1169 datademosfh cbio intro content refresh needed #1185

sitapriyamoorthi · 2025-04-18T16:12:29Z

This is a big re-write of cBioPortal content. It involves the following changes:

The main cBioPortal doc (left tab): has very specific content that a user needs to know about cBioPortal and the Fred Hutch instance in particular
There are 4 datademos that discuss very specific examples now for some of these steps. This modularity helps to reduce content load on the main page
There is now a new pathways article as well that helps user potentially quickly understand what are all the steps involved in getting a study uploaded into cBioPortal

deleting old version of upload instructions.

New upload instructions

Adding a data demo page for instructions on how to test if a user has the right access to the fh-dasl-cbio S3 bucket

Adding header

Adding preliminary content

…3_bucket.md changing file prefix for consistency

Creating a demo for how to prepare files for cBioPortal

Creating a demo for how to use cbioportal with specific examples

Creating demo to show how to upload data in fh-dasl-cbio S3 bucket

Draft of pathway article for uploading a study into the Fred Hutch instance of cBioPortal

Version 1 of the updated docs!

Outline of content for usage examples

Draft version

Adding new version of cbio_01_oncoprint_kras_different_studies.png

Updating figure cbio_02_KRAS_lollipop.png

Updating cbio_04_KRAS_clinical_covariates.png

Updating cbio_05_KRAS_clinical_mut.png

Horizontal version of cbio_05_KRAS_clinical_mut

Creating a new data demo for examples of using cBioPortal

Updated cbio_test_access_to_cbio_s3_bucket.md

Updating content on how to prepare files for cBioPortal as a demo

Content update for Uploading your study into `fh-dasl-cbio` S3 bucket

laderast

Really like the new structure. I think it will be super helpful for new users

sitapriyamoorthi · 2025-04-18T20:38:36Z

Really like the new structure. I think it will be super helpful for new users

Hopefully all the links work as expected!

tefirman

Sadly haven't finished reviewing everything, but wanted to provide feedback before the weekend. Two main points:

For hyperlinks, if you add the .md file extension to the hyperlink, it borks the link unfortunately, so make sure to get rid of those.
For the accordion dropdowns, I think you'll need to use old school HTML rather than Markdown to preserve formatting. Sadly they look weird when I built the site locally.

Will finish looking through the _datademos updates soon!

_pathways/path-cbio-fh-instance.md

_datascience/cbioportal.md

@tefirman

Adding all changes suggested by @tefirman Co-authored-by: Taylor Firman <[email protected]>

Removed accordian style drop downs.

Adding AWS CLI configuration

tefirman

Looks awesome, really like how you split up the different topics into separate articles! Just found some broken links because of the article re-org, but definitely approve once those are fixed. Thanks @sitapriyamoorthi !

_datademos/cbio_test_access_to_cbio_s3_bucket.md

_pathways/path-cbio-fh-instance.md

_datascience/cbioportal.md

Co-authored-by: Taylor Firman <[email protected]>

…-needed

sitapriyamoorthi · 2025-06-11T02:36:06Z

@tefirman only one comment on one of your comments

tefirman

Looks great, thanks @sitapriyamoorthi ! Excited for the docs upgrade, really appreciate your hard work on this!

sitapriyamoorthi added 30 commits April 14, 2025 11:16

Delete _datademos/assets/cbio_17_overview_of_FH_instance_upload.png

22f530c

deleting old version of upload instructions.

Add files via upload

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New upload instructions

Create test_access_to_cbio_s3_bucket.md

0ffc7ec

Adding a data demo page for instructions on how to test if a user has the right access to the fh-dasl-cbio S3 bucket

Update test_access_to_cbio_s3_bucket.md

a921dd8

Adding header

Update test_access_to_cbio_s3_bucket.md

6863606

Adding preliminary content

Rename test_access_to_cbio_s3_bucket.md to cbio_test_access_to_cbio_s…

cf75f12

…3_bucket.md changing file prefix for consistency

Create cbio_how_to_prepare_files.md

8a70120

Creating a demo for how to prepare files for cBioPortal

Create cbio_examples_of_using_cbio.md

889ada9

Creating a demo for how to use cbioportal with specific examples

Create cbio_how_to_upload_data_to_cbio_s3.md

b98aed3

Creating demo to show how to upload data in fh-dasl-cbio S3 bucket

Create path-cbio-fh-instance.md

b85694d

Draft of pathway article for uploading a study into the Fred Hutch instance of cBioPortal

Update cbioportal.md

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Version 1 of the updated docs!

