Changes to CFDE Portal tutorial structure and explanation to overview…

… pages of tutorials (#247) * added brief explanation to index pgs of tutorials * add exclamation pt * update tab org description * re-write of Bioinformatics landing page * slight re-write for web development tab * edits to cheat sheets landing pg * small txt edits * fixed order of lessons and minor text edits in bioinfo section * minor text edits to web devlp index * minor text edits to cfde int index * txt edit to web devo index * added ending statemnet in portal index * minor grammar edits * made word cloud align left on home pg * revert back img left align Co-authored-by: Marisa Lim <[email protected]> Co-authored-by: Jeremy Walter <[email protected]> Co-authored-by: marisalim <[email protected]>
nih-cfde · Oct 15, 2020 · 28c5cda · 28c5cda
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diff --git a/docs/Bioinformatics-Skills/.pages b/docs/Bioinformatics-Skills/.pages
@@ -1,12 +1,13 @@
 nav:
   - index.md
+  - Kids First Tutorials: Kids-First
+  - CFDE Portal Tutorials: CFDE-Portal
   - install_conda_tutorial.md
   - Introduction_to_Amazon_Web_Services
   - Command-Line-BLAST
   - GWAS in the Cloud: GWAS-in-the-cloud
   - Snakemake Workflow Management: Snakemake
-  - Kids First Tutorials: Kids-First
-  - CFDE Portal Tutorials: CFDE-Portal
+
 
 
 
diff --git a/docs/Bioinformatics-Skills/CFDE-Portal/.pages b/docs/Bioinformatics-Skills/CFDE-Portal/.pages
@@ -1,5 +1,5 @@
 nav:
  - index.md
- - Blood-Cancer
- - Movement-Related-Disorders
+ - Use Case 1: Blood-Cancer
+ - Use Case 2: Movement-Related-Disorders
 
diff --git a/docs/Bioinformatics-Skills/CFDE-Portal/index.md b/docs/Bioinformatics-Skills/CFDE-Portal/index.md
@@ -7,20 +7,27 @@ title: CFDE Portal Overview
 
 The [NIH Common Fund (CF)](https://commonfund.nih.gov) has funded a wide variety of data types and studies that are of interest to clinical and biomedical researchers, however those datasets are hosted on an equally large number of websites, with varying query systems. The [Common Fund Data Ecosystem (CFDE) Portal](https://app.nih-cfde.org) is a unified system for searching across the entire CF portfolio in a single search, and is the first step in addressing the goal of making CF data more [Find-able, Accessible, Interoperable and Reusable (FAIR)](https://www.nih-cfde.org/product/fair-cookbook/). The wide range of data types, models and formats used by Common Fund Programs are being harmonized using well-defined metadata, common controlled vocabularies using the [Crosscut Metadata Model](https://www.nih-cfde.org/product/cfde-c2m2/).
 
-By following these tutorials researchers and clinicians will learn to navigate within the [CFDE Portal](https://app.nih-cfde.org). Users will learn how to use this portal to find datasets from many different CF Programs in a single search to build a cohort, and to save that cohort as a single metadata manifest file. Users will also learn to use the information in the manifest to gather the associated data files from their originating CF data portals. While some discoverable datasets may be public-access, many are likely to be controlled-access. Researchers will learn how to apply for protected data access for files included in their manifest.
+By following these tutorials researchers and clinicians will learn to navigate within the [CFDE Portal](https://app.nih-cfde.org). Users will learn how to use this portal to find datasets from many different CF Programs in a single search to build a cohort, and to save that cohort as a single metadata manifest file. Users will also learn to use the information in the manifest to gather the associated data files from their originating CF data portals. While some discoverable datasets may be public-access, many are likely to be controlled-access. Researchers will be guided to resources for obtaining data access authorization.
+
+**Use Case 1: Gathering Blood Cancer Datasets**  
 
 Est. Time | Lesson name | Description
 --- | --- | ---
 10 mins | [Cohort Selection for Blood Cancer](./Blood-Cancer/blood-cancer-portal-export.md) | Identify RNA-seq and whole genome sequencing (WGS) datasets in CFDE portal
 15 mins | [Blood Datasets from CF Program Portals](./Blood-Cancer/blood-cancer-data-access.md) | Access identified cohort in individual CF data portals
+
+**Use Case 2: Compiling Datasets of Movement-Related Disorders**
+
+Est. Time | Lesson name | Description
+--- | --- | ---
 10 mins | [Multi-omics Data Discovery for Movement-Related Disorders](./Movement-Related-Disorders/movement-disorders-portal-export.md) | Identify multiomics datasets
 10 mins | [Movement Disorders Datasets in CF Program Portals](./Movement-Related-Disorders/movement-disorders-data-access.md) | Access identified datasets in individual CF data portals
 
 !!! note "Learning Objectives"
 
     In this tutorial you will learn:
 
-    - how to build cohorts for Acute Myeloid Leukemia
+    - how to build cohorts for Blood Cancer
 
     - how to build cohorts for Movement-Related Disorders
 
@@ -35,6 +42,6 @@ Est. Time | Lesson name | Description
 
     Vidlets:
 
-     - [Acute Myeloid Leukemia Demonstration](./Blood-Cancer/blood-cancer-portal-export.md)
+     - [Blood Cancer Demonstration](./Blood-Cancer/blood-cancer-portal-export.md)
 
      - [Movement-Related Disorders Demonstration](./Movement-Related-Disorders/movement-disorders-portal-export.md)
diff --git a/docs/Bioinformatics-Skills/index.md b/docs/Bioinformatics-Skills/index.md
@@ -6,7 +6,14 @@ title: Overview
 Bioinformatics Skills
 =======================
 
