diff --git a/docs/access/access_hpc.md b/docs/access/access_hpc.md
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+{width="340"}
+
+---
+
+# **The Secure Research Enclave and HPC Cluster**
+
+This user manual will guide you through the high-performance computing (HPC) features and functionalities of Soteria. The HPC cluster is equipped with multiple compute nodes (CPU) and two GPU nodes available for specific needs.
+
+To access Soteria, you can utilize the OnDemand graphical user interface, which provides a user-friendly interface for seamless interaction with the enclave.
+
+We hope this manual assists you in making the most of Soteria's capabilities while ensuring the confidentiality and security of your research data.
+
+---
+
+## Prerequisites: Accessing Soteria and Cluster Resources
+
+### Accessing the Soteria Enclave
+
+!!! Info "*Please refer to the [Obtaining Soteria Access via VPN](access_vpn.md) for Soteria access details.*"
+
+**Trainings**: Once your Soteria request form has been reviewed and approved, you will receive an email with the subject "*UA Soteria Access Request Approved*". This email will contain the next steps to take, including detailed instructions to get Soteria access and establish a VPN connection.
+
+!!! Warning "Required Trainings"
+
+ The trainings that Soteria requires completion of are:
+
+ - HIPAA Essentials
+ - UA Information Security Awareness Training
+ - Insiders Threat Training
+
+ These can be accessed at [uaccess.arizona.edu](https://uaccess.arizona.edu/) or [edgelearning.arizona.edu](https://edgelearning.arizona.edu/).
+
+**Access to Soteria**: After completing the required trainings, you will be notified via email when you have been granted access to the Soteria VPN. The Soteria VPN is crucial for maintaining HIPAA compliance and distinguishes Soteria usage from standard HPC clusters. Please note that Soteria access can only be established when connected to the VPN.
+
+- [Obtaining the Cisco VPN](access_vpn.md/#downloading-cisco-vpn)
+- [Connecting to the Soteria enclave](access_vpn.md/#connecting-to-the-soteria-enclave)
+
+!!! Info "Additional Instructions"
+
+ Ensure that the computer you will use to access Soteria services meets the following requirements:
+
+ - Keep your Operating System and applications updated.
+ - Use strong passwords (easy to remember, multiple character, letter, number combinations).
+ - Do not use a shared computer with other users.
+ - Maintain up-to-date antivirus software.
+
+### Cluster Resources
+
+Please refer to the regular [HPC documentation](https://uarizona.atlassian.net/wiki/spaces/UAHPC/overview) to learn how to use the HPC system. During the early testing phase, the time and space allocations will be similar to those of the HPC clusters, with a time allocation of 150,000 hours.
+
+The Soteria cluster consists of the following resources:
+
+- **Compute**:
+ - 4 Standard CPU nodes (`r1u26n1`, `r1u27n1`, `r1u28n1`, `r1u29n1`)
+ - Each CPU node has 94 cores and 512GB RAM memory available.
+ - 2 GPU Nodes (`r1u30n1`, `r1u32n1`)
+ - Each GPU node has access to 94 cores and 512GB RAM memory available.
+ - Access to 4 V100 GPUs.
+- **Storage**:
+ - Your Soteria account will come with space available in the `/home` and `/groups` directories, where you can store your research data. Currently, these directories do not have a quota limit.
+
+---
+
+## Accessing the HPC Soteria Enclave and GUI Applications
+
+!!! Info "*To access the HPC Soteria enclave, please ensure that you are connected to the Soteria VPN as explained in the previous section.*"
+
+To access GUI applications, follow these steps after connecting to the Soteria VPN:
+
+1. Open your preferred web browser.
+2. Visit the following URL: [**https://ondemand-hipaa.hpc.arizona.edu**](https://ondemand-hipaa.hpc.arizona.edu/). Log in using your UA credentials.
+3. The available GUI applications on Soteria are **:simple-rstudio: RStudio**, **:material-chart-bell-curve: Matlab**, **:simple-jupyter: Jupyter**, **:material-apps-box: Stata** and an **:octicons-device-desktop-16: Interactive Desktop**.
+
+??? Warning "First time logging in? Home directory not found?"
+
+ If this is your first logging onto the OnDemand Soteria service, it is likely that you're going to be greeted with the following message:
+
+
+ {width="650"}
+
+ If that is the case, follow the onscreen instructions:
+
+ 1. Open the shell (which will automatically create your home folder).
