BICAN Tools and Infrastructure

BICAN supports open tools and infrastructure for data access, analysis, integration, visualization, and reuse. These resources help users work with BICAN data and enable developers to build on shared pipelines, viewers, and operational platforms.
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Core BICAN infrastructure includes the platforms, partner resources, and data systems that support consortium-scale data generation and sharing. These components help coordinate biospecimen sourcing, sequencing workflows, cloud-based processing, public communication, and dataset discovery so that BICAN products can move from collaborative production into accessible community resources.

INFRASTRUCTURE
(RRID/PID)

BICAN USAGE

DESCRIPTION

Neuroanatomy-anchored Information Management Platform (NIMP) RRID:SCR_024684

• Developed by BICAN
• Used to manage specimen and sequencing workflows
• Supports anatomical provenance tracking

Centralized system for tracking BICAN specimen and sequencing workflows. NIMP includes the Specimen Portal and Sequence Library Portal, which together manage tissue requests, specimen tracking, sequencing library submission, and data deposition workflows. The system supports linkage of multimodal genomic data back to anatomical origins using Allen Brain Atlas resources.

NIH NeuroBioBank
RRID:SCR_003131

• Used by BICAN
• Source of human postmortem brain tissue and associated biospecimens

National resource that provides investigators with access to human postmortem brain tissue and related biospecimens for research on the nervous system.

Terra
RRID:SCR_021648

• Used by BICAN
• Supports secure cloud-based data analysis and sharing

Open-source, cloud-native platform developed by the Broad Institute in collaboration with Verily and Microsoft. Terra enables biomedical researchers to access, analyze, and share large-scale data securely.

Broad Institute Genomics Platform
RRID:SCR_027987

• Used by BICAN
• Supports high-throughput sequencing and genomic data generation

Large-scale genomics facility that generates, analyzes, and interprets high-throughput genomic data. In BICAN, the platform supports sequencing-based data generation workflows.

New York Genome Center Research Sequencing Platform

• Used by BICAN
• Supports high-throughput sequencing and genomic data generation

Independent nonprofit genomics research center and technology platform that supports sequencing, genomic technology development, and data analysis. In BICAN, the platform contributes to large-scale genomic data production.

Brain Knowledge Platform
RRID:SCR_027180

• Used by BICAN
• Provides access to BICAN data, tools, and visualization resources

Multi-species neuroscience platform for exploring brain cells, anatomy, and related datasets. The Brain Knowledge Platform includes catalogs of relevant data and projects, along with visualization tools for understanding brain cell types and brain organization.

BICAN Portal

• Developed by BICAN
• Main public website for the BICAN project

Public-facing website for BICAN information, outreach, consortium updates, standards, resources, and links to data products.

BICAN Data Catalog
RRID:SCR_027884

• Developed by BICAN
• Catalogs BICAN datasets and release products
• Links users to primary data in archives

Catalog of BICAN datasets, projects, and release products. Entries provide descriptive metadata and links to primary data stored in appropriate archives and partner repositories.

BICAN data are shared through established archives that support long-term access, preservation, and reuse. Different archives serve different data types, allowing sequencing, imaging, neurophysiology, and related datasets to be deposited in systems designed for those modalities. Together, these repositories help ensure that BICAN data products remain discoverable, citable, and available for downstream analysis.

Archive (RRID/PID)

BICAN USAGE

DESCRIPTION

Distributed Archives for Neurophysiology Data Integration (DANDI)
‍RRID:SCR_017571

• Used by BICAN
• Archive for neurophysiology and electrophysiology data
• Supports Patch-seq-related data deposition

Platform for publishing, sharing, and processing neurophysiology data. DANDI is funded by the BRAIN Initiative and supports standardized deposition and reuse of neurophysiology datasets.

Brain Image Library (BIL)
RRID:SCR_017272

• Used by BICAN
• Archive for large-scale brain imaging data
• Supports light microscopy, spatial, and morphology-related data deposition

Platform for publishing, sharing, and visualizing large light-microscopic 2D and 3D brain datasets.

