From b32e0885af0773010c60db032eb3be38ec265c76 Mon Sep 17 00:00:00 2001 From: Amanda Charbonneau Date: Thu, 9 Apr 2026 15:17:19 -0400 Subject: [PATCH 1/3] gemini suggestion --- docs/getting_started/index.md | 84 ++++++--------------------------- docs/index.md | 88 ++++++----------------------------- 2 files changed, 30 insertions(+), 142 deletions(-) diff --git a/docs/getting_started/index.md b/docs/getting_started/index.md index b585f766..c63a45f6 100644 --- a/docs/getting_started/index.md +++ b/docs/getting_started/index.md @@ -2,78 +2,24 @@ title: Re-Search made simple --- -

With CDA you search by harmonized, common language terms. Using simple language you can get information about the subjects, files, or specimens that you care about in a standard dataframe format (tsv) that you can open in Excel, integrate into a pipeline or upload to your favorite cloud resource.

+# Find the Cancer Data You Needβ€”No Coding Required +The **Cancer Data Aggregator (CDA)** connects you to subjects, files, and specimens across **GDC**, **PDC**, and **IDC** through one simple interface. Filter by common clinical terms and export results directly to Excel or the Cloud. -
- -- :material-clock-fast:{ .lg .middle } __Don't code? No problem!__ - - --- - - Browse through a curated dataset of all subjects that have data at multiple data centers using an intuitive filtering tool right in this website. -Head to our interactive page to try it out. -

- -- :material-clock-fast:{ .lg .middle } __Low code, no install__ - - --- - - Fill in the blanks in our pre-built queries to find the data you need without installing a thing.

Send your results to [Broad Institute FireCloud:octicons-link-external-16:](https://datacommons.cancer.gov/analytical-resource/broad-institute-firecloud){:target="_blank"} or [Velsera Cancer Genomics Cloud:octicons-link-external-16:](https://www.cancergenomicscloud.org/){:target="_blank"} for a complete cloud experience. Find the data you need, fetch all the files, and run your favorite bioinformatics pipeline *all without ever leaving your web browser.*

-Launch CDA in the cloud -

- -- :fontawesome-brands-python:{ .lg .middle } __Power users__ - - --- - - Install `cdapython` with `pip` and get up - and running in no time - - ```bash - pip3 uninstall -y cdapython; pip3 install git+https://github.com/CancerDataAggregator/cdapython.git@develop - python3 - ``` - - ```python - from cdapython import * - ``` - -- :fontawesome-brands-python:{ .lg .middle } __Code in the Cloud__ - - --- - - Bring lists of files or subjects found with CDA to the [ISB Cancer Gateway in the Cloud (ISB-CGC):octicons-link-external-16:](https://isb-cgc.org/){:target="_blank"} to instantly access both associated derived data and raw files, for use in cloud processing pipelines -- either in your own preferred environment or using ISB-CGC's free Google Cloud Platform credits program. - Test it out on Google Colab -

- -- :simple-swagger:{ .lg .middle } __Developers__ - - --- - - Are you building a metadata microservice? Connecting even more databases? Hosting a computational resource?

Whatever your use case, CDA can help. - - [:octicons-arrow-right-24:**API documentation**](../documentation/developers/index.md) - -- :material-bell-alert-outline:{ .lg .middle } __What's new?__ - - --- - - Recently Updated Pages: - - - [Data Release](../release_notes/data_updates.md) - - [Code Release](../release_notes/cdapython.md) - -- :simple-mysql:{ .lg .middle } __Need even more data?__ - - --- - - Do you dream of having a CDA database instance of your very own? Or CDA but bigger somehow? - We can make those dreams come true. Let's chat! - - :material-email: cancerdataaggregator `@` gmail +!!! abstract "Start Here" + If you want to browse data visually without writing any code, our interactive tool is the best place to begin. + + [πŸš€ Start Searching Interactively](https://cda.readthedocs.io/en/latest/interactive_search.html){ .md-button .md-button--primary } + *(No installation or account needed)* +--- +### Three Ways to Access Data -

+| No Code | Low Code | Power Users | +| :--- | :--- | :--- | +| **Interactive Search** | **Cloud Notebooks** | **Python Library** | +| Best for clinical researchers and quick cohort building. | Fill-in-the-blank queries in [FireCloud](https://cda.readthedocs.io/en/latest/) or [CGC](https://cda.readthedocs.io/en/latest/). | Full API access for bioinformatics pipelines and large-scale analysis. | +| [Try it now β†’](https://cda.readthedocs.io/en/latest/interactive_search.html) | [Launch in Cloud β†’](https://cda.readthedocs.io/en/latest/#low-code-no-install) | [View API Docs β†’](https://cda.readthedocs.io/en/latest/developer_tools.html) | +--- \ No newline at end of file diff --git a/docs/index.md b/docs/index.md index 58d7815f..3fb43ee7 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,79 +1,21 @@ ---- -title: Re-Search made simple ---- - -

With CDA you search by harmonized, common language terms. Using simple language you can get information about the subjects, files, or specimens that you care about in a standard dataframe format (tsv) that you can open in Excel, integrate into a pipeline or upload to your favorite cloud resource.

