ABSTRACT:

This is a HydroShare resource to demonstrate an approach for open and reproducible Environmental Environmental Modeling during EarthCube2020 meeting (https://www.earthcube.org/EC2020).

You can start a Jupyter notebook ("First_NB_An_Approach_for_Open_Reproducible_Environmental_Modeling.ipynb") using "CyberGIS-Jupyter for water" on "Open with ..." Button.
Through the 1st notebook demonstration, you can experience open and reproducible environmental modeling using three main components which are online repository (HydroShare), computational environment (CyberGIS-Jupyter for water), and model API(pySUMMA).
Also, you will create a Sciunit container to encapsulate every dependency for SUMMA execution in CybeGIS-Jupyter into the Sciunit container.

Then you can move to the 2nd notebook (Second_NB_An_Approach_for_Open_Reproducible_Environmental_Modeling.ipynb) to evaluate reproducibility and replicability of the SUMMA Sciunit container in different cyberinfrastructure (CUAHSI JupyterHub).

ABSTRACT:

This is an example of Geoscience Use Case 4: Height Above the Nearest Drainage (HAND) of "Improving Reproducibility of Geoscience Models with Sciunit" in the Geological Society of America publication. In this resource, there are two notebooks: 1) HANDWorkFlow.ipynb and 2) HAND_Sciunit.ipynb.

Using these two notebooks, we demonstrate the capabilities of Sciunit to encapsulate the HAND TauDEM workflow and create a Sciunit Container, and evaluate differences in HAND due to changing the contributing area threshold used to map the drainage network. During computation of the drainage network, a minimum contributing area threshold is used to identify the channel beginning. With a lower threshold value, the density of the resulting drainage network increases. Scientists running this experiment might be interested in finding out how the threshold makes a difference in the execution and result of the HAND model.

The first notebook demonstrates the general procedure to calculate HAND (Height above the Nearest Drainage) using TauDEM (https://hydrology.usu.edu/taudem/taudem5/).
Then using the second notebook we demonstrate how to create a Sciunit container for HAND Workflow and compare two Sciunit containers (5000 vs 50000 thresholds) using `diff` command.

ABSTRACT:

This is a HydroShare resource to demonstrate an approach for open and reproducible Environmental Environmental Modeling during EarthCube2020 meeting (https://www.earthcube.org/EC2020).

You can start a Jupyter notebook ("First_NB_An_Approach_for_Open_Reproducible_Environmental_Modeling.ipynb") using "CyberGIS-Jupyter for water" on "Open with ..." Button.
Through the 1st notebook demonstration, you can experience open and reproducible environmental modeling using three main components which are online repository (HydroShare), computational environment (CyberGIS-Jupyter for water), and model API(pySUMMA).
Also, you will create a Sciunit container to encapsulate every dependency for SUMMA execution in CybeGIS-Jupyter into the Sciunit container.

Then you can move to the 2nd notebook (Second_NB_An_Approach_for_Open_Reproducible_Environmental_Modeling.ipynb) to evaluate reproducibility and replicability of the SUMMA Sciunit container in different cyberinfrastructure (CUAHSI JupyterHub).

ABSTRACT:

This HydroShare resource is an example to demonstrate the vPICO presentations in EGU General Assembly 2021 (https://meetingorganizer.copernicus.org/EGU21/session/40092#vPICO_presentations).
- Session: EOS5.3 session - The evolving open-science landscape in geosciences: open data, software, publications, and community initiatives
- Title: An Approach for Open and Reproducible Hydrological Modeling using Sciunit and HydroShare

Using this notebook, you can test how to create an immutable and interoperable Sciunit Container for open and reproducible hydrological modeling.

You can start using "NB_01_An_Approach_for_Open_and_Reproducible_Hydrological_Modeling_using_Sciunit_and_HydroShare.ipynb" notebook in "CyberGIS-Jupyter for water" after clicking "Open with...". in Right-Above.

ABSTRACT:

This resource contains the containerized code for the pre-processing pipeline for the Variable Infiltration Capacity(VIC) Model in Hydrology.

ABSTRACT:

This HydroShare resource provides the Jupyter Notebooks created for the study "An Approach for Creating Immutable and Interoperable End-to-End Hydrological Modeling Computational Workflows" led by researcher Young-Don Choi submitted to the 2021 EarthCube Annual meeting, Notebook Sessions.

To find out the instructions on how to run Jupyter Notebooks, please refer to the README file provided in this resource.

For the sake of completeness, the abstract for the study submitted to the EarthCube session is mentioned below:

"Reproducibility is a fundamental requirement to advance science. Creating reproducible hydrological models that include all required data, software, and workflows, however, is often burdensome and requires significant work. Computational hydrology is a rapidly advancing field with fast-evolving technologies to support increasingly complex computational hydrologic modeling. The growing model complexity in terms of variety of software and cyberinfrastructure capabilities makes achieving computational reproducibility extremely challenging. Through recent reproducibility research, there have been efforts to integrate three components: 1) (meta)data, 2) computational environments, and 3) workflows. However, each component is still separate, and researchers must interoperate between these three components. These separations make verifying end-to-end reproducibility challenging. Sciunit was developed to assist scientists, who are not programming experts, with encapsulating these three components into a container to enable reproducibility in an immutable form. However, there were still limitations to support interoperable computational environments and apply end-to-end solutions, which are an ultimate goal of reproducible hydrological modeling. Therefore, the objective of this research is to advance the existing Sciunit capabilities to not only support immutable, but also interoperable computational environments and apply an end-to-end modeling workflow using the Regional Hydro-Ecologic Simulation System (RHESSys) hydrologic model as an example. First, we create an end-to-end workflow for RHESSys using pyRHESSys on the CyberGIS-Jupyter for Water platform. Second, we encapsulate the aforementioned three components and create configurations that include lists of encapsulated dependencies using Sciunit. Third, we create two HydroShare resources, one for immutable reproducibility evaluation using Sciunit and the other for interoperable reproducibility evaluation using library configurations created by Sciunit. Finally, we evaluate the reproducibility of Sciunit in MyBinder, which is a different computational environment, using these two resources. This research presents a detailed example of a user-centric case study demonstrating the application of an open and interoperable containerization approach from a hydrologic modeler’s perspective."

ABSTRACT:

Sciunit (https://sciunit.run/) is a tool that encapsulates a set of executions into an isolated, independent container. It allows computational scientists to create research objects, which can be reused and transferred to other computational environments for reproducibility. Sciunit containerizes a program by capturing the trace of its execution using system utilities. It stores the sequence of instructions to run the program and the input and output data content used by that program. Programs in this self-contained sandbox are reproduced on the system or transported to another system for re-execution.

In this resource, users can show how to reproduce a Sciunit Container that encapsulates MODFLOW-NWT Use Case in the James River watershed upstream of Richmond, VA, USA

ABSTRACT:

This resource illustrates how data and code can be combined together to support hydrologic analyses. It was developed June 2020 as part of a HydroLearn Hackathon.

ABSTRACT:

This is a resource for demonstrating Sciunit export functionality between multiple machines.
There is a corresponding resource on CUAHSI JupyterHub here:
https://www.hydroshare.org/resource/16023fc1a0954b488bfe602fbecbe886/