oSPARC Hub : An Extensible ETL Framework for Streamlining the SPARC Ecosystem

Table of Contents

• Video Overview
• Introduction
• Presenting oSPARC Hub
• oSPARC Applications
• oSPARC Services
• License
• Team Members

Video Overview

Introduction

The SPARC Database offers a variety of datasets, including anatomical models, neural connectivity data available on the SCKAN database, physiological and electrophysiological data, genomics data, and more. These datasets are spread across different websites and typically require preprocessing before they can be visualized. Additionally, many models are not immediately usable and require significant preliminary work by the end-user to extract meaningful insights.

oSPARC is a platform provided by SPARC that offers services, code templates, and modules for managing various SPARC data types. However, not all datasets have dedicated visualization tools available on the oSPARC platform.

Presenting oSPARC Hub

The oSPARC Hub framework is a comprehensive suite of SPARC pipelines, modules, and applications designed to enhance the capabilities of the oSPARC platform. It introduces an integrated pipeline that allows users to navigate datasets directly from the SPARC portal within the platform.

Depending on the data type, there are three specialized applications available: one for accessing and utilizing data on the SCKAN database, another for exploring anatomical models on the SPARC Portal, and a third for working with genomics datasets. In addition, several modules have been developed to efficiently process various data types, ensuring seamless integration and usability.

In total, we have developed:

-3 oSPARC Application available on the oSPARC platform.

-And 6 oSPARC Services, that are accessible via the oSPARC platform.

oSPARC-Hub Applications

Name	Utility	Tutorial	Source Code	Zenodo
Visualize Anatomical Modules Demonstration	Visualizes Anatomical 3D Scaffold	Tutorial	Source Code
Transcriptomics data visualization	Analyzes and visualizes transcriptomics data	Tutorial	Source Code
Visualize SCKAN database data	Accesses and visualizes SCKAN database data	Tutorial	Source Code

oSPARC Services

Name	Utility	Tutorial	Source Code	Zenodo
File Format Converter	Converts files between various formats	Tutorial	Dedicated GitHub Repo	Zenodo
VTK Converter	Converts .vtk files to .stl and .obj formats	Tutorial	Dedicated GitHub Repo	Zenodo
Visualize 3D Model	Visualizes 3D scaffold models	Tutorial	Dedicated GitHub Repo	Zenodo
Fetch Scaffold From SPARC Portal	Fetches scaffold .vtk files from SPARC Portal	Tutorial	Dedicated GitHub Repo	Zenodo
Tabular Data Viewer	Views tabular data within studies	Tutorial	Dedicated GitHub Repo	Zenodo
Transcriptomics Data Explorer	Explores and visualizes transcriptomic data	Tutorial	Dedicated GitHub Repo	Zenodo

Models Deployment Status

The services are awaiting deployment to oSPARC production. The GitHub actions fail, as we do not have the required permissions for the build stage:

/home/scu/.venv/bin/python3: can't open file '/home/scu/.venv/bin/ooil': [Errno 13] Permission denied

Service has been deployed and tested locally via:

make publish-local

License

This project is licensed under the MIT License - see the LICENSE file for details.

Team Members

• Shailesh Appukuttan - Aix-Marseille Université, CNRS, INT, Marseille, France - @appukuttan-shailesh
• Hiba Ben Aribi - University of Tunis El Manar, Tunis, Tunisia - @HibaBenAribi
• Fynn Rievers - Tilburg University, Tilburg, The Netherlands - @schrievicode

Have an issue or question?

Please open an issue here.