Update fh-cbio-intro.md

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Outline of content for usage examples

Update cbio_test_access_to_cbio_s3_bucket.md

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Draft version

Add files via upload

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Adding new version of cbio_01_oncoprint_kras_different_studies.png

Add files via upload

8caec00

Updating figure cbio_02_KRAS_lollipop.png

Add files via upload

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Updating cbio_04_KRAS_clinical_covariates.png

Add files via upload

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Updating cbio_05_KRAS_clinical_mut.png

Add files via upload

cbf9a9a

Horizontal version of cbio_05_KRAS_clinical_mut

Update cbio_examples_of_using_cbio.md

33fc744

Creating a new data demo for examples of using cBioPortal

Update cbio_test_access_to_cbio_s3_bucket.md

949f67e

Updated cbio_test_access_to_cbio_s3_bucket.md

Update cbio_how_to_prepare_files.md

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Update cbio_how_to_upload_data_to_cbio_s3.md

78bcf73

Update cbio_test_access_to_cbio_s3_bucket.md

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Update cbio_how_to_prepare_files.md

4877dc5

Updating content on how to prepare files for cBioPortal as a demo

Update cbio_how_to_upload_data_to_cbio_s3.md

53e1d2c

Update cbio_how_to_upload_data_to_cbio_s3.md

06042e6

Content update for Uploading your study into `fh-dasl-cbio` S3 bucket

Update cbio_examples_of_using_cbio.md

64883a2

Update cbio_how_to_prepare_files.md

0f315e4

Update cbio_examples_of_using_cbio.md

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Update cbio_how_to_upload_data_to_cbio_s3.md

8f83e31

sitapriyamoorthi self-assigned this Apr 18, 2025

sitapriyamoorthi requested a review from a team as a code owner April 18, 2025 16:12

sitapriyamoorthi linked an issue Apr 18, 2025 that may be closed by this pull request

Update the cBioPortal page and transfer content #1182

Closed

laderast approved these changes Apr 18, 2025

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sitapriyamoorthi linked an issue Apr 18, 2025 that may be closed by this pull request

_datademos/fh-cbio-intro content refresh needed #1169

Closed

tefirman requested changes Apr 18, 2025

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sitapriyamoorthi and others added 5 commits April 22, 2025 09:10

Apply suggestions from code review

323b2f5

Adding all changes suggested by @tefirman Co-authored-by: Taylor Firman <[email protected]>

Update path-cbio-fh-instance.md

b5659d4

Update cbioportal.md

3b9c3ee

Removed accordian style drop downs.

Update path-cbio-fh-instance.md

db97510

Adding AWS CLI configuration

Update cbio_how_to_prepare_files.md

b5695b4

sitapriyamoorthi requested a review from tefirman May 9, 2025 16:11

tefirman requested changes Jun 4, 2025

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sitapriyamoorthi and others added 10 commits June 10, 2025 18:44

Update _datademos/cbio_test_access_to_cbio_s3_bucket.md

99030d9

Co-authored-by: Taylor Firman <[email protected]>

Update _pathways/path-cbio-fh-instance.md

3a63e71

Co-authored-by: Taylor Firman <[email protected]>

Update _pathways/path-cbio-fh-instance.md

f273e14

Co-authored-by: Taylor Firman <[email protected]>

Update _pathways/path-cbio-fh-instance.md

5400db2

Co-authored-by: Taylor Firman <[email protected]>

Update _pathways/path-cbio-fh-instance.md

94ec206

Co-authored-by: Taylor Firman <[email protected]>

Update _datascience/cbioportal.md

c3e46cb

Co-authored-by: Taylor Firman <[email protected]>

Update _datascience/cbioportal.md

7babf32

Co-authored-by: Taylor Firman <[email protected]>

Update _datascience/cbioportal.md

5217a0b

Co-authored-by: Taylor Firman <[email protected]>

Update _datascience/cbioportal.md

6c2fdb5

Co-authored-by: Taylor Firman <[email protected]>

Merge branch 'main' into 1169-_datademosfh-cbio-intro-content-refresh…

d8c4a44

…-needed

tefirman approved these changes Jun 11, 2025

View reviewed changes

tefirman merged commit 8b29075 into main Jun 11, 2025
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tefirman deleted the 1169-_datademosfh-cbio-intro-content-refresh-needed branch June 11, 2025 19:28

sitapriyamoorthi restored the 1169-_datademosfh-cbio-intro-content-refresh-needed branch June 11, 2025 19:46

sitapriyamoorthi deleted the 1169-_datademosfh-cbio-intro-content-refresh-needed branch June 11, 2025 19:52

1169 datademosfh cbio intro content refresh needed #1185

1169 datademosfh cbio intro content refresh needed #1185

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sitapriyamoorthi commented Apr 18, 2025

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sitapriyamoorthi commented Jun 11, 2025

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