Code: SPARC Marker Paper

About

This is the code associated with the SPARC Marker Paper. SPARC is one of the NIH Common Fund's Program that seeks to accelerate the development of therapeutic devices that modulate electrical activity in the ANS to improve internal organ functions and suppress dysfunction. The SPARC Marker paper currently being prepared is aimed at providing an overview of the SPARC program, presenting its major outcomes, and giving an assessment of the impact of the program on bioelectronic medicine-related research and development. The repository contains the Jupyter notebook developed to analyze data for the paper and generate figures. See this inventory for all related resources, including the paper.

Standards followed

The overall code is structured according to the FAIR-BioRS guidelines. The Python code in the Jupyter notebook main.ipynb follows the PEP8 guidelines. Functions are documented with docstring formatted following Google's style guide. All the dependencies are documented in the environment.yml file.

Using the Jupyter notebook on your computer

Prerequisites

We recommend using Anaconda to create and manage your development environment and using JupyterLab to run the notebook. All the subsequent instructions are provided assuming you are using Anaconda (Python 3 version) and JupyterLab.

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 .sparc-marker-paper

```

Setup conda env

sh $ conda env create -f environment.yml

Setup kernell for Jupyter lab

sh $ conda activate sparc-marker-paper $ conda install ipykernel $ ipython kernel install --user --name=<any_name_for_kernel> $ conda deactivate

Launch Jupyter lab

Launch Jupyter lab and naviguate to open the main.ipynb file. Make sure to change the kernel to the one created above (e.g., see here). We recommend to use the JupyterLab code formatter along with the Black and isort formatters to facilitate compliance with PEP8 if you are editing the notebook.

Using the Jupyter notebook on o²S²PARC (no installation required)

SPARC has also developed o²S²PARC, a cloud platform to build and explore modeling and data analysis pipelines. You will find the code in this repository, all the necessary software dependencies, and the input data at this o²S²PARC link.

To access the o²S²PARC link, you need an o²S²PARC account; you will find more information on how to create an account at the o²S²PARC platform URL osparc.io.

Inputs/outputs

The Jupyter notebook makes use of files in the dataset associated with the SPARC Marker Paper (see here). You will need to download the dataset at add it in the input folder.

Outputs of the code include tables displayed directly in the notebook and plots displayed in the notebook but also saved as files. These saved plot files are included in the output folder.

License

This work is licensed under MIT. See LICENSE for more information.

Feedback and contribution

Use the GitHub issues for submitting feedback or making suggestions. You can also work the repository and submit a pull request with suggestions.

How to cite

If you use this code, please cite the SPARC Marker Paper (it will be listed here when available) and also cite this repository as:

bash Patel, Bhavesh. Code: SPARC Marker Paper [Software]. Zenodo. https://doi.org/10.5281/zenodo.11361363