- Introduction
- Presenting oSPARC Hub
- oSPARC Applications
- oSPARC Services
- Deployment Status
- License
- Team Members
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.
| Data Type on SPARC | Dataset Count | Associated oSPARC Module/Service | Action Required |
|---|---|---|---|
| SCKAN Database | Various | X | Created one |
| Anatomical Models | 40 | + - | Created one |
| Navigate SPARC Portal Datasets | X | Created one | |
| Datasets | |||
| - Microscopy | 100 | V | Tutorial |
| - Anatomy | 96 | V | Tutorial |
| - Physiology | 96 | Tutorial | |
| - Electrophysiology | 62 | V | Tutorial |
| - Connectivity | 52 | V | Tutorial |
| - Histology | 35 | - | - |
| - Spatial Transcriptomics | 22 | - | - |
| - Expression; Expression Characterization; Transcriptomics | 22 | + - | Update + Add a UI |
| - Other | <20 each | - | - |
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, and
- 6 oSPARC Services
that are accessible via the oSPARC platform.
Source Code: https://github.com/SPARC-FAIR-Codeathon/oSPARC-Hub/tree/main/Apps/Visualize%20Anatomical%20Modules
This is an App for transcriptomics data analysis and visualization.
Source Code: https://github.com/SPARC-FAIR-Codeathon/2024-team-5/tree/main/Apps/Transcriptomics%20data%20visualization
This app allows you to access data fromm the SCKAN database.
Source Code: https://github.com/SPARC-FAIR-Codeathon/2024-team-5/tree/main/Apps/Visualize%20SCKAN%20datadase%20data
This module allows conversion of files between various formats such as CSV, JSON, YAML, XLS, XLSX, NWB (Neurodata Without Borders) and many others.
Dedicated GitHub Repo: https://github.com/SPARC-FAIR-Codeathon/2024-team-5-service-1
Citation: Appukuttan, S., Benaribi, H., & Rievers, F. (2024). oSPARC Service #1: File Format Converter. Zenodo. https://doi.org/10.5281/zenodo.13308896
This module converts .vtk files to their .stl and .obj equivalents, which have wider support with visualization libraries.
Dedicated GitHub Repo: https://github.com/SPARC-FAIR-Codeathon/2024-team-5-service-2
Citation: Appukuttan, S., Benaribi, H., & Rievers, F. (2024). oSPARC Service #2: VTK Converter. Zenodo. https://doi.org/10.5281/zenodo.13308927
This module offers a quick and simple visualization of 3D scaffold models.
Dedicated GitHub Repo: https://github.com/SPARC-FAIR-Codeathon/2024-team-5-service-3
Citation: Appukuttan, S., Benaribi, H., & Rievers, F. (2024). oSPARC Service #3: Visualize 3D Model. Zenodo. https://doi.org/10.5281/zenodo.13308931
This module can fetch scaffold .vtk file from SPARC Portal for specified datasets.
Dedicated GitHub Repo: https://github.com/SPARC-FAIR-Codeathon/2024-team-5-service-4
Citation: Appukuttan, S., Benaribi, H., & Rievers, F. (2024). oSPARC Service #4: Fetch Scaffold From SPARC Portal. Zenodo. https://doi.org/10.5281/zenodo.13308937
This module enables users to view tabular data fromw within study.
Dedicated GitHub Repo: https://github.com/SPARC-FAIR-Codeathon/2024-team-5-service-5
Citation: Appukuttan, S., Benaribi, H., & Rievers, F. (2024). oSPARC Service #5: Tabular Data Viewer. Zenodo. https://doi.org/10.5281/zenodo.13308941
This module allows users to explore and visualize transcriptomic data.
Dedicated GitHub Repo: https://github.com/SPARC-FAIR-Codeathon/2024-team-5-service-6
Citation: Appukuttan, S., Benaribi, H., & Rievers, F. (2024). oSPARC Service #6: Transcriptomics Data Explorer. Zenodo. https://doi.org/10.5281/zenodo.13308944
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
This project is licensed under the MIT License - see the LICENSE file for details.
- 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
Please open an issue here.