cBioPortal Newsletter August 2025

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Tali Mazor

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Aug 11, 2025, 11:38:18 AMAug 11

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August 2025

Welcome to the August 2025 edition of the cBioPortal Newsletter!

In this issue, we highlight some exciting new data and performance improvements, and provide updates from our latest hackathon.

Data Highlight: Explore microregion transcriptomic data and multiplex imaging in cBioPortal!

A new spatial multi-omics dataset on high-grade serous ovarian cancer (HGSOC) is now available in cBioPortal. This study by Kader et al. (2025) maps the molecular and immune changes from fallopian tube precursor lesions to invasive cancer, highlighting early interferon signaling, chromosomal instability, and immune suppression during progression.

You can explore microregional gene expression from GeoMx in the Plots tab and Group Comparison, and view CyCIF imaging data in the Minerva Viewer on the Patient View. This resource supports research into early detection and therapeutic targets for HGSOC.

Google Summer of Code Updates

We have 3 ongoing projects through the Google Summer of Code (GSoC) program that have been making good progress towards reaching their goals. These projects include:

Showing VAF on the plots tab for the OncoPrint
AI/LLM tool for identifying relevant genes to each OncoTree Code
Metadata harmonization pipeline to automate data curation for the cBioPortal

Stay tuned for further updates showcasing these projects and future work planned!

Spring Hackathon Highlights: Ideas to Impact in Just 2 Days

In June, we hosted the annual cBioPortal Hack & Specathon at MSK, bringing together participants from Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Children's Hospital of Philadelphia, The City University of New York, and remote collaborators in the Netherlands (The Hyve, SE4BIO). Over two packed days, teams prototyped a range of innovative features, from AI-generated patient summaries and natural language querying tools, to ClickHouse integration, longitudinal analysis enhancements, and H&E image viewers.

Projects included:

cBioPubChat: A chatbot that helps users explore cBioPortal studies using natural language and links to relevant publications.
AI-Generated Patient Summaries: Automatically generates short clinical summaries for individual patients based on their data.
AI OQL Helper: Uses AI to help users write and understand OncoQuery Language (OQL) expressions. Try it here by logging in and going to the query page.
AI Curation Tools for OncoKB: Assists curators in finding and evaluating relevant papers using AI-powered recommendations.
Longitudinal Querying Enhancements: Prototypes filters and displays for time-aware queries across treatment timelines.
ClickHouse Integration: Implements ClickHouse support for more pages to speed up performance for large studies.
H&E Viewer Integration: Embeds histopathology image viewers directly into the Patient View for deeper visual analysis.
Image Embeds in R: Adds support for visualizing CyCIF and other embedded images within plots and reports in the R client.

These events are an exciting annual tradition in the cBioPortal community. Interested in joining the next one? Let us know here.

Performance Improvements: Study View Now Backed by ClickHouse

We’ve kicked off a long-term performance improvement initiative to address growing study sizes and sluggish page loads, especially in large datasets like GENIE. As a major milestone, both the public cBioPortal and the GENIE portal are now running the Study View on ClickHouse, delivering significantly faster load times. You can watch this demo video to see the speed in action. We strongly recommend testing ClickHouse if your private cBioPortal instance has studies with 100,000+ samples. Documentation for running cBioPortal in ClickHouse mode is available here. Other key pages in cBioPortal are also planned to move to ClickHouse; you can follow the performance roadmap ticket to stay updated on ongoing and future developments.

New Feature for Local Installations of cBioPortal: Dynamic Study Export

The “Download All Clinical and Genomic Data for This Study” button in cBioPortal can now generate data exports dynamically, eliminating the need for static archive files, which can be outdated and require manual maintenance. To enable this feature in your local cBioPortal installation, set feature.study.export=true in the application properties file. Once enabled, users can download up-to-date study data, including for virtual studies, via /export/study/{studyId}.zip.

Learn More

To learn more about cBioPortal, review our documentation, which includes FAQs, webinars, and tutorials. If you have questions, please don't hesitate to reach out to us at cbiop...@googlegroups.com.

Stay tuned for more updates, and thank you for your continued support in advancing cancer genomics research with cBioPortal.