GitHub GitHub OctoTales • Team Stories, 5 Apr 2016

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From YouTube: Octotales • Fred Hutch

Description

The Fred Hutchinson Cancer Research Center is working to break down silos across cancer research by open sourcing their data. Help them build Oncoscape at github.com/fredhutch/oncoscape.

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A

I think the people who are going to cure cancer are going to be the people who have computational skills.

A

If people have programming skills,, they can jump on and be a part of this.

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And that's what we want,! We want to get everyone involved.

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We really think that the solution to unlocking cancer.

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Is really going to be from all of us. ♪ (music) ♪.

B

(Eric holland) the fred hutchinson cancer research center is a research center in seattle that specializes in understanding cancer,.

B

And coming up with new cures, and that we can use for patients with diseases that are incurable..

C

(Lisa mcferrin), our goal is to both research, the cancer biology,.

C

But also treat patients, so we're part of a consortium that includes hospitals,, but it also includes a large number of researchers.

B

(Eric) historically,, when people were trying to decide what a cancer type was, they would look under a microscope, and because of the way things look,. They would give it a name..

B

But recently, we've had the ability to sequence, huge amounts of dna,.

B

And so,, all of the sudden there's a whole lot more sort of digital data that completely describes a tumor in a much better way.

B

Than simply the way of a microscope, but. This is both a good thing and a bad thing..

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It poses a problem in that the amount of data.

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For any given person is enormous..

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And all that information has to be compiled together in some giant database, and then manipulated and visualized, and, so we were able to get a team together to attack this problem, and we've built some of these tools,.

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That we're pretty happy with.

A

(Desert horse-grant) oncoscape is an open source web application.

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Where we take a cancer, patient's information and we easily visualize it for doctors and scientists to understand what's, going on in the patient's disease., the fields right, now,, there's cancer, biologists,.

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So the people who are studying cancer, and, then there's the computational people,, and so we wanted a tool that really could speak to both groups, and then at that same time. Just how can we make them work? Together.

D

(Jenny zhang), my work includes dry lab,, computational side, plus the wet lab,.

D

Which means processing human tissues,, so I work on both sides., so the tissue is freezed, I'll, just put it on the dry ice,.

D

And then switch to my thermal glove.

D

a lot of times. We only look at data as a computer, scientist,.

D

But you don't know how the data were generated., and I have this opportunity to look at the tissue,.

D

And, when the data doesn't make sense,, then you go back to the specimen..

D

Every aspect matters to generate good quality, data.

D

There is a lot of advantages to be able to work on both sides.

B

(Eric) well, I've been in this field for 20 years..

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I've learned more about the disease that I'm particularly interested in,, which is brain cancer, with simply this visualization tool to all I've learned over many of the previous years,.

B

Because I'm not necessarily looking at only what the street light, you know, is illuminating.

B

If you look at all of the dna, you actually,, it's like turning the lights on the entire room,, you see everything, and you see it all at once, and you can see the things that you know exist,, but then there's all this other stuff that you didn't even know to look for.

B

But it's sitting right in front of you.

A

(Desert) so,, we wanted oncoscape to be open source,, because our goal, and our goal from the beginning has really been about collaboration.

A

this year. We got this idea because someone contacted us.

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Whose father had lung cancer,, but he really didn't, have a way to help, except for programming,.

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And it really gave us this idea that coders out there could really help us.

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And so,, we thought this would be a great thing to put on github,.

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And we felt like we could still give credit to people and use their name and really celebrate them for helping us in this fight against cancer.

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(Lisa), you don't have to be an expert in biology or computational biology..

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We want to allow people to be an expert in their own field,.

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And so, we've created all these "help wanted" tasks on things that we're not experts, at,, that you might be an expert at,.

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And we want our github repository to be a place where people can come to and contribute their own knowledge,, their own software and their own efforts..

D

(Jenny), I know just by far how much I've been learning.

D

From, the github community. I've been checking a lot of the repositories.

D

Just looking at how they code., we cannot work as competitors anymore in cancer research,.

D

Because people die,, so we really need to work together with different cancer centers,.

D

With different fields, with people all from different expertise.

B

(Eric), it's a very exciting time. If these tools can be really brought.

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To the level that just any old person can do this, and you know,.

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It really opens up science and cancer research to everybody,.

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Which is actually really exciting..

A

(Desert), I don't know,, I mean, cancer will be solved on a computer.

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We want people to join us in making a tool.

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That really all of us can benefit from., ♪, (music), ♪.