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.

About us

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.

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Technologies

  • java
  • javascript
  • reactjs
  • database
  • web apps

Topics

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cBioPortal for Cancer Genomics 2019 Projects

  • Lizabeth Katsnelson
    Addition of novel CPTAC proteogenomic datasets to the cBioPortal
    This project will aim to create a pipeline for all CPTAC data transformation into cBioPortal compatible files for public access. Conversion and...
  • Wenjie Sun
    Clonal evolution visualization web-tools
    The sequencing technology produces the DNA sequence information of tumor cells. And cBioPortal is one of the leading web-tools which collected tumor...
  • Zachary Heins
    ETL pipeline development for TCGA data from GDC Portal
    The Genomic Data Commons (GDC) Portal serves as a large-scale genomic data repository hosting data from NCI cancer genome projects in standardized...
  • Ziya ERKOÇ
    Integrating PathwayMapper into cBioPortal and Separating the Network View as a standalone module
    PathwayMapper provides a pathway visualization environment which biologists are mostly familiar with. Currently, it works as a standalone application...
  • Andrew Cvekl
    OncoKB Analysis in Study View
    I would like to work on issue #70, “OncoKB Analysis in Study View”. An inconvenience for both biologists trying to get valuable information to make...
  • Doori Rose
    Spark and Parquet Backend for cBioPortal Web API
    cBioPortal utilizes a Spring MVC architecture with MyBatis for the persistence layer and a relational database (MySQL) for data storage. As the...
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2019