improvement: various improvements to the docs site

docs/citing-stjude-cloud/index.md

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+---
+title: Citing St. Jude Cloud
+---
+
+# Citing St. Jude Cloud
+
+The St. Jude Cloud manuscript is currently under review. Until further notice, when St. Jude Cloud or data accessed therein is used in your work, please ensure that you:
+
+1. Cite the St. Jude Cloud manuscript preprint on BioRxiv:
+
+    [St. Jude Cloud - a Pediatric Cancer Genomic Data Sharing Ecosystem](https://www.biorxiv.org/content/10.1101/2020.08.24.264614v1)
+
+2. Cite the relevant paper for each dataset and/or resource that you used in your study (see ‘Dataset’ and ‘Resource’ reference tables below)
+
+3. State in the **Results** and/or **Methods** section that the relevant data and/or resource was obtained from St. Jude Cloud. Example statement:
+>"Whole genome sequencing data for relapse tumor samples from 345 pediatric patients were obtained from St. Jude Cloud."
+           
+4. State in the **Data availability** section of the manuscript that data and/or resource can be accessed via St. Jude Cloud. Example statement:
+>"Whole genome sequencing data for pediatric relapse tumor samples used for analysis in this study were obtained from St. Jude Cloud (https://www.stjude.cloud) – a publicly accessible pediatric genomic data resource requiring approval for controlled data access."
+
+## Dataset Reference Table
+
+Please download the Schedule 1(s) (linked in table below) to find dataset specific wording of acknowledgement(s).
+
+| St. Jude Cloud Dataset             |  Reference     |
+| -------------------------------- | ----------------- |
+| Pediatric Cancer Genome Project (PCGP) dataset  | [PCGP perspectives paper](https://www.ncbi.nlm.nih.gov/pubmed/22641210) and the [relevant tumor type paper(s)](http://pecan.stjude.cloud/pcgp-explore); [<i class="material-icons material-icons-sjcloud-custom">file_download</i> PCGP Schedule 1](../../files/PCGP-Schedule1.pdf)   |
+| St. Jude Lifetime (SJLIFE) dataset                   | [SJLIFE paper](https://www.ncbi.nlm.nih.gov/pubmed/?term=29847298); [<i class="material-icons material-icons-sjcloud-custom">file_download</i> SJLIFE Schedule 1](../../files/SJLIFE-Schedule1.pdf)  |
+| Clinical Genomics (Clinical Pilot, Genomes for Kids, Real-Time Clinical Genomics) dataset | [Clinical Pilot paper](https://www.ncbi.nlm.nih.gov/pubmed/30262806); [<i class="material-icons material-icons-sjcloud-custom">file_download</i> Clinical Genomics Schedule 1](../../files/ClinGen-Schedule1.pdf) |
+| Sickle Cell Genome Project (SGP) dataset | paper in progress; [<i class="material-icons material-icons-sjcloud-custom">file_download</i> SGP Schedule 1](../../files/SGP-Schedule1.pdf) |
+| Childhood Cancer Survivor Study (CCSS) dataset | [CCSS study design paper](https://www.ncbi.nlm.nih.gov/pubmed/11920786); [<i class="material-icons material-icons-sjcloud-custom">file_download</i> CCSS Schedule 1](../../files/CCSS-Schedule1.pdf) |
+| Pan-Acute Lymphoblastic Leukemia (PanALL) dataset | [<i class="material-icons material-icons-sjcloud-custom">file_download</i> PanALL Schedule 1](../../files/PanALL-Schedule1.pdf) |
+
+!!!note
+If you are unsure what dataset(s) the data that you have been vended belongs to, you can find this information in the sj_datasets column of the [SAMPLE_INFO.txt](../../genomics-platform/requesting-data/about-our-data/#metadata) file.
+!!!
+
+!!!warning
+Publishing using any of the data files _before_ the [embargo date](../../genomics-platform/requesting-data/glossary/#embargo-date) has passed is strictly prohibited as outlined in the [Data Access Agreement (DAA)](../../genomics-platform/requesting-data/glossary/#data-access-agreement).
+!!!
+
+## Resource Reference Table
+
+| St. Jude Cloud Resource             |  Reference     |
+| -------------------------------- | ----------------- |
+| ProteinPaint | [ProteinPaint paper](https://www.nature.com/articles/ng.3466) | 
+| GenomePaint | paper in progress | 
+| PeCan Pie | [PeCan Pie paper](https://genome.cshlp.org/content/29/9/1555.full) |
+| ChIP-Seq Peak Calling | unpublished | 
+| Rapid RNA-Seq Fusion Detection | paper in progress | 
+| WARDEN  | unpublished | 
+| Mutational Signatures | [Mutational Patterns paper](https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-018-0539-0) | 
+| cis-x  | paper in progress | 
+| XenoCP  | paper in progress | 
+
+<!-- NeoepitopePred | [NeoepitopePred paper](https://www.ncbi.nlm.nih.gov/pubmed/28854978) -->
+
+## Contact Us
+
+Any questions, comments, or concerns can be directed to our ["Contact Us"](https://stjude.cloud/contact) form or you can email us directly at support@stjude.cloud.

