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

cd .GI-review-dataset/code

Setup conda env

$ conda env create -f environment.yml

Setup kernell for Jupyter lab

$ 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).