Developing open source solutions for precision medicine for cancer patients

What is 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.

Who is using cBioPortal?

The public instance of cBioPortal is now one of the most popular online resources for cancer genomics data and attracts more than 3,000 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 1,900 and 1,400 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. Notably, cBioPortal has been adopted as the analysis and visualization platform by AACR GENIE, an international multi-institutional data-sharing project to catalyze precision oncology.

Who are we?

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.

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Technologies

  • javascript
  • java
  • web
  • reactjs
  • web services

Topics

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cBioPortal for Cancer Genomics 2017 Projects

  • Leonard Dervishi
    Collaborative construction of cancer pathways with PathwayMapper
    The tool used in cBioPortal for network visualization is a powerful one with many implemented features. However, researchers and biologists are more...
  • Dixit Patel
    Implement a Pipeline to Extract and Transform GDC Data
    The goal of this project is to extract Cancer Genomic data available from NCI's Genomic Data Commons and transform them according to the file formats...
  • Ishu Kalra
    Improved genome overview in patient view page.
    Through this project I plan to improve the genome overview in the patient view page. By adding- 1) Zoom Feature 2) Introducing Probe Level Copy...
  • sathyabandara
    Integrating MolecularMatch clinical trials data into cBioPortal
    One of the main challenges in CBioPortal is to interpret the great amount of genomic data it has accumulated. It has currently integrated a few...
  • bsir
    Standardizing clinical data from cBioPortal to for easier comparison and analysis
    cBioPortal provides clinical data from a number of different cancer studies. The clinical data from the studies is conveniently organized in a...
  • Pamela Wu
    Visualizing circulating tumor DNA results in the cBioPortal patient view
    A major need in cancer research is the development of non-invasive cancer detection and monitoring methods. Circulating tumor DNA (ctDNA) is DNA that...
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2017