Overview
The Seven Bridges Cancer Genomics Cloud developed by Velsera (SB-CGC), is a cloud-based platform for cancer research funded by the NCI. It co-localizes in a single environment:
- Access to data
- Tools for data analysis
- The computational power for large-scale analyses
Users can access many large NCI datasets across multiple fields, including genomics, proteomics, and data from multiple species, as well as bring in their own data quickly and easily. SB-CGC provides a curated library of over 850 tools and workflows that have been optimized for the cloud, covering many major areas of data analysis. Users can bring in their own pipelines or edit our existing tools by using our simple workflow editor to wrap and edit tools in Common Workflow Language. Users can then continue their analyses in the cloud using JupyterLab or RStudio (Galaxy and SAS are coming soon!) packages. The entire platform is built with both security and collaboration in mind, so users can work with other researchers around the world while knowing their data are safely controlled.
Data
The Seven Bridges Cancer Genomics Cloud makes data from various programs and initiatives accessible. Below is an outline of the most used datasets and the CRDC data commons where they can be found.
| Dataset | Data Commons |
|---|---|
| CBTN (Children’s Brain Tumor Network) | GDC, PDC |
| CCDI (Childhood Cancer Data Initiative) | PDC |
| CMB (Cancer Moonshot Biobank) | GC |
| CMPC (The Comparative Molecular Characterization Program) | CTDC |
| COP (Comparative Oncology Program) | ICDC |
| CPTAC (Clinical Proteomic Tumor Analysis Consortium) | GDC, PDC |
| HTAN (Human Tumor Atlas Network) | GC |
| ICPC (International Cancer Proteogenomic Consortium) | PDC |
| PCCR (The Purdue University Center for Cancer Research) | ICDC |
| PPTC (Pediatric Preclinical Testing consortium) | GC |
| TARGET (Therapeutically Applicable Research to Generate Effective Treatments) | GDC |
| TCGA (The Cancer Genome Atlas) | GDC |
Note that these are the most commonly requested datasets from each Data Commons and the Cloud Resource that provides access.
Learn more about Datasets and how to access them.
Users can also go to each Data Commons for a complete list of the datasets they house.
Tools
The Seven Bridges Cancer Genomics Cloud offer thousands of publicly available analytical tools and features of interest to researchers with varying skills and needs. Below is an overview of what SB-CGC has to offer.
| Tool Category | Available Tools |
|---|---|
| Workflows | CWL, WDL and Nextflow Workflow Support, Publicly Available Workflows from Dockstore |
| Analysis Types | Variant calling (long and short reads), GWAS, Bulk RNAseq, Single-Cell RNAseq, ML, Epigenomics, Multiomics, Proteomics, Fusion Detection, Imaging Analysis |
| Tutorials | Example Tool Analysis Projects, Videos |
| Interactive Applications | Jupyter, Rstudio, RShiny Apps, Galaxy, SAS, Command Line Sessions, Interactive Querying |
| User-Driven Content | User Written Workflow Support, User Created Interactive Apps, User Defined Project Resources |
| Analytic Workspaces | APIs for scripting, Bring your own data, Access Controlled Data |
| Cloud Native Tool Support | Integrated Billing, Python/R Command Line Tools, STRIDES Support |
Visit SB-CGC’s Public Apps page to browse over 1,000 Common Workflow Language and Nextflow workflows and tools.