docs/ecosystem/index.md

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+---
+title: About our Ecosystem
+---
+
+# About our Ecosystem
+
+## Overview
+
+The St. Jude Cloud ecosystem has been designed with three main entry points, called Research Domains, to guide users along a path of content that will be most relevant to their research interests. Cards for these top-level Research Domains (Pediatric Cancer, Cancer Survivorship, and Non-Cancerous Diseases) are the first selections you will be presented with on [our homepage](https://stjude.cloud). 
+
+The diagram below shows an abstraction of our ecosystem. Research Domains are presented as vertical panels which cascade down through the sets of Apps and Studies, the building blocks of content along the Research Domains.
+
+![](./figure_overall_structure.png)
+
+Apps are interactive and facilitate data sharing and discovery. Studies are
+static pages of content that discuss how St. Jude has generated and used a
+particular dataset. Apps and Studies are disjoint ecosystem elements, yet they
+are distributed non-uniquely among the Research Domains in order to facilitate a
+focused sharing of content. For a complete list of Applications and Studies
+please visit the [Welcome to St. Jude](../) documentation page.
+
+## Migration to new structure
+
+St. Jude Cloud's original architecture of Data, Tools, and Visualizations
+has been retired. You can learn more about what changed in the [announcement
+blog post](https://stjude.cloud/announcements/st-jude-cloud-restructure). We hope this redesigned
+ecosystem will better facilitate data sharing, discovery, and community
+engagement.
+
+![](./figure_restructure-map.png)

docs/faq/index.md

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+---
+title: Frequently Asked Questions
+---
+
+
+# Frequently Asked Questions
+
+!!!info
+
+This page contains information about site-wide St. Jude Cloud frequently asked questions. For more detailed information, we highly recommend that you also visit the dedicated frequently asked questions page for the application you are using.
+
+* [St. Jude Cloud Genomics
+    Platform FAQ](../../genomics-platform/faq)
+* [St. Jude Cloud
+    PeCan FAQ](../../pecan/faq)
+* [St. Jude Cloud Visualization
+    Community FAQ](../../visualization-community/faq)
+!!!
+
+```toc
+from-heading: 2
+```
+
+## General Questions
+
+### Where can I find the Terms of Service or the Privacy Policy?
+
+You can find the Terms of Service [here](https://stjude.cloud/terms-of-use) and
+the Privacy Policy [here](https://stjude.cloud/privacy-policy). They are updated
+regularly, so as we note out in the text there, please check back regularly!
+
+### How can I sign up for updates?
+
+To receive updates on St. Jude Cloud, such as new data releases and new
+applications released, please [subscribe to our email
+list](https://hospital.stjude.org/apps/forms/fb/st-jude-cloud-subscribe/).
+
+## Billing Questions
+
+### Will I be charged for using St. Jude Cloud?
+
+Please see the following questions in each application's dedicated frequently
+asked questions page.
+
+* [St. Jude Cloud Genomics
+  Platform](../../genomics-platform/faq/#will-i-be-charged-for-using-st-jude-cloud-genomics-platform)
+* [St. Jude Cloud
+  PeCan](../../pecan/faq/#will-i-be-charged-for-using-st-jude-cloud-pecan)
+* [St. Jude Cloud Visualization
+  Community](../../visualization-community/faq/#will-i-be-charged-for-using-st-jude-cloud-visualization-community)
+
+## Publication Questions
+
+### How do I cite St. Jude Cloud?
+
+The manuscript for St. Jude Cloud is currently in preparation. In the
+meantime, please refer to the [citation guide](../citing-stjude-cloud).
+
+### When can I publish my findings using St. Jude Cloud data?
+
+* Within St. Jude Cloud Genomics Platform, all of the samples are marked with an [embargo
+date](../../genomics-platform/requesting-data/glossary#embargo-date). Once the embargo date has passed for **all** of the data sets you've used in your research, you are permitted to publish results based on that data. You
+can find this by looking at the tags for each file or in the `SAMPLE_INFO.txt`
+file that is included with each data request. To learn more, please visit the dedicated section in our [guide](../../genomics-platform/requesting-data/about-our-data/#standard-metadata).
+* Any data in St. Jude Cloud Visualization Community or St. Jude Cloud PeCan is considered published.
+* For any data not covered here, or if you have any questions, please [contact us](mailto:support@stjude.cloud).
+

