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|Created:||Dec 21, 2020 at 8:45 a.m.|
|Last updated:|| Apr 03, 2022 at 6:26 p.m.
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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.
How to run the Hand Workflow and Sciunit
This workflow has been developed and tested on the CyberGIS-Jupyter for Water platform linked to HydroShare using the TauDEM-2021-09 Kernel. To execute the full workflow elsewhere you may need to account for differences between this platform and the platform being used.
STEP_0 Join the CyberGIS-Jupyter for Water HydroShare Group
To use the CyberGIS-Jupyter for Water platform you need to have a HydroShare user account be a member of the CyberGIS-Jupyter for Water HydroShare Group. - Create a HydroShare account at http://www.hydroshare.org - Request to become a member of the CyberGIS-Jupyter for Water (CJW) group at the CyberGIS-Jupyter for Water platform
Group membership is used manage the use of the community computing resources available in CyberGIS-Jupyter for Water
STEP_1 Open With CyberGIS-Jupyter for Water.
- Click the OpenWith button in the upper-right corner of this HydroShare resource webpage;
- Select "CyberGIS-Jupyter for Water";
- Authenticate and allow access to HydroShare content from CJW;
This should open the CyberGIS-Jupyter for Water Jupyter computing platform and transfer the files from HydroShare to the platform for work there. Note that the CJW file workspace is different from HydroShare resource file space, so any work you do in CJW would need to be copied back to HydroShare or elsewhere if you want to preserve or share it.
STEP_2 Execute HANDWorkFlow using HANDWorkFlow.ipynb
This notebook demonstrates the general procedure to calculate HAND (Height above the Nearest Drainage) using TauDEM (https://hydrology.usu.edu/taudem/taudem5/). Run all cells to completely execute the notebook, or run one cell at a time to see the process involved. The Hand_Sciunit.ipynb notebook uses this notebook to create a python script from the code in this notebook. This notebook does not have to have been executed for Hand_Sciunit.ipynb to run, so you can skip running this notebook if you just want to see Sciunit reproducibility
STEP_3 Create Sciunit using HAND_Sciunit_create.ipynb
This notebook demonstrates how to create a Sciunit container for the HAND Workflow and compares two Sciunit executions (5000 vs 50000 cell channelization thresholds) using the sciunit
diff command and visualization of the results. This notebook is best executed cell by cell to see how it works.
HANDWorkFlow.zip is the sciunit containerized results from these workflows. Use the sciunit open command to open this
STEP_4 Repeat workflow from Sciunit using HAND_Sciunit_repeat.ipynb
This notebook illustrates the commands used for repeating the sciunit executions. This notebook can be run without any of the above notebooks as it repeats all the work from the content containerized in the Sciunit.
sciunit open HANDWorkflow.zip
sciunit repeat e1
|The content of this resource is derived from||http://www.hydroshare.org/resource/9fd03c3c20564008af98bad83ce2304f|
This resource was created using funding from the following sources:
|Agency Name||Award Title||Award Number|
|National Science Foundation||EarthCube Data Capabilities: Collaborative Research: Integration of Reproducibility into Community CyberInfrastructure||ICER 1928369, 1928288 and 1928315|
How to Cite
This resource is shared under the Creative Commons Attribution CC BY.http://creativecommons.org/licenses/by/4.0/