Merge pull request #592 from isb-cgc/Deena-Staging-Theme

Deena staging theme
isb-cgc · Jun 24, 2021 · 35c1897 · 35c1897
2 parents 4bec9bc + e418d5c
commit 35c1897
Show file tree

Hide file tree

Showing 17 changed files with 89 additions and 73 deletions.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -14,7 +14,7 @@ Contained within this documentation are descriptions of ISB-CGC features along w
 .. image:: overview_image.png
    :align: left
 
-The `ISB-CGC <https://isb-cgc.org>`_ aims to serve the needs of a broad range of cancer researchers ranging from scientists or clinicians who prefer to use an interactive web-based application to access and explore the rich TCGA, TARGET, CCLE, and COSMIC datasets, to computational scientists who want to write their own custom scripts using languages such as R or Python, accessing the data through APIs, and to algorithm developers who wish to spin up thousands of virtual machines to analyze hundreds of terabytes of sequence data.
+The `ISB-CGC <https://isb-cgc.org>`_ aims to serve the needs of a broad range of cancer researchers ranging from scientists or clinicians who prefer to use an interactive web-based application to access and explore the rich TCGA, TARGET, CCLE, COSMIC and other data sets, to computational scientists who want to write their own custom scripts using languages such as R or Python, accessing the data through APIs, and to algorithm developers who wish to spin up thousands of virtual machines to analyze hundreds of terabytes of sequence data.
 
 -- the ISB-CGC team
 

diff --git a/docs/source/sections/BigQuery/BigQueryTableSearchUI.png b/docs/source/sections/BigQuery/BigQueryTableSearchUI.png
diff --git a/docs/source/sections/Hosted-Data.rst b/docs/source/sections/Hosted-Data.rst
@@ -4,7 +4,7 @@ Programs and Data Sets
 
 The National Cancer Institute (NCI) `Genomic Data Commons <https://gdc.cancer.gov/>`_ (GDC) and  `Proteomics Data Commons (PDC) <https://pdc.cancer.gov/pdc/>`_ provide the cancer research community with data repositories that enables data sharing across cancer genomic and proteomic studies (known as Programs) in support of precision medicine. 
 
-The ISB-CGC started with The Cancer Genome Atlas (TCGA) data sets but has expanded to include other data sets from programs such as Therapeutically Applicable Research To Generate Effective Treatments (TARGET). Along with the NCI GDC and PDC data sets, ISB-CGC hosts data sets from programs such as Catalogue Of Somatic Mutations In Cancer (COSMIC) from the `Wellcome Trust Sanger Institute <http://www.sanger.ac.uk/>`_. We are always interested in adding new data sets, so if you have any suggestions or requests for additional data, please let us know (feedback@isb-cgc.org).
+The ISB-CGC started with The Cancer Genome Atlas (TCGA) data sets but has expanded to include other data sets from programs such as Therapeutically Applicable Research to Generate Effective Treatments (TARGET). Along with the NCI GDC and PDC data sets, ISB-CGC hosts data sets from programs such as Catalogue Of Somatic Mutations In Cancer (COSMIC) from the `Wellcome Trust Sanger Institute <http://www.sanger.ac.uk/>`_. We are always interested in adding new data sets, so if you have any suggestions or requests for additional data, please let us know (feedback@isb-cgc.org).
 
 Clinical, Biospecimen and Processed -Omics Data Sets
 ----------------------------------------------------
@@ -62,7 +62,7 @@ Clinical, biospecimen and processed -omics data (such as RNASeq, etc.) are avail
    * - `FM <data/FM_about.html>`_
      - |checkmark|
      - |checkmark| *
-     - 
+     - |checkmark|
    * - `GENIE <data/GENIE_about.html>`_
      - |checkmark|
      - |checkmark| *
@@ -74,15 +74,15 @@ Clinical, biospecimen and processed -omics data (such as RNASeq, etc.) are avail
    * - `MMRF <data/MMRF_about.html>`_
      - |checkmark|
      - |checkmark| *
-     - 
+     - |checkmark|
    * - `NCICCR <data/NCICCR_about.html>`_
      - |checkmark|
      - |checkmark| *
      - 
    * - `OHSU <data/OHSU_about.html>`_
      - |checkmark|
      - |checkmark| *
-     - 
+     - |checkmark|
    * - `ORGANOID <data/ORGANOID_about.html>`_
      - |checkmark|
      - |checkmark| 
@@ -161,7 +161,7 @@ PDC protein expression data are available in ISB-CGC BigQuery tables. The table
    * - `Georgetown Proteomics Research Program <data/GPRP_about.html>`_
      - 
      - |checkmark| 
-     - 
+     - |checkmark|
    * - `ICPC <data/ICPC_about.html>`_
      - 
      - |checkmark|

diff --git a/docs/source/sections/ReleaseNotes/WebAppReleaseNotes.rst b/docs/source/sections/ReleaseNotes/WebAppReleaseNotes.rst
@@ -2,6 +2,28 @@
 ISB-CGC Web App Release Notes
 #############################
 
+*June xx, 2021* 
+
+**New Features** 
+
+- The Citations link on the top-level menu has been replaced with a Publications link. The page now includes ISB-CGC publications and posters, as well as citations.
+- Enhance the Cohort Builder UI and Cohort Details UI so that additional node based GDC and PDC Programs can be selected and edited. The Programs now available are:
+
+  - GDC
+
+    - TCGA
+    - TARGET
+    - CCLE
+    - BEATAML1.0
+    - FM
+    - MMRF
+    - OHSU
+
+  - PDC
+
+    - Georgetown Proteomics (GPRP) 
+- On the Cohort Builder, replace the Selected Filters panel with the Cohort Filters panel. This panel displays all selected filters for all selected Programs.
+
 *April 13, 2021* 
 
 **New Features** 

diff --git a/docs/source/sections/Tutorials/KidneyCancerDemo/ISB-homepage.png b/docs/source/sections/Tutorials/KidneyCancerDemo/ISB-homepage.png
diff --git a/docs/source/sections/webapp/CreateCohort.png b/docs/source/sections/webapp/CreateCohort.png
diff --git a/docs/source/sections/webapp/CreateCohorts-noSignIn.png b/docs/source/sections/webapp/CreateCohorts-noSignIn.png
diff --git a/docs/source/sections/webapp/CreateDetails.png b/docs/source/sections/webapp/CreateDetails.png
diff --git a/docs/source/sections/webapp/Menu.rst b/docs/source/sections/webapp/Menu.rst
@@ -33,7 +33,7 @@ The **MENU** bar supplies links for the following Web App features:
 
     - Public Programs - Here you can:
 
-      *  View the public programs (TCGA, CCLE, TARGET) that are currently in the ISB-CGC system. 
+      *  View the public programs that are currently in the ISB-CGC system. 
 
 * **ANALYSES** - From here you can Create, Edit Details, Duplicate, Delete, or Share Analyses. You can use a specific analysis type to create a new workbook customized with the specific data (Genes and miRNAs, Variables, Cohorts) you have selected.  The plot types that you can select are:
 

diff --git a/docs/source/sections/webapp/Overview.rst b/docs/source/sections/webapp/Overview.rst
@@ -18,6 +18,8 @@ Also on this page are links to:
 - Pipelines and APIs
 - Notebooks
 - Controlled Access Data
+- Documentation
+- ISB-CGC Publications and Citations
 
 
 **If your screen looks like this:** 

diff --git a/docs/source/sections/webapp/Register_Step_2.png b/docs/source/sections/webapp/Register_Step_2.png