docs/index.md

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+---
+title: Overview
+---
+
+# St. Jude Cloud Documentation
+
+Welcome to the St. Jude Cloud documentation! Here, you will find authoritative guides for accessing St. Jude Cloud data, creating and running analysis workflows on the cloud, and exploring curated data from numerous published studies by St. Jude and our collaborating institutions.To learn more about our ecosystem, read this [guide](../ecosystem). 
+
+Sign up [here](https://hospital.stjude.org/apps/forms/fb/st-jude-cloud-subscribe/) to receive email notifications when we add new datasets, analysis pipelines, or other exciting features.
+
+## Features
+
+You can apply many different capabilities of St. Jude Cloud to your research, such as:
+
+* Explore the [raw genomics data](https://platform.stjude.cloud/data/diseases) we currently offer. You can browse by diagnosis, publication, or curated dataset while applying a number of different filters. For more information, see our [data request guide](../genomics-platform/requesting-data/making-a-data-request).
+* Run your tools on *our* data by [requesting data](../genomics-platform/requesting-data/making-a-data-request) and packaging your tools in a secure cloud environment. See this [guide](../genomics-platform/analyzing-data/creating-a-cloud-app) for an example.
+* Run our in house analysis workflows on *your* data by [moving your data](../genomics-platform/managing-data/upload-local) to the cloud and selecting a [workflow](https://platform.stjude.cloud/workflows) to run. See this [guide](../genomics-platform/analyzing-data/running-sj-workflows) for an example. 
+* Explore St. Jude datasets through interactive visualizations that we have packaged for the community. For example, visit [PeCan](https://pecan.stjude.cloud) to visually investigate pediatric cancer mutation data.
+* Create manuscript quality figures with *your* data to use in publications or to host on your website with [ProteinPaint](https://proteinpaint.stjude.org/) or [GenomePaint](https://genomepaint.stjude.cloud/). See the [ProteinPaint documentation](../visualization-community/proteinpaint) and [GenomePaint documentation](../visualization-community/genomepaint) for help.
+
+!!!note
+Please note that while it is free to receive and store our data in St. Jude Cloud, there are [compute and storage fees associated with working in the cloud, as well as egress fees for downloading data](./faq/#will-i-be-charged-for-using-st-jude-cloud). 
+!!!
+
+## Apps
+
+St. Jude Cloud provides a number of applications which you can use for various purposes. Click on the links below to checkout one or more of our applications.
+
+* [Genomics Platform](https://platform.stjude.cloud): browse our publicly available genomics datasets, make a data request, and run analyses in a secure cloud environment. View the documentation for this app [here](./guides/genomics-platform/index.md). 
+
+* [Pediatric Cancer Portal (PeCan)](https://pecan.stjude.cloud): interactively explore mutational recurrence and pathogenicity assessment of variants in pediatric cancer using a wide variety of St. Jude + publicly available data. View the documentation for this app [here](./guides/pecan/index.md).
+
+* [Visualization Community](https://viz.stjude.cloud/): explore, create, and share interactive visualizations using tools such as ProteinPaint and GenomePaint. View the documentation for this app [here](./guides/visualization-community/index.md).
+
+## Studies
+
+The following projects currently distribute data through St. Jude Cloud. Click [here](./guides/genomics-platform/requesting-data/about-our-data.md#data-access-units) for a brief description of each project listed below. Or click on a project in the bulleted list below to go straight to the corresponding Study page.
+
+* [Pediatric Cancer Genome Project (PCGP)](https://stjude.cloud/studies/pediatric-cancer-genome-project)
+* [St. Jude Lifetime (SJLIFE)](https://sjlife.stjude.org/)
+* [Clinical Genomics (Clinical Pilot and G4K)](https://stjude.cloud/studies/clinical-genomics)
+* [Sickle Cell Genome Project (SGP)](https://sickle-cell.stjude.cloud)
+* [Childhood Cancer Survivor Study (CCSS)](https://ccss.stjude.org/)
+
+## Analysis Workflows
+
+St. Jude shares a number of end-to-end analysis workflows as part of the Genomics Platform application. Click on the links below to learn more about the workflow.
+
+<!-- * [NeoepitopePred](https://platform.stjude.cloud/workflows/neoepitopepred) -->
+* [ChIP-Seq Peak Calling](https://platform.stjude.cloud/workflows/chip-seq)
+* [Rapid RNA-Seq Fusion Detection](https://platform.stjude.cloud/workflows/rapid_rna-seq)
+* [WARDEN Differential Expression Analysis](https://platform.stjude.cloud/workflows/warden)
+* [Mutational Signatures](https://platform.stjude.cloud/workflows/mutational_signatures)
+* [SequencErr](https://platform.stjude.cloud/workflows/sequencerr)
+* M2A (coming soon)
+
+## Contact Us
+
+Any questions, comments, or concerns can be directed to our ["Contact Us"](https://stjude.cloud/contact) form or you can email us directly at support@stjude.cloud.

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