-Setup & Computing Software:
+Tutorials in this section provide lessons for finding data sets, setting up compute environments for analysis, and running hands-on bioinformatics analyses. 
+
+Common Fund Data - Finding Datasets for Analysis:
+
+- [Kids First Tutorials](Kids-First/index.md)
+- [CFDE Portal Tutorials](CFDE-Portal/index.md)
+
+Software and Compute Set up for Analysis:
 
 - [Set up Conda Computing Environment](install_conda_tutorial.md)
 - [Introduction to Amazon Web Services](Introduction_to_Amazon_Web_Services/introtoaws1.md)
@@ -16,8 +23,3 @@ Bioinformatics Analysis:
 - [Command Line BLAST](Command-Line-BLAST/BLAST1.md)
 - [GWAS in the Cloud](GWAS-in-the-cloud/index.md)
 - [Snakemake Workflow Management](Snakemake/index.md)
-
-Common Fund Data:
-
-- [Kids First Tutorials](Kids-First/index.md)
-- [CFDE Portal Tutorials](CFDE-Portal/index.md)
diff --git a/docs/CFDE-Internal-Training/Website-Style-Guide/1WebsiteNavStyle.md b/docs/CFDE-Internal-Training/Website-Style-Guide/1WebsiteNavStyle.md
@@ -4,7 +4,7 @@ The website uses several forms of navigation:
 
 Navigation type | Specified in | About
 --- | --- | ---
-Navigation tabs | name of tutorial folder, separated by hyphens (e.g., 'Bioinformatics-Tutorials/' is rendered as 'Bioinformatics Tutorials')* | Organized by tutorial type (**at the moment**)
+Navigation tabs | name of tutorial folder, separated by hyphens (e.g., 'Bioinformatics-Skills/' is rendered as 'Bioinformatics Skills')* | Currently organized by topic and user type 
 Left TOC | `.pages` | Table of contents for each tab and tutorial (if there are multiple pages)
 Right TOC | `#`, `##`, etc. markdown headers | Table of contents for each tutorial page
 Tab overview | `index.md` for tab section | Landing page describing the contents of the tab

diff --git a/docs/CFDE-Internal-Training/index.md b/docs/CFDE-Internal-Training/index.md
@@ -5,7 +5,10 @@ title: Overview
 
 CFDE Internal Training
 =========================
-CFDE-CC:
+
+This section lists tutorials for working in GitHub, the preferred project management platform for CFDE, along with essential resources for contributing to the website. The tutorial for identifying MIME type is specifically aimed at Common Fund Programs as part of their data ingest workflow for the CFDE Portal.
+
+CFDE-Coordination Center:
 
    - [Website Style Guide](./Website-Style-Guide/0index.md)
    - [Editing MkDocs Websites with cfde-bot](cfdebot_website_editing.md)

diff --git a/docs/Cheat-Sheets/index.md b/docs/Cheat-Sheets/index.md
@@ -6,6 +6,8 @@ title: Overview
 Cheat Sheets
 ==============
 
+The cheat sheets below are a quick reference to commonly used commands in bash, conda, and Snakemake.
+
 - [Bash and nano Commands](./bash_cheatsheet.md)
 - [Conda Commands](./conda_cheatsheet.md)
 - [Snakemake Commands](./snakemake_cheatsheet.md )
diff --git a/docs/Web-Development/index.md b/docs/Web-Development/index.md
@@ -7,6 +7,8 @@ title: Overview
 Web Development
 ==================
 
+The Building Websites tutorials describe how to render GitHub websites locally on a variety of platforms and hardware. The Customization section includes a Javascript tutorial for creating a dropdown list in web pages enabling users to choose from different versions of page content.
+
 Building Websites:
 
 - [Rendering a GitHub Website Locally with Jekyll](Jekyll_Tutorial.md)

diff --git a/docs/index.md b/docs/index.md
@@ -5,12 +5,13 @@ title: Home
 
 # Welcome to the CFDE Training Resource Center!
 
-Our mission as the **Common Fund Data Ecosystem (CFDE)** Coordination Center is to make **Common Fund (CF)** data accessible to researchers like you. Choose from our growing list of tutorials and resources to learn how to perform bioinformatic analyses and access data. 
+Our mission as the **Common Fund Data Ecosystem (CFDE)** Coordination Center is to make **Common Fund (CF)** data accessible to researchers like you! Choose from our growing list of tutorials and resources to learn how to perform bioinformatic analyses and access data.
 
-To get started, visit the [Bioinformatics Skills](./Bioinformatics-Skills/index.md) section for tutorials on setting up a computing environment and conducting common bioinformatic analyses. 
+To get started, visit the [Bioinformatics Skills](./Bioinformatics-Skills/index.md) section for tutorials on setting up a computing environment and conducting common bioinformatic analyses.
 
 Learn how to build cohorts and export metadata at the [Kids First Portal](./Bioinformatics-Skills/Kids-First/index.md) and across multiple CF datasets using the [CFDE Portal](./Bioinformatics-Skills/CFDE-Portal/index.md).
 
-![](./images/CFDEwordcloud.png "CFDE word cloud")
+
+![CFDE word cloud](./images/CFDEwordcloud.png "CFDE word cloud")
 
 Check the [release notes](./Release-Notes/index.md) for our latest tutorial updates. If you have comments or suggestions, please [contact us](mailto:[email protected])!
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -24,11 +24,9 @@ markdown_extensions:
 - pymdownx.superfences
 - pymdownx.tabbed
 - pymdownx.emoji
-
 - pymdownx.tabbed
 - pymdownx.extra
 - pymdownx.superfences
-
 - pymdownx.extra
 - pymdownx.highlight
 - pymdownx.keys