Question for the SPARC community?
The Stimulating Peripheral Activity to Relieve Conditions (SPARC) program is supported by the NIH Common Fund to provide a scientific and technological foundation for future bioelectronic medicine devices and protocols. Learn more about SPARC.
Take a walkthrough of the SPARC Portal to learn how to access high quality multimodal, multi-species data and powerful tools for exploring the organization and function of ANS-end organ interactions. Through the portal, users can search, browse, view, and download datasets.
But SPARC does more, linking these data to 2D interactive maps where you can explore these data in the context of a ANS connections, or view spatial distributions of cells and nerve processes within 3D computational scaffolds.
These 3D scaffolds are available for download along with tools. The SPARC Portal provides access to the powerful o²S²PARC simulation platform, where you can run and tune dynamic models of ANS function, or create your own simulations.
(See also: Using computers to simulate, optimize, and understand neural responses to electrical signals to treat disease by SPARC investigator Nikki Pelot.)
|Access and explore anatomical multi-species datasets on the vagus nerve||Anatomical dataset|
|Access and explore functional multi-species datasets on the vagus nerve||Functional dataset|
|Explore connections of the vagus nerve||Example dataset|
|Predict parameter-dependent vagal nerve responses using an AI-informed computational model running on OSPARC||Predict parameter-dependent vagal nerve responses|
|Use a Jupyter Notebook with SPARC data||tutorial|
You can also browse our YouTube tutorials to learn more about what SPARC offers. For help with our more advanced features, we suggest contacting us. For more information on the SPARC Data and Resource Center, which oversees development of the portal, see here.
The SPARC Portal provides viewers for different data types that let you explore and view data through the portal without downloading the files.
Here we demonstrate how to view 2D and 3D microscopic images and movies through the Portal.
Example 1: iWAT (inguinal White Adipose Tissue) sympathetic innervation circuit pseudorabies viral tracing in reporter mice contributed by Muenzberg et al. (2021) DOI: 10.26275/mhq6-csy1
[View] (https://sparc.science/datasets/biolucidaviewer/6640?view=NjY0MC1jb2wtMTY2&dataset_version=1&dataset_id=175&item_id=N%3Apackage%3Afc9d4311-0a2c-415e-8421-1122b20957ad) a confocal light sheet microscopy image of iWAT using the image gallery viewer.
Example 2: Visualizing sympathetic projections in the intact brown adipose tissue depot in the mouse contributed by Seoeun Lee and Lori Zeltser (2020) DOI: 10.26275/ge74-ypxd
View a movie of sympathetic innervation of brown adipose tissue using confocal microscopy with iDISCO prepared tissue.
How do I do this myself? Movies can be viewed in two ways depending on the format. All .mp4 movies may be viewed through the File tab; other formats are sometimes made available through the Gallery Viewer). For the dataset, above, select the File tab for this dataset, and click the icon indicated below to view this movie.
SPARC Maps offers a visual interface for exploring SPARC data and tools in the context of knowledge about ANS connectivity and provides 3D organ scaffolds for mapping the 3D distribution of ANS axons and cells. View tutorials on MAP Viewer and the 3D Scaffold Viewer.
Example 1: Identification of peripheral neural circuits that regulate heart rate using optogenetic and viral vector strategies by Hanna et al. (2021) DOI:10.26275/0ce8-cuwi.
View a 3D mapping of the parasympathetic innervation of the heart on a 3D SPARC organ scaffold.
How do I do this myself? To view data mapped onto scaffolds, select the "derivatives" folder under the File menu, and look for the folder labeled "Scaffolds." Look for the eye icon in the action menu.
SPARC provides access to multiple tools for creating scaffolds and mapping data to them. For more information, contact [email protected].
- Access 3D organ scaffolds: Select the "Scaffold" facet under the "Models and Simulations" Tab.
- Access 3D scaffold tools for fitting data and making scaffolds: Search for "scaffold" in our Tools and Resources catalog.
All datasets on the SPARC portal are directly accessible to the research community. Users can download datasets directly from the SPARC portal, or access the data on AWS for large-scale downloads and/or cloud-based analytics.
Each dataset is highly curated in accordance with all FAIR principles of data sharing. Check out documentation to access data in AWS to find out how to start accessing SPARC data in the cloud.
The SPARC portal provides access to the o²S²PARC simulation platform, a cloud-based platform for developing, running, and sharing computational models and data analysis pipelines. Through the SPARC Portal, any user can directly investigate a contributed simulation through a “Run Simulation” link. Registered users with an o²S²PARC account have access to greater functionality such as editing existing simulation workflows and creating their simulations.
Examples of contributed simulations with detailed tutorials available on o²S²PARC
To run each simulation, click the "Run Simulation" button under the thumbnail image. See the abstract for details about model and access to a detailed tutorial on o²S²PARC.
The SPARC Nerve Activity Predictor (SNAP) by Ward (2022) [DOI: 10.26275/9ly6-az0n] (https://sparc.science/datasets/6): Predict parameter-dependent vagal nerve responses using an AI-informed computational model running on o²S²PARC.
[Multi-scale rabbit cardiac electrophysiology models] (https://sparc.science/datasets/4?type=simulation) by Lewis et al. (2022) DOI: 10.26275/vgd9.b4yv: a reusable and reproducible rabbit cardiac multi-scale electrophysiology model.
Updated 6 months ago