tutorial updates

docs/visualization-community/faq/index.md

@@ -7,26 +7,26 @@ KeyWord(s): VisCom (Visualization Community)
 * [Visualization Community](https://viz.stjude.cloud/) is a safe environment where you can explore public research visualizations, learn how to use [ProteinPaint](https://proteinpaint.stjude.org/)/[GenomePaint](https://genomepaint.stjude.cloud/), and even create visualizations that can be privately or publicly accessed from your own dataset.
 
 **How does Visualization Community work?**
-* VisCom is hosted in St. Jude's cloud enviornment where there is no outsource program or application to download. It only requires a computer and internet connection and is completely free for non-profit/academic use. Your data set must be hosted on St. Jude's HPC in a specific directory outlined in our [Manage your Data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section or have a URL to access the data. 
+* VisCom is hosted in St. Jude’s cloud environment so there is no application to download. It only requires a computer and internet connection and is completely free for non-profit/academic use. Your data set must be hosted on St. Jude's HPC in a specific directory outlined in our [Manage your Data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section or have a URL to access the data. 
 
 * You will ***not*** incur any costs except in the following situations:
 
 *When data driving a visualization is stored in St. Jude Cloud Genomics Platform or DNAnexus, a monthly fee will be incurred for storage costs. See your [DNAnexus billing information](https://platform.dnanexus.com/profile/settings/billing) for the cost per GB.*
 
 **What do the visualizations represent?**
-* The visuals are curated by researchers, those composed of St Jude Cloud or others within a research team. These visuals represent high dimensional proteomic or genomic data sets. 
+* The visualizations represent the integration of high dimensional genomic or proteomic data sets or the summarization of such data sets .
 
 **Can I create my own visualizations?**
 * Yes, users have access to create visuals once they sign up for an account. Visualizations cannot become public until they are assigned to a team where a PI or Team Lead must approve through our internal workflow. To be added to a team, you must contact [support@stjude.cloud](support@stjude.cloud). 
 
 **Can I share my visuals with others?**
-* Yes, you may share your visualization(s) if our PI or team lead approves. We can enable a feature for you to share the direct link administratively if the visualization is still private. Coming soon will be a sharing option within the Visualization Community platform once the visualization is public. 
+* Yes, you may share your visualization(s) once your PI or team lead approves. We can share the direct link administratively,  if the visualization is still private, on request at [support@stjude.cloud](support@stjude.cloud).
 
 **Can I keep my visualizations private?**
 * Yes, we have an access control workflow where you can create visualizations which will remain private until you get approval from the team PI or Team Lead to make it public. 
 
 **Can I use these in a publication?**
-* Yes, you may use these sophisticated figures in your publications. We currently have published visualizations in over 11 prestigious journals including, but not limited to, Nature, Cancer Discovery, Blood, and Cell Reports. You may search which Journals are associated by using our search engine. 
+* Yes, we encourage you to use these figures in your publications. We currently have published visualizations in over 11 prestigious journals including, but not limited to, Nature, Cancer Discovery, Blood, and Cell Reports. You may search for a journal by entering a key word in our search engine.
 
 **Do I have to upload my own PDF or what do I need to generate the interactive visualization?**
 * You do not need to upload a PDF. You will signin to your account and use one of our two editors: Easy View or Traditional Code. Easy view allows you to render visualizations without knowing the code block. Traditional code is encouraged for more advanced users who know how to develop the code blocks. 

docs/visualization-community/index.md

@@ -13,13 +13,15 @@ Once you find the visualization you need within VisCom, you can easily re-create
 2.) by viewing our [library](https://university.stjude.cloud/docs/visualization-community/basics) of curated code blocks.*
 3.) or explore our new visualization editor with curated pre-filled examples.
 
-*If you want to use the new VisEditor with a curated example data found in VisCom, then just be sure to copy/paste the file or url key hyperlink to re-create it. Add the hyperlink to the URL field that populates for that track or app. 
+*To use a curated example data found in VisCom within the VisEditor, be sure to copy/paste the file or url key hyperlink to re-create it. Add the hyperlink to the URL field appropriate for that track or app.
 