Neuroscience Multi-Omic Archive (NeMO) RRID:SCR_016152

• Used by BICAN
• Primary archive for sequencing-based omics data
• Supports storage and dissemination of BICAN molecular datasets

Data repository focused on storage and dissemination of omics data generated by BRAIN Initiative and related brain research projects.

National Institute of Mental Health Data Archive (NDA) RRID:SCR_004434

• Used by BICAN where applicable
• Archive for de-identified human subjects research data
• Supports controlled sharing of harmonized human research data

NIMH-hosted data archive that makes human subjects data available across many research domains. NDA supports sharing of research data, tools, methods, and analyses. De-identified data harmonized to common standards are available to qualified researchers, while summary data are broadly available.

Brain Observatory Storage Service and Database (BOSSDB)
RRID:SCR_017273

• Used by BICAN where applicable
• Supports storage and access for large-scale volumetric neuroscience datasets

Cloud-based service for storing, accessing, and sharing large-scale volumetric brain imaging datasets.

Tools provide practical entry points for working with complex BICAN resources. They help users move beyond static files by supporting interaction with data, annotations, visualizations, and related knowledge in ways that make the resources easier to find, understand, and use.

TOOl (RRID/PID)

BICAN USAGE

DESCRIPTION

Brain Cell Type Annotation and Integration using Distributed AI (BRAINCELL-AID)
RRID:SCR_027398

• Developed by BICAN
• Supports cell cluster interpretation and literature-grounded annotation

Resource for mouse brain cell cluster annotation that integrates marker gene sets, large language models, Gene Ontology information, and PubMed-linked evidence. The platform supports exploration of brain cell clusters and transparent annotation workflows.

Annotation Comparison Explorer
RRID:SCR_026496

• Used by BICAN
• Supports comparison of cell type assignments and cell-level annotations

Web application for comparing cell type assignments and other cell-based annotations, including donor demographics, anatomical locations, batch variables, and quality control metrics. It has been used to connect brain cell types across studies of health and Alzheimer’s disease.

Cell Annotation Platform (CAP)
RRID:SCR_022797

• Used by BICAN
• Supports creation, sharing, and review of cell annotations

Community-driven platform to create, explore, store, and analyze cell annotations. CAP supports annotation terms with associated molecular signatures and helps researchers converge on consensus nomenclature.

Human Connectome Workbench RRID:SCR_008750

• Used by BICAN
• Supports visualization and mapping of neuroimaging data

Open-source visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project.

Brain Cell Data Viewer RRID:SCR_023321

• Used by BICAN
• Supports visualization, interaction, and download of brain cell data

Web application for exploring brain cell data through linked views for gene expression, single-cell data, and spatial localization.

Cellarium Cell Annotation Service (CAS) RRID:SCR_025438

• Used by BICAN
• Supports automated cell type annotation and dataset comparison

Cell type annotation resource co-developed by 10x Genomics and the Broad Institute Data Sciences Platform. CAS provides a Python client library and API for querying single-cell omics data against a large reference index derived from public single-cell transcriptomics datasets.

Cytosplore Viewer
RRID:SCR_018330

• Used by BICAN
• Supports interactive exploration of single-cell and spatial transcriptomics data
• Provides access to HMBA and basal ganglia release data

Interactive visual analytics system for exploring single-cell and spatial transcriptomics data, including curated BICAN and Human and Mammalian Brain Atlas resources.

Basal Ganglia Epigenome Portal
RRID:SCR_027887

• Developed for BICAN-related basal ganglia resources
• Supports exploration of human basal ganglia epigenomic and transcriptomic data

Integrative web resource for exploring epigenetic regulation in the human brain. The portal unifies single-cell transcriptomic and epigenomic data from the basal ganglia.

MapMyCells
RRID:SCR_024672

• Developed BICAN contributors
• Used to map user datasets to reference cell type taxonomies
• Supports integration of community datasets with BICAN reference resources

Tool for mapping single-cell and spatial transcriptomics datasets to high-quality, high-resolution cell type taxonomies. MapMyCells helps researchers align new datasets to shared reference atlases.

