cBioPortal for Cancer Genomics
Aid discovery in complex cancer genomics data
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.
2024 Program
Successful Projects
Contributor
gautamsarawagi
Mentor
AARON S LISMAN
Organization
cBioPortal for Cancer Genomics
Add the ability to spawn code notebooks from cBioPortal queries
This project aims to enhance cBioPortal functionality by allowing users to seamlessly launch code notebook environments like JupyterLite directly...
Contributor
Ivy Zou
Mentor
Onur Sumer, Xiang Li
Organization
cBioPortal for Cancer Genomics
Integration of AlphaMissense Pathogenicity Predictions into Genome Nexus and cBioPortal
This project involves the integration of AlphaMissense, an innovative tool for predicting the pathogenicity of missense mutations, into two...
Contributor
Abhilash Dhal
Mentor
Sehyun Oh, Jonathan Davenport, Michele W.
Organization
cBioPortal for Cancer Genomics
Automated Curation and Harmonization of cBioPortal Clinical Metadata using Sentence Transformers
Omics data repositories often contain heterogeneous data from multiple studies and diverse sources. This lack of structure in the metadata is...
Contributor
Xinling Wang
Mentor
AugustinL, Meysam Ghaffari, Ruslan Forostianov
Organization
cBioPortal for Cancer Genomics
Chatbot trained on documentation site and conversations
This project is about build and train a streaming chatbot on four datasets: Documentation site of cBioportal, Google group conversations, PMC papers...
Contributor
Yameng Ge
Mentor
Hongxin, jfkonecn
Organization
cBioPortal for Cancer Genomics
Create pipeline/interface to prioritize variants for OncoKB curation
The cBioPortal organization is dedicated to assisting clinicians and researchers in the analysis of complex cancer genomics data. And cBioPortal...
Contributor
SURAJ SHARMA
Mentor
Zeynep Karagöz, Sowmiyaa Kumar, Mary Chapman
Organization
cBioPortal for Cancer Genomics
Frontend visualization and incorporation of single cell data in cBioPortal
My project aims to bridge the gap between single-cell gene expression data analysis and existing cancer genomics workflows, particularly within the...
Contributor
Aishika Nandi
Mentor
Hongxin, Ben Preiser
Organization
cBioPortal for Cancer Genomics
Visualize OncoKB annotation and patient report generation
OncoKB™ is a crucial resource which provides comprehensive information about genomic alterations in cancer. However, despite the availability of APIs...