diff --git a/docs/getting_started/index.md b/docs/getting_started/index.md index b585f766..dd45c61a 100644 --- a/docs/getting_started/index.md +++ b/docs/getting_started/index.md @@ -2,78 +2,106 @@ 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.

+# Search cancer data across multiple NCI data commons—instantly +Cancer data is distributed across multiple systems—CDA brings it together. -
+Find subjects, files, and studies using harmonized terms across repositories. No coding required. -- :material-clock-fast:{ .lg .middle } __Don't code? No problem!__ +```{admonition} +:class: important - --- +👉 **[Start exploring data](interactive.html)** +Try interactive search or view the API docs. +
+ 👉 Start exploring data
+ Try interactive search · + View API docs +
+``` + +--- + +## 🔎 Find what you need—your way + +### 🔍 Explore (No coding) +Search and filter cancer datasets in a visual interface +👉 [Open interactive search](interactive.html) + +--- + +### 📓 Analyze (Low code) +Run queries and explore results in a ready-to-use notebook +👉 [Launch notebook in the cloud](notebooks.html) - 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__ +### ⚙️ Build (API) +Integrate CDA into pipelines and applications +👉 [View API documentation](api.html) - --- +--- - 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 -

+## 🖥️ See it in action -- :fontawesome-brands-python:{ .lg .middle } __Power users__ +Search across datasets with one query: - --- +- Filter by disease type, demographics, or study +- View harmonized results across repositories +- Export data for downstream analysis - Install `cdapython` with `pip` and get up - and running in no time +👉 **Try a sample search:** +[Find adenocarcinoma subjects across datasets](interactive.html) - ```bash - pip3 uninstall -y cdapython; pip3 install git+https://github.com/CancerDataAggregator/cdapython.git@develop - python3 - ``` +--- - ```python - from cdapython import * - ``` +## 💡 Why use CDA? -- :fontawesome-brands-python:{ .lg .middle } __Code in the Cloud__ +CDA removes the hardest parts of finding cancer data: - --- +- 🔗 **Search multiple data commons at once** + No need to query each repository separately - 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 -

+- 🧠 **Harmonized data model** + Use consistent terms across datasets -- :simple-swagger:{ .lg .middle } __Developers__ +- ⚡ **From exploration to analysis quickly** + Move from search → notebook → pipeline - --- +- 🧪 **Flexible for all users** + Works for researchers, analysts, and 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) +## 🧭 What you can find -- :material-bell-alert-outline:{ .lg .middle } __What's new?__ +Use CDA to discover: - --- +- Subjects across studies +- Clinical and genomic data files +- Metadata across CRDC repositories +- Cohorts matching specific criteria - Recently Updated Pages: +--- - - [Data Release](../release_notes/data_updates.md) - - [Code Release](../release_notes/cdapython.md) +## 🚀 Start in 10 seconds -- :simple-mysql:{ .lg .middle } __Need even more data?__ +Not sure where to begin? - --- +👉 [Open interactive search with a pre-built example](interactive.html) +Explore adenocarcinoma datasets across repositories. - 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 +## 📚 Learn more +- [About CDA](about_us.html) +- [Data model](data_model.html) +- [Tutorials](tutorials.html) +- [API reference](api.html) +--- -

+## 🔬 Developed by +The National Cancer Institute’s Cancer Research Data Commons (CRDC) \ No newline at end of file diff --git a/docs/index.md b/docs/index.md index 58d7815f..41645984 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,79 +1,100 @@ --- title: Re-Search made simple --- +# Search cancer data across multiple NCI data commons—instantly -

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.

+Cancer data is distributed across multiple systems—CDA brings it together. +Find subjects, files, and studies using harmonized terms across repositories. No coding required. -
+
+ 👉 Start exploring data
+ Try interactive search · + View API docs +
+ +--- -- :material-clock-fast:{ .lg .middle } __Don't code? No problem!__ +## 🔎 Find what you need—your way - --- +### 🔍 Explore (No coding) +Search and filter cancer datasets in a visual interface +👉 [Open interactive search](interactive.html) - 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. -

+--- + +### 📓 Analyze (Low code) +Run queries and explore results in a ready-to-use notebook +👉 [Launch notebook in the cloud](notebooks.html) + +--- -- :material-clock-fast:{ .lg .middle } __Low code, no install__ +### ⚙️ Build (API) +Integrate CDA into pipelines and applications +👉 [View API documentation](api.html) - --- +--- - 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 -

+## 🖥️ See it in action -- :fontawesome-brands-python:{ .lg .middle } __Power users__ +Search across datasets with one query: - --- +- Filter by disease type, demographics, or study +- View harmonized results across repositories +- Export data for downstream analysis - Install `cdapython` with `pip` and get up - and running in no time +👉 **Try a sample search:** +[Find adenocarcinoma subjects across datasets](interactive.html) - ```bash - pip3 uninstall -y cdapython; pip3 install git+https://github.com/CancerDataAggregator/cdapython.git@develop - python3 - ``` +--- - ```python - from cdapython import * - ``` +## 💡 Why use CDA? -- :fontawesome-brands-python:{ .lg .middle } __Code in the Cloud__ +CDA removes the hardest parts of finding cancer data: - --- +- 🔗 **Search multiple data commons at once** + No need to query each repository separately - 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 -

+- 🧠 **Harmonized data model** + Use consistent terms across datasets -- :simple-swagger:{ .lg .middle } __Developers__ +- ⚡ **From exploration to analysis quickly** + Move from search → notebook → pipeline - --- +- 🧪 **Flexible for all users** + Works for researchers, analysts, and 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/) +## 🧭 What you can find -- :material-bell-alert-outline:{ .lg .middle } __What's new?__ +Use CDA to discover: - --- +- Subjects across studies +- Clinical and genomic data files +- Metadata across CRDC repositories +- Cohorts matching specific criteria - Recently Updated Pages: +--- - - [Data Release](release_notes/data_updates.md) - - [Code Release](release_notes/cdapython.md) +## 🚀 Start in 10 seconds -- :simple-mysql:{ .lg .middle } __Need even more data?__ +Not sure where to begin? - --- +👉 [Open interactive search with a pre-built example](interactive.html) +Explore adenocarcinoma datasets across repositories. - 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 +## 📚 Learn more +- [About CDA](about_us.html) +- [Data model](data_model.html) +- [Tutorials](tutorials.html) +- [API reference](api.html) +--- -

+## 🔬 Developed by +The National Cancer Institute’s Cancer Research Data Commons (CRDC) \ No newline at end of file diff --git a/docs/interactive/google.html b/docs/interactive/google.html new file mode 100644 index 00000000..637c5eb5 --- /dev/null +++ b/docs/interactive/google.html @@ -0,0 +1,24 @@ + + + +

+
+
diff --git a/mkdocs.yml b/mkdocs.yml
index 81914456..8358d297 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"]
 
@@ -93,6 +93,7 @@ extra_css:
 nav:
   - Getting Started:
     - getting_started/index.md
+    - google search: interactive/google.html
     - Interactive Search: interactive/index.ipynb
     - getting_started/no-install.md
     - getting_started/install.md