- - -
- -- :material-clock-fast:{ .lg .middle } __Don't code? No problem!__ - - --- - - Browse through a curated dataset of all subjects that have data at multiple data centers using an intuitive filtering tool right in this website. -Head to our interactive page to try it out. -

- -- :material-clock-fast:{ .lg .middle } __Low code, no install__ - - --- - - Fill in the blanks in our pre-built queries to find the data you need without installing a thing.

Send your results to [Broad Institute FireCloud:octicons-link-external-16:](https://datacommons.cancer.gov/analytical-resource/broad-institute-firecloud){:target="_blank"} or [Velsera Cancer Genomics Cloud:octicons-link-external-16:](https://www.cancergenomicscloud.org/){:target="_blank"} for a complete cloud experience. Find the data you need, fetch all the files, and run your favorite bioinformatics pipeline *all without ever leaving your web browser.*

-Launch CDA in the cloud -

- -- :fontawesome-brands-python:{ .lg .middle } __Power users__ - - --- - - Install `cdapython` with `pip` and get up - and running in no time - - ```bash - pip3 uninstall -y cdapython; pip3 install git+https://github.com/CancerDataAggregator/cdapython.git@develop - python3 - ``` +# Find the Cancer Data You Needβ€”No Coding Required - ```python - from cdapython import * - ``` +The **Cancer Data Aggregator (CDA)** connects you to subjects, files, and specimens across **GDC**, **PDC**, and **IDC** through one simple interface. Filter by common clinical terms and export results directly to Excel or the Cloud. -- :fontawesome-brands-python:{ .lg .middle } __Code in the Cloud__ - - --- - - Bring lists of files or subjects found with CDA to the [ISB Cancer Gateway in the Cloud (ISB-CGC):octicons-link-external-16:](https://isb-cgc.org/){:target="_blank"} to instantly access both associated derived data and raw files, for use in cloud processing pipelines -- either in your own preferred environment or using ISB-CGC's free Google Cloud Platform credits program. - Test it out on Google Colab -

- -- :simple-swagger:{ .lg .middle } __Developers__ - - --- - - Are you building a metadata microservice? Connecting even more databases? Hosting a computational resource?

Whatever your use case, CDA can help. - - [:octicons-arrow-right-24:**API documentation**](documentation/developers/) - -- :material-bell-alert-outline:{ .lg .middle } __What's new?__ - - --- - - Recently Updated Pages: - - - [Data Release](release_notes/data_updates.md) - - [Code Release](release_notes/cdapython.md) - -- :simple-mysql:{ .lg .middle } __Need even more data?__ - - --- - - Do you dream of having a CDA database instance of your very own? Or CDA but bigger somehow? - We can make those dreams come true. Let's chat! - - :material-email: cancerdataaggregator `@` gmail +!!! abstract "Start Here" + If you want to browse data visually without writing any code, our interactive tool is the best place to begin. + + [πŸš€ Start Searching Interactively](https://cda.readthedocs.io/en/latest/interactive_search.html){ .md-button .md-button--primary } + *(No installation or account needed)* +--- +### Three Ways to Access Data -

