Merge pull request #733 from isb-cgc/Deena-Staging-Theme

Deena staging theme

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, 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 <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 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
 

docs/source/sections/BigQueryTableSearchUI.rst

@@ -72,7 +72,7 @@ The tables are grouped into four high-level categories:
 
 * **File Metadata**: Information about raw data files including Google Cloud Storage Paths (includes tables with information                       about files available at the GDC, including GCS paths, creation dates, sizes, etc.)
 
-* **Genomic Reference Database**: Genomic information that can be used to cross-reference against processed-omics data tables                                   (examples include  COSMIC, ClinVar, cytoBand, dbSNP, Ensembl, Ensembl2Reactome)
+* **Genomic Reference Database**: Genomic information that can be used to cross-reference against processed-omics data tables                                   (examples include ClinVar, cytoBand, dbSNP, Ensembl, Ensembl2Reactome)
 
 * **Processed-omics Datasets**: Processed data primarily from the GDC (i.e. raw data that has gone through GDC pipeline                                        processing e.g. gene expression, miRNA expression, copy number, somatic mutations, methylation)
 

docs/source/sections/ExploringISB-CGC.rst

@@ -2,7 +2,7 @@
 ISB-CGC Data Overview
 ***********************
 
-ISB-CGC provides access to data from several research programs, such as **The Cancer Genome Atlas (TCGA)**, **Therapeutically Applicable Research to Generate Effective Treatments (TARGET)**, **Cancer Cell Line Encyclopedia (CCLE)** and **Catalogue of Somatic Mutations in Cancer (COSMIC)**. The full list is available `here <Hosted-Data.html>`_.  
+ISB-CGC provides access to data from several research programs, such as **The Cancer Genome Atlas (TCGA)**, **Therapeutically Applicable Research to Generate Effective Treatments (TARGET)**, and **Cancer Cell Line Encyclopedia (CCLE)**. The full list is available `here <Hosted-Data.html>`_.  
 
 The majority of the data made available through ISB-CGC originates from NCI `Genomic Data Commons <https://gdc.cancer.gov/>`_ (GDC). Users can access GDC data on the cloud through ISB-CGC. Users have access to both raw and processed data from cancer patients. 
 

docs/source/sections/Gaining-Access-To-Controlled-Access-Data.rst

@@ -7,8 +7,6 @@ In ISB-CGC, you can gain access to `controlled data via personal user credential
   * Provides access to controlled data for 24 hours at a time;
   * Uses your *personal* credentials;
   * Example uses: the ISB-CGC Web App, R Studio or running short jobs on Google Compute Engine that complete in under 24 hours
-
-.. note:: If you are looking to gain access to COSMIC data, please see the `COSMIC documentation <data/COSMIC_about.html>`_.
 
 Prerequisites
 --------------

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 Pan-Cancer Atlas and HTAN. 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
 ----------------------------------------------------
@@ -233,10 +233,6 @@ From Other Sources
      - GDC Google Cloud Storage
      - ISB-CGC BigQuery Tables
      - ISB-CGC Cohort Builder
-   * - `COSMIC <data/COSMIC_about.html>`_
-     - No, the COSMIC database is maintained by the Wellcome Sanger Institute, UK
-     - Yes, COSMIC data is in BigQuery for registered users. Learn more about how to gain access to the COSMIC data `here <data/COSMIC_about.html>`_   
-     - 
    * - `Pan-Cancer Atlas <PanCancer-Atlas-Mirror.html>`_
      - 
      - |checkmark|
@@ -250,7 +246,6 @@ From Other Sources
    :maxdepth: 1
    :hidden:
 
-   data/COSMIC_about
    PanCancer-Atlas-Mirror
    data/HTAN_about
 

docs/source/sections/HowTos.rst

@@ -43,9 +43,6 @@ I'm a novice, how do I...
    * - Join multiple tables?
      - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_perform_complex_joins.ipynb>`_
      -
-   * - Get started working with the COSMIC datasets?
-     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/Intro_to_COSMIC_in_BigQuery.ipynb>`_
-     -
    * - Convert a .bam file to a .fastq file with samtools?
      - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_convert_bams_to_fastq_with_samtools.ipynb>`_
      - 
@@ -103,9 +100,6 @@ I'm an advanced user, how do I...
    * - Compute Nearest Centroid Classification using BigQuery?
      - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_perform_Nearest_Centroid_Classification_with_BigQuery.ipynb>`_
      - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_perform_Nearest_Centroid_Classification_with_BigQuery.md>`_
-   * - Analyze data in the COSMIC Cancer Gene Census dataset?
-     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/Exploring_COSMICs_Cancer_Gene_Census_table.ipynb>`_
-     -
    * - Use a BigQuery user defined function to perform k-means clustering?
      - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_cluster_data_using_a_BigQuery_function.ipynb>`_
      -