https://github.com/bvhpatel/gi-review-dataset
Dataset associated with our review manuscript on the constitutive modeling of GI tissues
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 6 DOI reference(s) in README -
✓Academic publication links
Links to: preprints.org, zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.9%) to scientific vocabulary
Keywords
Repository
Dataset associated with our review manuscript on the constitutive modeling of GI tissues
Basic Info
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Metadata Files
README.md
Dataset: Biomechanical constitutive modeling of the gastrointestinal tissues
This is the dataset associated with our review manuscript on the biomechanical constitutive modeling of GI tissues [1]. It is structured according to the SPARC Data Structure [2] and curated using the SPARC data curation software SODA v4.7.0 [3,4]. We refer to the manuscript for details about the dataset content.
Using the Jupyter notebook under the code folder
Prerequisites
We recommend using Anaconda to create and manage your development environment. All the subsequent instructions are provided assuming you are using Anaconda (Python 3 version).
Clone repo
Clone the repo or download as a zip and extract.
cd into the code folder
Open Anaconda prompt (Windows) or the system Command line interface then naviguate to the code ```sh cd .GI-review-dataset/code
```
Setup conda env
sh
$ conda env create -f environment.yml
Setup kernell for Jupyter lab
sh
$ conda activate env-GI-review
$ ipython kernel install --user --name=<any_name_for_kernel>
$ conda deactivate
Launch Jupyter lab
Launch Jupyter lab and naviguate to open the post-processing-code.ipynb file under the code folder. Make sure to change the kernel to the one created above (e.g., see https://doc.cocalc.com/howto/jupyter-kernel-selection.html#cocalc-s-jupyter-notebook)
References
[1] Patel, B., Gizzi, A., Hashemi, J., Awakeem, Y., Gregersen, H., & Kassab, G. (2021). Biomechanical constitutive modeling of the gastrointestinal tissues: where are we?. preprints.org (https://doi.org/10.20944/preprints202109.0391.v1)
[2] Bandrowski, A., Grethe, J.S., Pilko, A., Gillespie, T.H., Pine, G., Patel, B., Surles-Zeiglera, M. and Martone, M.E., 2021. SPARC data structure: Rationale and design of a fair standard for biomedical research data. bioRxiv (https://doi.org/10.1101/2021.02.10.430563)
[3] https://github.com/bvhpatel/SODA
[4] Patel, B., Ngo, T., Soundarajan, S. SODA (Software to Organize Data Automatically) for SPARC: v4.7.0. Zenodo (https://doi.org/10.5281/zenodo.5392287).
Owner
- Name: Bhavesh Patel
- Login: bvhpatel
- Kind: user
- Location: San Diego, CA
- Company: California Medical Innovations Institute
- Repositories: 4
- Profile: https://github.com/bvhpatel
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