cBioPortal for Cancer Genomics

Aid discovery in complex cancer genomics data

Technologies
mysql, javascript, java, react, typescript
Topics
genomics, cancer, bioinformatics, big data, precision medicine
Aid discovery in complex cancer genomics data
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 instance of cBioPortal (https://cbioportal.org/) is now one of the most popular online resources for cancer genomics data and attracts more than 4,000 unique visitors (cancer researchers and clinicians) per day. The two papers documenting the cBioPortal Cerami et al. Cancer Discov. 2012 & Gao et al. Sci. Signal. 2013 have been cited more than 5,600 and 5,100 times, respectively, since their publication. There are more than 30 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, the Dana-Farber Cancer Institute, Princess Margaret Cancer Centre, Children's Hospital of Philadelphia, and The Hyve, a bioinformatics company from the Netherlands.

Projects

Contributor
Aditya Garg
Mentor
Onur Sumer, Charles Haynes, Bryan Lai
Organization
cBioPortal for Cancer Genomics
Add Mutation Diagram on Study View for Enhanced Mutation Analysis
This proposal aims to add a mutation diagram to the study view will enhance the mutation analysis capabilities of cBioPortal. The mutation diagram...
Contributor
Biqing Su 1
Mentor
Ryan Fu, Jeremy R. Easton-Marks
Organization
cBioPortal for Cancer Genomics
Proposal_Interactive web tour_Biqing Su
The cBioPortal provides access to a wealth of cancer genomics data, but new users often struggle to navigate its features, and existing users may not...
Contributor
Gorkem
Mentor
Onur Sumer, Ugur Dogrusoz
Organization
cBioPortal for Cancer Genomics
Pathway Improvements in cBioPortal
The project aims to enhance the functionality and usability of the PathwayMapper tool in cBioPortal. The project will have two tasks: The first task...
Contributor
JiahangLi
Mentor
Gaofei, Ryan Fu
Organization
cBioPortal for Cancer Genomics
Group Comparison - Generic Assay Categorical and Binary data implementation
The objective of this project is to improve the functionality of cBioPortal by introducing support for categorical and binary data analysis and...
Contributor
Justin Jao
Mentor
Charles Haynes, Walle, Avery Wang
Organization
cBioPortal for Cancer Genomics
Automating Quality Control of Datahub Submissions
cBioPortal allows submission of data sets to enrich its open-access cancer genomics database. Currently, new data sets can be uploaded to a separate...
Contributor
Justin Singh
Mentor
"Jag" Prasanna Kumar Jagannathan, Hongxin, jfkonecn
Organization
cBioPortal for Cancer Genomics
Create a clinical trial curation tool based on CTML from MatchMiner
Scope: To create a standalone React component from MatchMiner that will use Firebase to provide trial curation across multiple projects uses...