Slide-Tags Viewer
SCR_028255

• Developed for BICAN-related basal ganglia resources
• Supports visualization of human striatal Slide-tags spatial transcriptomics data

Online viewer for a human striatal Slide-tags spatial transcriptomics dataset comprising approximately 1.1 million cells from 19 human striatum donors.

Shared pipelines support standardization of data in BICAN by giving participating groups a common route from raw data to analysis-ready outputs. Rather than requiring each lab to make separate processing decisions, these workflows create a more consistent basis for quality review and cross-dataset comparison. They also help ensure that data released through BICAN can be interpreted in the context of the methods used to generate it.

PIPELINE (RRID/PID)

BICAN USAGE

DESCRIPTION

Human Connectome Pipelines
RRID:SCR_026575

• Used by BICAN where applicable
• Supports processing of human neuroimaging data

Processing pipelines for Human Connectome Project-style neuroimaging data.

Slide-tags Pipeline
RRID:SCR_027567

• Used by BICAN
• Supports processing of Slide-tags spatial transcriptomics data

Open-source, cloud-optimized workflow for processing spatial transcriptomics data from spatially barcoded sequencing technologies. The pipeline converts raw sequencing data into spatially resolved gene expression matrices.

ATAC Pipeline RRID:SCR_024656

• Used by BICAN
• Supports processing of single-nucleus ATAC-seq data

Open-source, cloud-optimized pipeline developed with BRAIN Initiative and SCORCH collaborators. It supports processing of 10x single-nucleus chromatin accessibility data, including ATAC data generated with 10x Multiome assays.

Multiome Single-cell ATAC and Gene Expression Pipeline
RRID:SCR_024217

• Used by BICAN
• Supports processing of paired gene expression and chromatin accessibility data

Open-source, cloud-optimized pipeline for 10x single-cell and single-nucleus gene expression and ATAC data generated with the 10x Genomics Multiome assay.

Paired-Tag Pipeline RRID:SCR_025042

• Used by BICAN
• Supports processing of Paired-Tag and related multiomic data

Open-source, cloud-optimized pipeline developed with BICCN and BICAN collaborators. It supports processing of 3′ single-nucleus histone modification data generated with the Paired-Tag protocol, as well as related 10x gene expression data.

Single Nucleus Methyl-Seq and Chromatin Capture Pipeline (snm3C) RRID:SCR_025041

• Used by BICAN
• Supports processing of single-nucleus methylome and chromatin contact data

Open-source, cloud-optimized workflow for processing snm3C sequencing data. The workflow demultiplexes and aligns raw reads, calls chromatin contacts, and generates summary metrics.

Smart-seq2 Single Nucleus Multi-Sample Pipeline RRID:SCR_021312

• Used by BICAN and BICCN
• Supports processing of Smart-seq2 single-nucleus RNA-seq data

Pipeline for processing single-nucleus RNA-seq data generated with Smart-seq2 assays. The workflow is written in WDL, is available through the WARP GitHub repository, and can be run with a compliant WDL runner.

Slide-Seq Pipeline RRID:SCR_023379

• Used by BICAN
• Supports processing of Slide-seq spatial transcriptomics data

Open-source, cloud-optimized pipeline developed with BICCN and BICAN collaborators. It supports processing of spatial transcriptomics data generated with the Slide-seq assay, commercialized as Curio Seeker.

BuildIndices Pipeline RRID:SCR_027630

• Used by BICAN
• Supports creation of reference bundles for sequencing workflows

Open-source, cloud-optimized pipeline developed with BICCN and BICAN collaborators. The workflow filters GTF files, calculates chromosome sizes, and builds reference bundles required by STAR and bwa-mem2 aligners.

Optimus Pipeline RRID:SCR_018908

• Used by BICAN and related BRAIN Initiative projects
• Supports processing of 10x single-cell and single-nucleus count data

Open-source, cloud-optimized pipeline developed by the Human Cell Atlas Data Coordination Platform with BICCN collaboration. It supports processing of 3′ single-cell and single-nucleus count data generated with 10x Genomics v2 or v3 assays.