sparc-assemble 0.1.0

A Python tool to find and automatically assemble tools and workflows to process SPARC datasets in accordance with FAIR principles.

SPARC Assemble (sparc-assemble)

A Python tool to find and automatically assemble tools and workflows to process SPARC datasets in accordance with FAIR principles.

Table of contents

• About
• Introduction
• The problem
• Our solution - sparc-assemble
• Impact and vision
• Future developments
• Setting up sparc-assemble
• Using sparc-assemble
• Reporting issues
• Contributing
• Cite us
• FAIR practices
• License
• Team
• Acknowledgements

About

This is the repository of Team sparc-assemble (Team #2) of the 2024 SPARC Codeathon. Click here to find out more about the SPARC Codeathon 2024. Check out the Team Section of this page to find out more about our team members.

Please see the Acknowledgements section of this readme for a list of tools that have been used in this project.

Introduction

The NIH Common Fund program on Stimulating Peripheral Activity to Relieve Conditions (SPARC) focuses on understanding peripheral nerves (nerves that connect the brain and spinal cord to the rest of the body), how their electrical signals control internal organ function, and how therapeutic devices could be developed to modulate electrical activity in nerves to improve organ function. This may provide a potentially powerful way to treat a diverse set of common conditions and diseases such hypertension, heart failure, gastrointestinal disorders, and more. 60 research groups spanning 90 institutions and companies contribute to SPARC and work across over 15 organs and systems in 8 species.

The SPARC Portal provides a single user-facing online interface to resources that can be shared, cited, visualized, computed, and used for virtual experimentation. A key offering of the portal is the collection of well-curated datasets in a standardised format, including anatomical and computational models that are being generated both SPARC-funded researchers and the international scientific community. These datasets can be found under the "Find Data" section of the SPARC Portal. Information regarding how to navigate a SPARC dataset and how a dataset is formatted can be found on the SPARC Portal.

The scientific community is developing tools to process the original data and generate new results, outcomes, and knowledge

Workflows can be developed that apply tools (e.g. segmentation of images, or running of computational physiology simulations) in a series of steps **to . These results (derived data) can be stored in a new standardised dataset and potentially be contributed to the SPARC Portal to support further scientific advances.

The problem

There is currently no option for users to:

• easily find and access existing tools and workflows developed by the SPARC community for processing SPARC data
• easily find and access external tools that could be used for processing SPARC data
• easily reuse these tools to assemble and run new workflows for:
  • processing existing SPARC data
  • helping identify new data that could be collected to fill in gaps in our knowledge
• easily run such workflows locally or from cloud computing platforms such as oSPARC
• easily reproduce workflow results

Our solution - sparc-assemble

To address this problem, we have developed a Python module called the SPARC Assemble (sparc-assemble) that can be used to find and automatically assemble workflows and tools to process SPARC datasets in accordance with FAIR principles:

• Provides an easy-to-use python-based application programming interface (API) to enable searching of available tools and workflows

If you find sparc-assemble useful, please add a GitHub Star to support developments!

Designed to enable FAIRness

Impact and vision

Future developments

• Workflow and tool registry in SPARC portal

Setting up sparc-assemble

Pre-requisites

• Git
• Python. Tested on:
  • 3.10
• Operating system. Tested on:
  • Ubuntu 18

PyPI

Here is the link to our project on PyPI

pip install sparc-assemble

From source code

Downloading source code

Clone the sparc-assemble repository from github, e.g.:

git clone https://github.com/SPARC-FAIR-Codeathon/2024-team-2.git

Installing dependencies

1. Setting up a virtual environment (optional but recommended). In this step, we will create a virtual environment in a new folder named venv, and activate the virtual environment.

   • Linux

   python3 -m venv venv
   source venv/bin/activate
   

   • Windows

   python3 -m venv venv
   venv\Scripts\activate
   

2. Installing dependencies via pip

   pip install -r requirements.txt
   

Using sparc-assemble

Running tutorials

Guided Jupyter Notebook tutorials have been developed describing how to use sparc-assemble in different scenarios:

Tutorial	Description
1	INSERT
2	Use sparc-assemble to ...
3	Use sparc-assemble to run ...
4	Use sparc-assemble to run ...
5	Use sparc-assemble to run ...
6	Use sparc-assemble to run ...

Reporting issues

To report an issue or suggest a new feature, please use the issues page. Issue templates are provided to allow users to report bugs, and documentation or feature requests. Please check existing issues before submitting a new one.

Contributing

Fork this repository and submit a pull request to contribute. Before doing so, please read our Code of Conduct and Contributing Guidelines. Pull request templates are provided to help guide developers in describing their contribution, mentioning the issues related to the pull request and describing their testing environment.

Project structure

• /sparc_assemble/ - Parent directory of sparc-assemble python module.
• /sparc_assemble/core/ - Core classes of sparc-assemble.
• /resources/ - Resources that are used in tutorials (e.g. SDS datasets containing workflow and tool descriptions).
• /tutorials/ - Parent directory of tutorials for using sparc-assemble.
• /development_examples/ - Parent directory of examples that were created during the development of sparc-assemble.
• /docs/images/ - Images used in sparc-assemble tutorials.

Cite us

If you use sparc-assemble to make new discoveries or use the source code, please cite us as follows:

Mathilde Verlyck, Jiali Xu, Max Dang Vu, Thiranja Prasad Babarenda Gamage, Chinchien Lin (2024). sparc-assemble: v1.0.0 - A Python tool to find and automatically assemble tools and workflows to process SPARC datasets in accordance with FAIR principles. Zenodo. https://doi.org/XXXX/zenodo.XXXX.

FAIR practices

We have assessed the FAIRness of our sparc-assemble tool against the FAIR Principles established for research software. The details are available in the following [document](INSERT GOOGLE DOC).

License

sparc-assemble is fully open source and distributed under the very permissive Apache License 2.0. See LICENSE for more information.

Team

• Mathilde Verlyck [e-mail] (Developer, Writer - Documentation)
• Jiali Xu (Developer, Writer - Documentation)
• Max Dang Vu [e-mail] (Developer, Writer - Documentation)
• Thiranja Prasad Babarenda Gamage (Writer - Documentation)
• Chinchien Lin (Lead, SysAdmin)

Acknowledgements

• We would like to thank the organizers of the 2024 SPARC Codeathon for their guidance and support during this Codeathon.