Powering the World's Largest Public Single-Cell Repository: CZ CELLxGENE Discover Census & TileDB
New technologies and analysis tools have led to the explosive growth of single-cell RNA sequencing (scRNA-seq) data, requiring new solutions that can accommodate datasets at scale. The formats used to distribute these data are not optimized for large volumes, and lack support for cloud storage. Furthermore, choice of file format is often determined by the language or analysis framework, creating silos of data that are difficult to share.
To address these challenges, TileDB and the single-cell biology team at the Chan Zuckerberg Initiative (CZI) collaborated to build SOMA: a unified open-source API specification for single-cell data access. SOMA is the foundation of Census — a feature of CZ CELLxGENE Discover that provides open access to the largest aggregation of analysis-ready single-cell data. Built from over 33 million cells and more than 500 datasets, Census cuts down parts of single-cell analysis from weeks to minutes. Powering efficient access to Census data is TileDB-SOMA, TileDB's implementation of the SOMA spec for R and Python that allows researchers to rapidly query and slice subsets of the data for analysis directly from the cloud.
In this recorded webinar, Pablo Garcia-Nieto, computational biologist at the Chan Zuckerberg Institute, and Aaron Wolen, principal software engineer and product leader for single cell at TileDB, cover:
The basics of the SOMA data model.
How TileDB-SOMA integrates directly with popular single-cell analysis frameworks like Seurat and Scanpy.
TileDB Cloud offers a unified data access, sharing, and scalable analysis platform for multiple constituents across pharma, biotech, and academia to accelerate collaborative insights.
The CZ CELLxGENE Discover Census open dataset.
Contents of this video
0:00:00 – Welcome
0:00:45 – Current state of single-cell biology (Pablo)
0:07:17 – Intro to TileDB-SOMA and TileDB Cloud (Aaron)
0:21:21 – CZ CELLxGENE Discover (Pablo)
0:25:50 – CELLxGENE Discover Census
0:31:36 – Census data access in Python
0:37:10 – Census PyTorch loaders
0:45:02 – Q&A
GitHub
https://github.com/single-cell-data/T...
https://github.com/single-cell-data/SOMA
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