model sharing, online computational environments along with containerization technology and notebooks for capturing reproducible computational studies, and Application Programming Interfaces (APIs) for simulation models to foster intuitive programmatic control. The objective of this research is to show how these efforts can be integrated to support reproducible environmental modeling. We present first the high-level concept and general approach for integrating these three components. We then present one possible implementation that integrates HydroShare (an online repository), CUAHSI JupyterHub and CyberGIS-Jupyter for Water (computational environments), and pySUMMA (a model API) to support open and reproducible hydrologic modeling. We apply the example implementation for a hydrologic modeling use case to demonstrate how the approach can advance reproducible environmental modeling through the seamless integration of cyberinfrastructure services.",
keywords = "Containers, JupyterHub, Modeling frameworks, Open hydrology, Reproducibility",
author = "Choi, {Young Don} and Goodall, {Jonathan L.} and Sadler, {Jeffrey M.} and Castronova, {Anthony M.} and Andrew Bennett and Zhiyu Li and Bart Nijssen and Shaowen Wang and Clark, {Martyn P.} and Ames, {Daniel P.} and Horsburgh, {Jeffery S.} and Hong Yi and Christina Bandaragoda and Martin Seul and Richard Hooper and Tarboton, {David G.}",
note = "Funding Information: Along with containers, computational gateway interfaces are also critical to lowering the barrier to entry and supporting more open and reproducible modeling in online computational environments. With the emergence of JupyterHub as a gateway innovation, there has been an increased interest in cloud-based modeling environments for creating, editing, and running computational notebooks. Markham (2019) reviewed five popular cloud services that support computational notebooks (Table 1). We reviewed two additional cloud services, 1) CUAHSI JupyterHub (hereafter CUAHSI JH) and 2) CyberGIS-Jupyter for Water (hereafter CyberGIS JW), and included them in Table 1 as well. The environments range from scientific services (e.g., the CUAHSI JH and CyberGIS JW that are used in this work) to more general services such as Binder (Jupyter Project et al., 2018). Large technology companies including Google and Microsoft have provided notebook execution environments such as Google Colab and Microsoft Azure Notebooks, demonstrating the popularity and growing interest in a variety of fields. Many cloud services have adopted the default Jupyter interface available from the Jupyter project without modification, while others have modified this interface to customize it for their own purposes (Markham, 2019). Furthermore, many cloud services support Python, R and other languages as well. Interface similarity in Table 1 considers available menus, buttons, and other visual elements that make up the user interface, and how different they are from a default Jupyter interface. All services listed in Table 1 are candidates for integration into an implementation of the modeling system described in this paper.This work was supported by the National Science Foundation under collaborative grants OAC-1664061, OAC-1664018, OAC-1664119, ICER-1928369, and ICER-1928315. We acknowledge the work of the larger HydroShare team (https://help.hydroshare.org/about-hydroshare/team) that made this research possible. Funding Information: This work was supported by the National Science Foundation under collaborative grants OAC-1664061 , OAC-1664018 , OAC-1664119 , ICER-1928369 , and ICER-1928315 . We acknowledge the work of the larger HydroShare team ( https://help.hydroshare.org/about-hydroshare/team ) that made this research possible. Publisher Copyright: {\textcopyright} 2020 The Authors",
year = "2021",
month = jan,
doi = "10.1016/j.envsoft.2020.104888",
language = "English (US)",
volume = "135",
journal = "Environmental Modelling and Software",
issn = "1364-8152",
publisher = "Elsevier BV",
}