EarthCube2020: Reproducible and Replicable Scientific Use Cases with CyberGIS-Jupyter for water and Sciunit tool using SUMMA and pySUMMA


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Created: Apr 10, 2020 at 7:07 a.m.
Last updated: Apr 13, 2020 at 9:04 p.m.
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Abstract

These notebooks are created to evaluate the reproducibility and replicability using Sciunit in different computational environment.
You can open these notebooks using CyberGIS-Jupyter for water from `Open with button`.
Notebook1 and notebook2 were created in local computer to test computational environment and create Sciunit containers to encapsulate SUMMA simulation workflow.
- Notebook1: N_1_Reproducibility_Evaluation_of_the_SUMMA_Model_in_the_Model_Agnostic_Framework.ipynb
- Notebook2: N_2_Creating_and_Executing_the_Sciunit_Container_to_Encapsulating_and_Evaluating_the_immutable_computational_environment.ipynb

So you can start with notebook3.
- Notebook3: N_3_Reproducibility_and_Replicability_Evaluation_using_the_Sciunit_Container_in_CyberGIS_for_water.ipynb

From this process, you can evaluate the reproducibility and replicability of SUMMA simulation with repeating of Sciunit container and changing the SUMMA configuration.
- Reproduced SUMMA application: Three different stomatal Resistance Parameterizations (BallBerry, Jarvis, and Simple Stomatal Method)
- Replicated SUMMA application: Changing the function for the soil moisture control on stomatal resistance from NoahType to CLM_Type

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Content

README.md

Objectives

The importance of acknowledgement and awareness for open, reproducible and replicable computational modeling is growing in environmental modeling fields. Recent research to improve these significant requirements has focused on (1) advancing data sharing of online repositories, (2) using containers and Jupyter notebooks for encapsulating computational environments and workflows, and (3) developing Application Programming Interfaces (APIs) to interact with the models. In this study, we develop a new integrated approach to leverage recent efforts into a model agnostic framework. The agnostic framework consists of (1) an online repository for sharing modeling data, (2) cyberinfrastructure and software supporting containerized dependencies and notebook-based modeling analyses, and (3) model APIs enabling the abstraction of lower-level details for modeling. Then we present an example implementation of the approach using (1) HydroShare as an online repository, (2) CUAHSI JupyterHub and CyberGIS for water as cyberinfrastructure for flexible reproducible and replicable environments, and Sciunit as software tool for immutable reproducible and replicable environment, and (3) pySUMMA as an example model API for the Structure for Unifying Multiple Modeling Alternative (SUMMA) hydrologic model.

Notebook-1: Reproducibility Evaluation of the SUMMA Model in the Model Agnostic Framework (HydroShare, CUAHSI JupyterHub, pySUMMA)

  • Introduce the SUMMA model and brief theory of different stomatal Resistance Parameterizations
  • Use pySUMMA to set up model configuration
  • Run SUMMA using three different stomatal Resistance Parameterizations (BallBerry, Jarvis, and Simple Stomatal Method)
  • Reproduce evaportanspiration plot comparing to Figure 7 of Clark et al., (2015b)
  • Discuss the reproducibility of this model agnostic framework (HydroShare, CUAHSI JupyterHub, pySUMMA)

Notebook-2: Creation and Execution of the Sciunit Container to Encapsulate and Evaluate the Immutable Computational Environment in CUAHSI JupyterHub

  • Create Sciunit container to encapsulate SUMMA modeling workflow
  • Save the Sciunit container in HydroShare as a new HydroShare resource

Notebook-3: Reproducibility and Replicability Evaluation using the Sciunit Container in CyberGIS for water (different cyberinfrastructure)

  • Move to CyberGIS for water to evaluate reproducibility and replicability of SUMMA modeling in different modeling environment
  • Change the SUMMA configuration and execute the Sciunit container again to evaluate replicability
  • Discuss and conclude this study

Software availability

  • Software: SUMMA2.0, pySUMMA2.0.0, Sciunit2.0
  • Contact Email: yc5ef@virginia.edu or choiyd1115@gmail.com
  • Software Required: Python 3.6 or above
  • Availability:

    1) The SUMMA source code - https://github.com/NCAR/summa

    2) The pySUMMA source code - https://github.com/UW-Hydro/pysumma

    3) Sciunit - https://sciunit.run/

References

Related Resources

This resource cites: Clark, M. P., B. Nijssen, J. D. Lundquist, D. Kavetski, D. E. Rupp, R. A. Woods, J. E. Freer, E. D. Gutmann, A. W. Wood, D. J. Gochis, R. M. Rasmussen, D. G. Tarboton, V. Mahat, G. N. Flerchinger and D. G. Marks, (2015), "A unified approach for process-based hydrologic modeling: 2. Model implementation and case studies," Water Resources Research, 51(4): 2515-2542, http://doi.org/10.1002/2015wr017200.

Credits

Funding Agencies

This resource was created using funding from the following sources:
Agency Name Award Title Award Number
National Science Foundation EarthCube Building Blocks: Collaborative Proposal: GeoTrust: Improving Sharing and Reproducibility of Geoscience Applications ICER-1639655, ICER-1639759, ICER-1639696
National Science Foundation Collaborative Research: SI2-SSI: Cyberinfrastructure for Advancing Hydrologic Knowledge through Collaborative Integration of Data Science, Modeling and Analysis OAC-1664061, OAC-1664018, OAC-1664119

How to Cite

CHOI, Y. (2020). EarthCube2020: Reproducible and Replicable Scientific Use Cases with CyberGIS-Jupyter for water and Sciunit tool using SUMMA and pySUMMA, HydroShare, http://www.hydroshare.org/resource/87a7feaf1178444b83365d7133198f5e

This resource is shared under the Creative Commons Attribution CC BY.

 http://creativecommons.org/licenses/by/4.0/
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