+| No Code | Low Code | Power Users | +| :--- | :--- | :--- | +| **Interactive Search** | **Cloud Notebooks** | **Python Library** | +| Best for clinical researchers and quick cohort building. | Fill-in-the-blank queries in [FireCloud](https://cda.readthedocs.io/en/latest/) or [CGC](https://cda.readthedocs.io/en/latest/). | Full API access for bioinformatics pipelines and large-scale analysis. | +| [Try it now β†’](https://cda.readthedocs.io/en/latest/interactive_search.html) | [Launch in Cloud β†’](https://cda.readthedocs.io/en/latest/#low-code-no-install) | [View API Docs β†’](https://cda.readthedocs.io/en/latest/developer_tools.html) | +--- \ No newline at end of file From bd795a02978a599480733ae1db8d1920ff7f5e4e Mon Sep 17 00:00:00 2001 From: Amanda Charbonneau Date: Thu, 9 Apr 2026 15:28:01 -0400 Subject: [PATCH 2/3] don't need to render --- mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index 81914456..0c8c41ac 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -44,7 +44,7 @@ plugins: remove_input_tags: - hide_code include_source: True - execute: True + execute: False allow_errors: False ignore: ["documentation/cdapython/vignettes/005_TCIA.ipynb"] From 240fbbfb91adb23009b37bd79addd3cf270841c8 Mon Sep 17 00:00:00 2001 From: Amanda Charbonneau Date: Thu, 9 Apr 2026 15:32:34 -0400 Subject: [PATCH 3/3] Update index.md --- docs/getting_started/index.md | 77 +++++++++++++++++++++++++++++++---- 1 file changed, 69 insertions(+), 8 deletions(-) diff --git a/docs/getting_started/index.md b/docs/getting_started/index.md index c63a45f6..473ecf69 100644 --- a/docs/getting_started/index.md +++ b/docs/getting_started/index.md @@ -1,7 +1,6 @@ --- title: Re-Search made simple --- - # Find the Cancer Data You Needβ€”No Coding Required The **Cancer Data Aggregator (CDA)** connects you to subjects, files, and specimens across **GDC**, **PDC**, and **IDC** through one simple interface. Filter by common clinical terms and export results directly to Excel or the Cloud. @@ -14,12 +13,74 @@ The **Cancer Data Aggregator (CDA)** connects you to subjects, files, and specim --- -### Three Ways to Access Data +## Choose Your Research Path + +Whether you prefer a visual interface, cloud-based notebooks, or a full Python environment, the CDA meets you where you are. + +=== "No Code (Interactive)" + + ### Explore Data Visually + Perfect for clinical researchers and building cohorts quickly. + + * **No Install:** Works entirely in your browser. + * **Intuitive Filtering:** Search by harmonized terms (age, diagnosis, project). + * **Export:** Download your cohort as a `.tsv` to open in Excel. + + [Try the Interactive Search β†’](https://cda.readthedocs.io/en/latest/interactive_search.html){ .md-button } + +=== "Low Code (Cloud)" + + ### Analyze in the Cloud + Fill in the blanks in our pre-built queries to find and process data without local setup. + + * **Connected:** Send results directly to [Broad Institute FireCloud](https://cda.readthedocs.io/en/latest/) or [Velsera Cancer Genomics Cloud](https://cda.readthedocs.io/en/latest/). + * **Scalable:** Run bioinformatics pipelines on the data you find without leaving your browser. + + [Launch CDA in the Cloud β†’](https://cda.readthedocs.io/en/latest/#low-code-no-install){ .md-button } + +=== "Power Users (Python)" + + ### Integrate with Python + For bioinformaticians building automated pipelines. + + ```bash + pip install cdapython + ``` + + ```python + from cdapython import Q + # Example: Find subjects with specific diagnosis + r = Q('primary_diagnosis = "Adenocarcinoma"').run() + print(r) + ``` -| No Code | Low Code | Power Users | -| :--- | :--- | :--- | -| **Interactive Search** | **Cloud Notebooks** | **Python Library** | -| Best for clinical researchers and quick cohort building. | Fill-in-the-blank queries in [FireCloud](https://cda.readthedocs.io/en/latest/) or [CGC](https://cda.readthedocs.io/en/latest/). | Full API access for bioinformatics pipelines and large-scale analysis. | -| [Try it now β†’](https://cda.readthedocs.io/en/latest/interactive_search.html) | [Launch in Cloud β†’](https://cda.readthedocs.io/en/latest/#low-code-no-install) | [View API Docs β†’](https://cda.readthedocs.io/en/latest/developer_tools.html) | + [View Developer Tools β†’](https://cda.readthedocs.io/en/latest/developer_tools.html){ .md-button } ---- \ No newline at end of file +--- + +## Master the CDA in Minutes + +Check out our video guides to see how the CDA simplifies complex data cross-referencing. + +* [πŸ“Ί Video: Intro to CDA](https://cda.readthedocs.io/en/latest/vignettes/video_intro.html) +* [πŸ“Ί Video: Build a Cohort Interactively](https://cda.readthedocs.io/en/latest/vignettes/video_build_a_cohort_interactively.html) +* [πŸ“Ί Video: Cohort Building with Python](https://cda.readthedocs.io/en/latest/vignettes/video_cohort_building_with_cdapython.html) + +--- + +## Why Use the CDA? + +| Feature | The CDA Advantage | +| :--- | :--- | +| **Harmonization** | We translate different data center terms into one common language. | +| **Cross-Center** | Find subjects that have data in GDC, PDC, and IDC simultaneously. | +| **Versatility** | Move from a simple search to a massive cloud pipeline in the same ecosystem. | + +--- + +### Stay Updated +* [Latest Data Releases](https://cda.readthedocs.io/en/latest/) +* [CDA Python Library Updates](https://cda.readthedocs.io/en/latest/release_notes/cdapython_releases.html) + +--- +[Back to top]