What is cBioPortal?

cBioPortal is a free, user-friendly platform for exploring publicly available cancer genomics data—no coding required. It lets you explore genomic and clinical data across multiple studies in a highly visual and interactive way.

You can:

  • Visualize mutations, gene expression, copy number changes, and more

  • Compare genetic data with clinical factors like stage, survival, and diagnosis age

  • Generate publication-ready plots like oncoprints and Kaplan-Meier survival curves

🔍 Explore more usage examples here

What is the Fred Hutch Instance of cBioPortal?

Fred Hutch’s internal cBioPortal instance is a secure, research-only platform developed by the Office of the Chief Data Officer (OCDO) and Scientific Computing (SciComp). It provides a safe and supported environment for researchers to explore their own study data.

Key features:

🔐 Controlled access – Only approved users can view & upload data

🧬 Sensitive data allowed – IRB-approved studies with identifiable data can be included

Uploading Your Own Data

Follow these steps to upload your own data into the Fred Hutch insance of cBioPortal

Pre-requisites

  • You should have Fred Hutch credentials or HutchNet ID

  • You should be logged in to the Fred Hutch network or if off-campus, connect via VPN.

1. Request Upload Access

Fill out the Access Request Form.

You’ll need:

  • Info on whether your data includes identifiable patient information
  • Your IRB details (IRB #, RG #, approval letter, protocol)

⚠️ Only upload data approved for the IRB and data types listed in your form. Violations may result in study removal.

✅ The Data Governance & Protection team will review and email you with next steps.

📝 Note:

  • Your approval is specific to the IRB and data types you list in the form.
  • It’s your lab’s responsibility to make sure only approved data types are uploaded.
  • If unapproved data is uploaded, your study may be removed from cBioPortal.
  • To add new data types to an approved study, email Data Governance & Protection for additional review.
  • Want to add data or start a new project? Just submit a new Access Request Form and email dataprotection@fredhutch.org.

2. Get AWS Credentials

Make sure your lab has an AWS lab account, and that each uploader has individual credentials.

📝 Note: If your team already has credentials, skip this step. Be sure to test your credentials.

3. Request S3 Bucket Access

Once your AWS credentials are ready:

📝 Note: Before emailing us make sure to test access to fh-dasl-cbio

4. Prepare & Upload Your Study

Preparing your study files involves following very specific instructions. We have some helpful information on how to format your data files here

Once your study files are formatted correctly follow there upload steps to upload your study folder into the fh-dasl-cbio.

🚀 Our automated system will load your data and notify you by email.

📝 Note: 📩 If upload fails, you’ll receive a “validation report” with error details. Didn’t get an email? Contact us.

🎉 Once uploaded, start exploring!

📎 Quick Links

🧭 Explore cBioPortal

🔍 What is cBioPortal? 📊 Visualize mutations, gene expression, and CNVs 🧬 Compare mutations to clinical factors 📈 Generate publication-ready plots 📚 Explore more usage examples

🔐 Fred Hutch cBioPortal Instance

🏥 What is the Fred Hutch Instance? 🔐 Request Access to Upload Data 🧪 Pathway for the whole process specific to Fred Hutch

📤 Upload Your Data

🧾 Request Upload Access 🔑 Get AWS Credentials 🪣 Request S3 Bucket Access 🗂️ Prepare Your Files for Upload 🚀 Upload Files to S3 Bucket 📩 Test Access to S3 Bucket

🎓 Learn by Example

📽️ Fred Hutch cBioPortal Demo Day Check out the recording to see how to use the portal, upload data, and more. 👉 Watch the recording (Panopto)

❓ Frequently Asked Questions

Can I add more data to my study? Yes, if it’s covered under your approved IRB. Email dataprotection@fredhutch.org if unsure.

How do I update a study? Just reupload a new version to the S3 bucket—this will replace the existing version.

Can collaborators access my study? Maybe. If they’re covered under your IRB and have Hutch credentials, yes. If external, contact us—this needs review.

Can the OCDO team help format our data? Not directly, but we offer resources and Data House Calls to help troubleshoot.

📝 Release Notes

September 2024

  • First release of Fred Hutch cBioPortal instance
  • Deployed with user documentation
  • Running version v5.4.10

Fixes

  • No fixes yet.

📬 Contact Us

Updated: