cBioPortal Scavenger Hunt

[Taylor Firman]

Hello all!

As a part of the rollout of the Fred Hutch instance of cBioPortal, we are planning a public event to introduce members of our community to the tool and show them what it's capable of.

To start, we'll provide a demo of the basic functionalities of cBioPortal, but to make things interactive and fun, we would like to create a "cBioPortal Scavenger Hunt" of sorts:

• Assign users an existing public dataset to explore and give them breadcrumbs as to the conclusions of the publication associated with that dataset.
• Have the user try to produce statistics/graphs that support those conclusions using the tools available in cBioPortal.
• If a user gets stuck, TA's could provide additional clues along the way:
  • "Have you tried the 'Plots' tab for that study?", "It seems like you're focusing on KRAS, maybe you can just query by that gene specifically?"
  • If they're really stuck, you could even provide the actual graphs from the publication and have them try to reproduce it.
• At the end, everyone could come together to show off their findings and compare them to the actual results.

Does anyone know if this has already been done? If so, we would love to hear how it went! If not, does anyone have any suggestions for publications that might be particular useful for these "scavenger hunt" purposes?

Thank you all for your help! Excited to further introduce this tool to the Fred Hutch community!

Sincerely,

Taylor Firman

tfi...@fredhutch.org

[JJ Gao]

Hi Taylor,

Apologies for the late response. I am not aware that a scavenger hunt has been done by the community. It sounds really fun! Please share with us how your experience is.

Best,

-JJ

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[Tali Mazor]

Hi Taylor - I'm so glad that helped! Please do let us know how it goes.

Getting contributors to properly format data is definitely a challenge. You have likely already seen this, but the cBioPortal curation team has developed a suite of tools to help with various aspects of the study generation process: https://github.com/cBioPortal/datahub-study-curation-tools. And the cBioPortal validator is a terrific tool for troubleshooting errors in the study files once they exist.

But in terms of getting started or training folks in how to do it, I don't have any great suggestions - I've never run a training from that perspective.

I've added the google group back to this email to see if anyone else has ideas.

-Tali

On Wed, May 7, 2025 at 2:35 PM Firman, Taylor E <tfi...@fredhutch.org> wrote:

Hi Tali,

 

Thank you so much for reaching out, these are perfect! This is exactly what we were thinking of, a set of directed questions that get people to poke around cBioPortal and see what it’s capable of. These will serve as ideal inspiration as we put together the event!

 

Out of curiosity, do you have any recommendations on how to train folks to format their data for upload? Once we start getting people excited about the tool, the next step will be to help them upload their own study data, but we’ve found that to be a much more difficult endeavour. Most existing tools are either overly simple or require deep knowledge of R/Python, but maybe that’s just how it is.

 

Thank you again for sending along these questions, incredibly helpful!

 

Sincerely,

Taylor Firman (he/him)

Research Informatics Lead

Data Science Lab (DaSL)

tfi...@fredhutch.org

(253)740-3456

 

 

From: Tali Mazor <tma...@ds.dfci.harvard.edu>
Date: Monday, April 28, 2025 at 6:52 PM
To: Firman, Taylor E <tfi...@fredhutch.org>
Subject: Re: [cbioportal] cBioPortal Scavenger Hunt

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

 

Hi Taylor - Apologies for the delayed response.

 

This is such a fun idea! I've spoken with a few others and we're not aware of anyone doing something like this. I occasionally run workshops to teach people how to use cBioPortal, and I'm happy to share the questions & answers that I use for that, in case that would be helpful for you. The questions are primarily focused on using the site rather than specifically replicating findings from a paper, but for the most part the questions are grounded in real cancer biology findings.

 

I'm attaching two documents. The PDF document is a set of questions which I just recently used, so the questions & answers should all be accurate. To give you a little more variety, I've also included a set of questions that I pulled together several years ago - these may need a little updating if you want to use them as the website & data may have changed in small ways since I put those questions together.

 

I hope these are helpful. If you have any more questions, just let us know.

 

-Tali

 

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Tali Mazor, Ph.D.

Knowledge Systems Group

Department of Data Sciences

Dana-Farber Cancer Institute

360 Longwood Ave, 5th floor, Boston, MA

Email: tma...@ds.dfci.harvard.edu

 

 

On Thu, Apr 17, 2025 at 1:50 PM Taylor Firman <tfi...@fredhutch.org> wrote:

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