 ![](./Explore.png)
 
 ## Purpose
 * You can explore shared visualizations by searching or filtering by institution, data type, lab, author, PubMedID, and even by diagnosis. 
-* By utilizing St. Jude's visualization tools [ProteinPaint](https://viz.stjude.cloud/tools/proteinpaint/) and [GenomePaint](https://viz.stjude.cloud/tools/genomepaint/), we allow world class genomic or proteomic visualizations to be easily developed, accessed, and/or shared globally. Each visualization saved in VisCom is private by default until a P.I. or team lead approves.
+* St. Jude's visualization tools ProteinPaint](https://viz.stjude.cloud/tools/proteinpaint/) and [GenomePaint](https://viz.stjude.cloud/tools/genomepaint/) allow world class genomic or proteomic visualizations.
+to be easily developed, accessed, and shared globally. Each visualization in VisCom is private until a P.I. or 
+team lead approves their release.
 * Visualizations can be shared and managed before becoming publicly available. Teams can be developed to provide a secure, private workspace for instant collaboration. Once public, adding a permalink or PubMedID to the visualization increases the profile and accessibility to your figure(s). 
 * We even offer [Communities](https://viz.stjude.cloud/communities) to share and unify research within a genre of research. 
 
@@ -31,7 +33,7 @@ Once you find the visualization you need within VisCom, you can easily re-create
 * Collaborate with others ***by exploring and sharing visualizations within a community or team***
 
 ## Support
-* [ProteinPaint](https://viz.stjude.cloud/tools/proteinpaint/) and [GenomePaint](https://viz.stjude.cloud/tools/genomepaint/) is developed & supported by [Xin Zhou's group](https://www.stjude.org/directory/z/xin-zhou.html)
+* [ProteinPaint](https://viz.stjude.cloud/tools/proteinpaint/) and [GenomePaint](https://viz.stjude.cloud/tools/genomepaint/) is developed & supported by [Xin Zhou's Lab](https://www.stjude.org/directory/z/xin-zhou.html)
 
 * Visualization Community is developed by the St. Jude Cloud team to facilitate scientific research using St. Jude-developed visualization tools. For more information, please read the [paper](https://cancerdiscovery.aacrjournals.org/content/11/5/1082) or contact us at [support@stjude.cloud](support@stjude.cloud). If you need to cite Visualization Community, please see this [page](https://university.stjude.cloud/docs/citing-stjude-cloud/).
 

docs/visualization-community/library/MA-Volcano/index.md

@@ -39,6 +39,11 @@ If you are using DNAnexus links, be sure to extend the duration. See our [manage
 }
 ```
 
+!!!tip
+If you are using a path on the HPC, the file must exist in a directory in the /tp directory.
+For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
+!!!
+
 # Path to file EXAMPLE
 **Be sure to update lines 4, 7, 9, 12, 14 and 17** 
 ```JS

docs/visualization-community/library/ai-check/index.md

@@ -12,7 +12,7 @@ Use: Displays the allelic imbalance of the heterozygous SNP markers in a tumor g
 
 !!!warning
 If you are using DNAnexus links, be sure to extend the duration. See our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
-In order to render <gz> files they must also have the <tbi> file associated. What happens is that the ProteinPaint looks for the <tbi> file and cannot parse the <gz> so we must give it an alternate path to the <tbi> file.>
+In order to render .gz files they must also have the .tbi file associated. What happens is that the ProteinPaint looks for the .tbi file and cannot parse the .gz so we must give it an alternate path to the .tbi file.
 !!!
 
 **Be sure to update lines 1, 3, 8, 9, and 10**
@@ -36,7 +36,7 @@ In order to render <gz> files they must also have the <tbi> file associated. Wha
 # File Key Example
 
 !!!warning
-If you are using a path on the HPC, the file must exist in a directory in the <tp> directory.
+If you are using a path on the HPC, the file must exist in a directory in the /tp directory.
 For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
 !!!
 

docs/visualization-community/library/arc/index.md

@@ -8,14 +8,14 @@ Use: Used to display chromatin capture data by focusing on the frequency of link
 [ProteinPaint Google Docs](https://docs.google.com/document/d/1MQ0Z_AD5moDmaSx2tcn7DyVKGp49TS63pO0cceGL_Ns/edit#heading=h.8zct8j3cscak)
 
 !!!warning
-<mode_arc> must be true with <mode_hm> set to false for the arc to render. If <mode_arc> is false, then it behaves like a Hi-C where the pyramid is up. Additional configs can be found in the UI of the visualization. <percentile_max> is for the resolution of the Hi-C plot. <gz> and <tbi> files are not accepted for Hi-C at this time. 
+mode_arc must be true with mode_hm set to false for the arc to render. If mode_arc is false, then it behaves like a Hi-C where the pyramid is up. Additional configs can be found in the UI of the visualization. percentile_max is for the resolution of the Hi-C plot. .gz and .tbi files are not accepted for Hi-C at this time. 
 !!!
 
