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Rapid Release: BICAN-2024-10-RR-SCO
Release
- Release Title: Rapid Release Inventory
- Release Date: Oct. 1, 2024
- Release Version: BICAN-2024-10-RR-SCO
- Superceded by BICAN-2026-01-RR-SCO
About
The BICAN is committed to rapid data sharing to increase the accessibility and impact of the data generated by constituent members. We have enabled sharing of data within a calendar quarter of its generation, utilizing a federated pipeline for metadata collection, sequencing, and data processing. The initial Rapid Release Inventory provides early search and access capabilities for single cell transcriptomic and epigenomic data.
This release features three core components:
- Data ingest pipelines integrated with specimen/sequencing data management at NIMP & NeMO archive.
- Dedicated BICAN program page in the Data Catalog with dashboard overview of BICAN data ecosystem
- BICAN rapid release project page and specimen viewer
The first public release of data from the BRAIN Initiative Cell Atlas Network (BICAN) is now available in the Data Catalog. BICAN is a continuation of the BRAIN Initiative Cell Census Network (BICCN) and features unprecedented diversity in cross-species specimens and data.
Release Organization
The first Rapid Release Inventory project includes single cell transcriptomic and epigenomic data generated by participating BICAN awardees. The project-level organization provides search across common features of all single cell data. Data is further packaged into 20 “collections” of files that are available individually from the Neuroscience Multiomic Archive (NeMO); each collection is grouped based upon technique, species, grant and participating laboratory.
Navigating the Release
A new dedicated BICAN program page serves as the visual entry point to BICAN data within the Data Catalog. It features a general description of the consortium effort and goals and interactive dashboards that give an overview of the BICAN data ecosystem, as well as featured projects and links to other highlighted web resources.
Scientists can explore data from 6 labs, totalling 255 donors, 1461 specimens(library aliquots), and 20 data collections. They are accessible via a dedicated project page and specimen browser. The latter features a multi-level viewing experience broken down by library aliquot or donor. Scientists can download specimen metadata and file manifests that match the filters selected in the user interface.
General Licensing and Usage Guidelines
Data are provided under different licenses. Please check the Data Catalog collection descriptions and the README file available for download alongside specimen and file manifests for the applicable license for each dataset. Generally non-human datasets are made available under a CC-BY-4.0 license. Human data derived from tissue consented for open access are provided under BICAN-BY-NR. The initial release does not include controlled access human data.
When data is reused, please provide attribution to the data generators by citing the data citation. Data citations can be found with the collection at the NeMO archive or in the Data Catalog collection description.
Release Documentation
- Release notes: BICAN consortium data now available in Data Catalog.
- Tutorial: Download a file manifest for all female chimpanzees from the UM1MH130981 BICAN grant.
- User docs: BICAN Rapid Release: Reference documentation
Contributors
Data in the rapid release were generated by multiple laboratories as part of the BRAIN Initiative Cell Atlas Network, including developmental mouse data from the Allen Institute for Brain Science (Zeng) & University of California, San Francisco (Nowakowski), cross-species data from the Allen Institute for Brain Science (Lein), marmoset data from Princeton University (Krienen), as well as multi-modal human data from Broad Institute (McCarroll) & Salk Institute for Biological Studies (Ecker). The NIH grant awards contributing to data in this initial release are shown below.
The data ecosystem that supports the initial product release includes three platforms: Brain Knowledge Platform (BKP; the brain science accelerator at Allen Institute), the Neuroanatomy-anchored Information Management Platform for Collaborative BICAN Data Generation (NIMP, RRID:SCR_024684; The University of Texas Health Science Center at Houston) and the fastq file storage at NeMO archive. These integrated platforms will continue to enable quarterly cross-consortium data releases going forward.
Metadata and resource identifiers (ID) for specimens and sequencing data are captured, managed, and cross-linked through the Neuroanatomy-anchored Information Management Platform (NIMP, RRID:SCR_024684) for Collaborative BICAN Data Generation, codifying critical BICAN data standards and standard operating processes to ensure trackable experimental workflow and data integrity for down-stream data archives of the entire BICAN consortium.
Single cell omics data processing pipelines were developed by the Broad Data Sciences Platform in partnership with the BICAN community. Pipelines are available on GitHub (RRID:SCR_002630), Dockstore, and the cloud workbench Terra (RRID:SCR_021648) Data operations (including data ingestion, storage, and release) are performed by the Neuroscience Multi-omic (NeMO) Archive team at the University of Maryland.
The following NIH Awards provided infrastructure support for the BICAN Data Ecosystem and initial Rapid Release.