cBioPortal for Cancer Genomics

Automated Clinical Metadata Harmonization Dashboard

cBioPortal hosts 400+ cancer genomics studies whose clinical metadata is wildly heterogeneous — treatment fields alone have 24+ variants. The...

AI-Assisted Curation Assistant Tool for cBioPortal

This project aims to extend the existing cBioAbstractor prototype into a schema-driven formatting pipeline that assists curators in transforming...

Enhance Similarity Maps (Embeddings) Visualization

cBioPortal introduced Similarity Maps, a feature that visualizes UMAP/PCA embeddings of cancer samples, allowing researchers to discover hidden...

MCP Apps: Interactive Genomic Visualisations for AI Clients

This proposal outlines a plan to extend the cBioPortal MCP server with interactive genomic visualisation applications via MCP Apps that allow AI...

Enhance 3D Protein Structure Viewer in cBioPortal using AlphaFold Data

This project enhances the 3D protein structure viewer in cBioPortal by integrating AlphaFold predicted structures alongside experimentally determined...

2025

3 projects

Automated Metadata Harmonization Tool

This project aims to automate metadata harmonization for cBioPortal, a widely used platform for cancer genomics research. Currently, metadata from...

Show Variant Allele Frequency on the Plots Tab and OncoPrint

This project aims to enhance cBioportal's analytical capabilities by integrating Variant Allele Frequency (VAF) visualization into the Plots Tab and...

AI/LLM Generated gene alteration and expression based subtyping for each tumor type

The project aims to enhance the cBioPortal platform by generating a list of recommended default genes for each OncoTree code, which are often used...

2024

9 projects

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...

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...

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...

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...

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...

Improve navigatability of the HTAN data standards

The goal of this project is to improve the navigability of the HTAN data standards in HTAN portal as well as in schema-visualization. To do this, we...

Extend Chart Types in Study View

Extend the "Chart" functionality on the Study View Page by supporting additional types of charts such as line charts and area charts. Support chart...

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...

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...

2023

6 projects

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...

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...

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...

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...

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...

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...

2022

2 projects

Improve Genome Nexus' Command Line Interface Experience

This will be the Genome Nexus' cli to rule them all. Main objectives: 1. All 3 projects will be merged into one Java project. 2. Interface will...

Broader use of pathway views in cBioPortal

The goal of this project is to improve the integration of PathwayMapper into cBioPortal as well as enhancing the full-blown, stand-alone editor...

2019

6 projects

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...

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...

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...

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...

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...

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...

2017

6 projects

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...

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...

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...

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...

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...

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...

2016

5 projects

Onco Query Language (OQL) editor

cBioPortal allows the analysis and visualization of published cancer genomic datasets. These datasets must be queried by entering symbols of genes of...

Build a web service and auto updating pipeline to provide 3D structure alignments for BioPortal

cBioPortal provides web resources in cancer genome research. Building a web service to provide protein alignments between ensembl and PDB sequences...

Integration of Proteomics Data to cBioPortal

A key step towards the development of effective personalized cancer treatments is the collection of vast stores of patient data on a variety of tumor...

Prototype Plugin framework for Authentication

My proposal outlines my project goals. I have detailed my vision about how could the problem be solved. Also, I tried to enhance my strengths. I feel...

Improving the clinical timeline of cBioPortal's patient view

The primary aim of this project is to improve the cBioPortal’s clinical-timeline. The present implementation...