 # URL Key Example
 
 !!!warning
 If you are using DNAnexus links, be sure to extend the duration. See our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
-In order to render <gz> files they must also have the <tbi> file associated. What happens is that the <runproteinpaint()> looks for the <tbi> file and cannot parse the <gz> so we must give it an alternate path to the <tbi> file.>
+In order to render .gz files they must also have the .tbi file associated. What happens is that the ProteinPaint looks for the .tbi file and cannot parse the .gz so we must give it an alternate path to the .tbi file.
 !!!
 
 **Be sure to update lines 1, 3, 8, 9, and 10**
@@ -44,7 +44,7 @@ In order to render <gz> files they must also have the <tbi> file associated. Wha
 # File Key Example
 
 !!!warning
-If you are using a path on the HPC, the file must exist in a directory in the <tp> directory.
+If you are using a path on the HPC, the file must exist in a directory in the /tp directory.
 For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
 !!!
 

docs/visualization-community/library/bam/index.md

@@ -13,7 +13,7 @@ Use: Visualizes the aligned reads and assists in understanding depth and quality
 
 !!!warning
 If you are using DNAnexus links, be sure to extend the duration. See our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
-In order to render <bam> files they must also have the <bai> file associated. What happens is that the ProteinPaint looks for the <abi> file and cannot parse the <bam> so we must give it an alternate path to the <bai> file.>
+In order to render .bam files they must also have the .bai file associated. What happens is that the ProteinPaint looks for the .bai file and cannot parse the .bam so we must give it an alternate path to the .bai file.
 !!!
 
 **Be sure to update lines 1, 3, 8, 9, and 10**
@@ -37,7 +37,7 @@ In order to render <bam> files they must also have the <bai> file associated. Wh
 # File Key Example
 
 !!!warning
-If you are using a path on the HPC, the file must exist in a directory in the <tp> directory.
+If you are using a path on the HPC, the file must exist in a directory in the /tp directory.
 For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
 !!!
 

docs/visualization-community/library/bigwig/index.md

@@ -35,7 +35,7 @@ If you are using DNAnexus links, be sure to extend the duration. See our [manage
 # File Key Example
 
 !!!warning
-If you are using a path on the HPC, the file must exist in a directory in the <tp> directory.
+If you are using a path on the HPC, the file must exist in a directory in the /tp directory.
 For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
 !!!
 

docs/visualization-community/library/bigwigstranded/index.md

@@ -41,7 +41,7 @@ If you are using DNAnexus links, be sure to extend the duration. See our [manage
 # File Key Example
 
 !!!warning
-If you are using a path on the HPC, the file must exist in a directory in the <tp> directory.
+If you are using a path on the HPC, the file must exist in a directory in the /tp directory.
 For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
 !!!
 

docs/visualization-community/library/expression-rank/index.md

@@ -11,7 +11,7 @@ Use: RNA-seq coverage data as a pair of bigWig tracks, with forward strand on to
 # URL Parameter EXAMPLE
 
 !!!warning
-If you are using DNAnexus links, be sure to extend the duration. See our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section. The <sample> parameter must be unique to the file otherwise it will **not** render. 
+If you are using DNAnexus links, be sure to extend the duration. See our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section. The sample parameter must be unique to the file otherwise it will **not** render. 
 !!!
 
 **Be sure to update lines 1, 3, 8, 9, 10, and 11**
@@ -37,7 +37,7 @@ If you are using DNAnexus links, be sure to extend the duration. See our [manage
 # Path to file EXAMPLE
 
 !!!warning
-If you are using a path on the HPC, the file must exist in a directory in the <tp> directory.
+If you are using a path on the HPC, the file must exist in a directory in the /tp directory.
 For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
 !!!
 

docs/visualization-community/library/genomepaint/index.md

@@ -12,7 +12,7 @@ Use: Explore coding and non-coding variants in pediatric cancer.
 
 !!!warning
 If you are using DNAnexus links, be sure to extend the duration. See our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
-In order to render <gz> files they must also have the <tbi> file associated. What happens is that the ProteinPaint looks for the <tbi> file and cannot parse the <gz> so we must give it an alternate path to the <tbi> file.>
+In order to render .gz files they must also have the .tbi file associated. What happens is that the ProteinPaint looks for the .tbi file and cannot parse the .gz so we must give it an alternate path to the .tbi file.
 !!!
 
