Engineering Commons^™

Reproducibility Starts At The Source: R, Python, And Julia Packages For Retrieving Usgs Hydrologic Data, Timothy O. Hodson, Laura A. Decicco, Jayaram A. Hariharan, Lee F. Stanish, Scott Black, Jeffery S. Horsburgh

Civil and Environmental Engineering Faculty Publications

Much of modern science takes place in a computational environment, and, increasingly, that environment is programmed using R, Python, or Julia. Furthermore, most scientific data now live on the cloud, so the first step in many workflows is to query a cloud database and load the response into a computational environment for further analysis. Thus, tools that facilitate programmatic data retrieval represent a critical component in reproducible scientific workflows. Earth science is no different in this regard. To fulfill that basic need, we developed R, Python, and Julia packages providing programmatic access to the U.S. Geological Survey’s National Water Information …

Toward Open And Reproducible Environmental Modeling By Integrating Online Data Repositories, Computational Environments, And Model Application Programming Interfaces, Young-Don Choi, Jonathan L. Goodall, Jeffrey M. Sadler, Anthony M. Castronova, Andrew Bennett, Zhiyu Li, Bart Nijssen, Shaowen Wang, Martyn P. Clark, Daniel P. Ames, Jeffery S. Horsburgh, Hong Yi, Christina Bandaragoda, Martin Seul, Richard Hooper, David G. Tarboton

Civil and Environmental Engineering Faculty Publications

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 …

Advancing Water Resources Systems Modeling Cyberinfrastructure To Enable Systematic Data Analysis, Modeling, And Comparisons, Adel Mohammad Kheir Abdallah

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Water resources systems models aid in managing water resources holistically considering water, economic, energy, and environmental needs, among others. Developing such models require data that represent a water system’s physical and operational characteristics such as inflows, demands, reservoir storage, and release rules. However, such data is stored and described in different formats, metadata, and terminology. Therefore, Existing tools to store, query, and visualize modeling data are model, location, and dataset-specific, and developing such tools is time-consuming and requires programming experience. This dissertation presents an architecture and three software tools to enable researchers to more readily and consistently prepare and reuse …

Developing Open Source Software Using Version Control Systems: An Introduction To The Git Language For Documenting Your Computational Research, Jared D. Smith, Jonathan D. Herman

All ECSTATIC Materials

Version control systems track the history of code as it is committed (saved) by any number of developers. Have you made a coding error and cannot debug it? Version control systems allow for resetting code back to when it worked, and show what code has changed since previous commits.

The contents of this lecture provide an introduction to the git version control language, GitHub for cloud hosting open source code repositories, and tutorials that demonstrate common and useful git and GitHub practices. This lecture is intended to be coupled with a discussion on creating reproducible computational research.

The zipped folder …

Integrating Hydrologic Modeling Web Services With Online Data Sharing To Prepare, Store, And Execute Hydrologic Models, Tian Gan, David G. Tarboton, Pabitra Dash, Tseganeh Z. Gichamo, Jeffery S. Horsburgh

Civil and Environmental Engineering Faculty Publications

Web based applications, web services, and online data and model sharing technology are becoming increasingly available to support hydrologic research. This promises benefits in terms of collaboration, computer platform independence, and reproducibility of modeling workflows and results. In this research, we designed an approach that integrates hydrologic modeling web services with an online data sharing system to support web-based simulation for hydrologic models. We used this approach to integrate example systems as a case study to support reproducible snowmelt modeling for a test watershed in the Colorado River Basin, USA. We demonstrated that this approach enabled users to work within …

Design Of A Metadata Framework For The Environmental Models With An Example Hydrologic Application In Hydroshare, Mohamed M. Morsy, Jonathan L. Goodall, Anthony M. Castronova, Pabitra Dash, Venkatesh Merwade, Jeffrey M. Sadler, Mohammad Adnan Rajib, Jeffery S. Horsburgh, David G. Tarboton

Civil and Environmental Engineering Faculty Publications

Environmental modelers rely on a variety of computational models to make predictions, test hypotheses, and address specific problems related to environmental science and natural resource management. Scientists and engineers must devote significant effort to preparing these computational models. While significant attention has been devoted to sharing and reusing environmental data, less attention has been devoted to sharing and reusing environmental models. A first step toward increasing environmental model sharing and reuse is to define a general metadata framework for models that is flexible and, therefore, applicable across the wide variety of models used by environmental modelers. This paper proposes a …