cBioPortal for Cancer Genomics
Developing open source solutions for discovery from complex cancer data
About the cBioPortal
The cBioPortal for Cancer Genomics is a resource designed to provide broad community access to cancer genomic data. It provides a unique user-friendly and "biology-centric computational user interface", with the goal of making genomic data more easily accessible to translational scientists, biologists, and clinicians. The interface was explicitly built and continues to evolve with careful usability studies involving multiple biological and clinical users, and an active and engaged user base.
The public cBioPortal is now one of the most popular resources for cancer genomics data and attracts more than 3,000 cancer researchers and clinicians per day. The cBioPortal paper (Cerami et al. Cancer Discov. 2012 has been cited more than 4,000 times since its publication.
The cBioPortal project has become an open source project under the Affero General Public License (AGPL), due to the high demand for local installations and contribution requests. There are more than 40 actively used cBioPortal instances in hospitals, universities, pharmaceutical companies, and other institutes all over the globe.
We are a group of software engineers, bioinformaticians, and cancer biologists building software solutions for precision medicine for cancer patients. Our overall goal is to build infrastructure to support clinical decisions for personalized cancer treatment by utilizing “big data” of cancer genomics and patient clinical profiles. Our multi-institutional team currently has more than 30 active members, primarily from Memorial Sloan Kettering Cancer Center in New York, the Dana-Farber Cancer Institute in Boston, Princess Margaret Cancer Centre in Toronto, Children's Hospital of Philadelphia, and The Hyve, a bioinformatics company from the Netherlands.
cBioPortal for Cancer Genomics 2019 Projects
Addition of novel CPTAC proteogenomic datasets to the cBioPortalThis project will aim to create a pipeline for all CPTAC data transformation into cBioPortal compatible files for public access. Conversion and...
Clonal evolution visualization web-toolsThe sequencing technology produces the DNA sequence information of tumor cells. And cBioPortal is one of the leading web-tools which collected tumor...
ETL pipeline development for TCGA data from GDC PortalThe Genomic Data Commons (GDC) Portal serves as a large-scale genomic data repository hosting data from NCI cancer genome projects in standardized...
Integrating PathwayMapper into cBioPortal and Separating the Network View as a standalone modulePathwayMapper provides a pathway visualization environment which biologists are mostly familiar with. Currently, it works as a standalone application...
OncoKB Analysis in Study ViewI would like to work on issue #70, “OncoKB Analysis in Study View”. An inconvenience for both biologists trying to get valuable information to make...
Spark and Parquet Backend for cBioPortal Web APIcBioPortal utilizes a Spring MVC architecture with MyBatis for the persistence layer and a relational database (MySQL) for data storage. As the...