 **Be sure to update lines 1, 3, 8, 9, 10, 12, 13, 16, 17** 
@@ -44,7 +44,7 @@ In order to render <gz> files they must also have the <tbi> file associated. Wha
 # File Key Example
 
 !!!warning
-If you are using a path on the HPC, the file must exist in a directory in the <tp> directory.
+If you are using a path on the HPC, the file must exist in a directory in the /tp directory.
 For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
 !!!
 

docs/visualization-community/library/hic/index.md

@@ -14,7 +14,7 @@ Not currently supported in the VisEditor. No URL key enabled.
 # File Key Example
 
 !!!warning
-If you are using a path on the HPC, the file must exist in a directory in the <tp> directory. For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section. <percentile_max> is for the resolution of the Hi-C plot. <pyramidup> must be 1 to be upward or 0 for downward. <enzyme> is the restriction enzyme used to cut. <gz> and <tbi> files are not accepted for Hi-C at this time. 
+If you are using a path on the HPC, the file must exist in a directory in the tp directory. For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section. percentile_max is for the resolution of the Hi-C plot. pyramidup must be 1 to be upward or 0 for downward. enzyme is the restriction enzyme used to cut. .gz and .tbi files are not accepted for Hi-C at this time. 
 !!!
 
 **Be sure to update lines 1, 3, 8, and 9** 

docs/visualization-community/library/json-bed/index.md

@@ -40,7 +40,7 @@ If you are using DNAnexus links, be sure to extend the duration. See our [manage
 # File Key Example
 
 !!!tip
-If you are using a path on the HPC, the file must exist in a directory in the <tp> directory.
+If you are using a path on the HPC, the file must exist in a directory in the /tp directory.
 For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
 !!!
 

docs/visualization-community/library/pgv/index.md

@@ -9,7 +9,7 @@ Use: Used to display gene. expression results from RNA seq across a cohort of sa
 [ProteinPaint Google Docs](https://docs.google.com/document/d/1yrRpDUZWSRGuCa0snGwRuo721WRHgdYTX7GWIsZ_fSY/)
 
 !!!warning
-If you are using DNAnexus links, be sure to extend the duration. See our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section. The <file> keys can be switched with <url> keys. Legendimg is optional.
+If you are using DNAnexus links, be sure to extend the duration. See our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section. The file keys can be switched with url keys. Legendimg is optional.
 !!!
 
 

docs/visualization-community/library/rna-splice-junction/index.md

@@ -11,7 +11,7 @@ Use: This visualization displays the number of mapped junction reads precisely a
 
 !!!warning
 If you are using DNAnexus links, be sure to extend the duration. See our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
-In order to render <gz> files they must also have the <tbi> file associated. What happens is that the <runproteinpaint()> looks for the <tbi> file and cannot parse the <gz> so we must give it an alternate path to the <tbi> file.>
+In order to render .gz files they must also have the .tbi file associated. What happens is that the runproteinpaint() looks for the .tbi file and cannot parse the .gz so we must give it an alternate path to the .tbi file.
 !!!
 
 # URL Parameter EXAMPLE
@@ -33,7 +33,7 @@ In order to render <gz> files they must also have the <tbi> file associated. Wha
 ```
 
 !!!tip
-If you are using a path on the HPC, the file must exist in a directory in the <tp> directory.
+If you are using a path on the HPC, the file must exist in a directory in the /tp directory.
 For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
 !!!
 

docs/visualization-community/library/singlecell/index.md

@@ -12,6 +12,11 @@ Use: A data driven dimensional reduction method used to display single cell RNA
 This currently is not supported with a url key at this time. 
 
 
+!!!tip
+If you are using a path on the HPC, the file must exist in a directory in the /tp directory.
+For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
+!!!
+
 # File Key Example
 
 **Be sure to update lines 6 and 7** 

docs/visualization-community/library/splice-junctions-cohort/index.md

@@ -13,6 +13,12 @@ Use: This visualization displays the number and color codes the type of mapped j
 # URL Key Example
 This currently is not supported with a url key at this time. 
 
+!!!tip
+If you are using a path on the HPC, the file must exist in a directory in the /tp directory.
+For more details, see our [manage data](https://university.stjude.cloud/docs/visualization-community/data-manage/) section.
+!!!
+
+
 # File Key Example
 
 **Be sure to update lines 1, 3, 8, and 9**