+ 2. Reload the page.
+
+ Once that is done, you should be greeted with the OnDemand home page.
+
+
+ {width="650"}
+
+
+### Connecting to the Applications
+
+!!! Tip "The following section uses RStudio as an example, however, these same instructions are applicable to **:material-chart-bell-curve: Matlab**, **:simple-jupyter: Jupyter**, **:material-apps-box: Stata** and the **:octicons-device-desktop-16: Interactive Desktop**."
+
+1. Once you access the OnDemand interface, navigate to the "Interactive Apps" dropdown menu.
+2. Select the desired application from the options, in this case "RStudio server" was chosen.
+
+ {width="650"}
+
+3. Apply the necessary resources and enter your laboratory/research group in the "PI Group" field.
+
+ {width="700"}
+
+4. Connect to the requested node by clicking "Connect to RStudio Server".
+
+ {width="700"}
+
+!!! Info "Choosing the **:octicons-device-desktop-16: Interactive Desktop** gives you access to more."
+
+ The :octicons-device-desktop-16: Interactive Desktop gives you access to the ability to load **modules**. Modules are pre-installed software that are not loaded upon starting the Application/terminal but users can load at any point during the node uptime.
+
+ Once logged into the :octicons-device-desktop-16: Interactive Desktop, users can open the Terminal and execute `module avail` to see what software are available. To load the software, users can then do `module load `; The loaded software will then be available until the :octicons-device-desktop-16: Interactive Desktop is terminated.
+
+ For a list of `module` commands, please refer to the [official UA HPC documentation page](https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75990663/Accessing+Software).
+
+ {width="650"}
+ Example of `module load ` where the user loads and launches Matlab through `module load matlab` and `matlab` within the :octicons-device-desktop-16: Interactive Desktop session.
+
+
+
+### Command Line Access
+
+To access Soteria through your computer's command line, you can use SSH (Secure Shell) with the following instructions:
+
+1. Open your preferred terminal application on your local machine.
+2. Use the SSH command to connect to Soteria. The hostname for Soteria command line access is: `shell.cougar.hpc.arizona.edu`. Enter the following command, replacing `` with your actual NetID:
+ ```
+ ssh @shell.cougar.hpc.arizona.edu
+ ```
+3. You will be prompted to enter your password. Please provide your password associated with your NetID. Make sure you have authorized access to use Soteria. All user activity may be monitored and reported.
+4. After successfully logging in, you will see a message similar to the following:
+ ```
+ Authorized uses only. All activity may be monitored and reported.
+ Last login: Tue Apr 30 13:14:23 2024 from shell.cougar.hpc.arizona.edu
+ Authorized uses only. All activity may be monitored and reported.
+ [cosi@taub ~]$
+ ```
+ The `taub` is a login node, and it provides the same functionality and follows the same policies as other HPC clusters.
+
+5. Please note that modules are available on Soteria's compute nodes but not on the login node. You can use the **`interactive`** command to request a session on a compute node, and jobs can be submitted using the standard **`sbatch`** command.
+
+ For more detailed information on running jobs with SLURM and utilizing Soteria's capabilities, please refer to the [UA HPC documentation on "Running Jobs with Slurm"](https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75989875/Running+Jobs+with+Slurm).
+
+If you do not have access to a command line, the OnDemand service allows you to start a cluster with Shell Access. On the menu at the top of the OnDemand dashboard select Clusters > Shell Access. A new tab should open giving you CLI capabilities.
+
+
+ {width="700"}
+
+
+---
+
+## Transferring and Accessing Data via Globus
+
+Globus is a recommended tool for efficiently transferring data to and from the Soteria environment. It provides a reliable and secure data transfer mechanism. To learn more about using Globus, please refer to the following link: [**Globus Documentation**](https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75989646/Globus).
+
+!!! Note "Soteria Endpoint for Globus: '`UA HPC HIPAA Filesystems`'"
+
+**File Paths:** When working with Soteria, you can access your files using the following file paths:
+
+1. Filexfer Nodes:
+ - **`/hipaa/groups/`**: This path allows access to the shared group directories associated with your PI's NetID.
+ - **`/hipaa/home//`**: This path provides access to your personal home directory under your NetID.
+
+2. When connected to a Soteria login or compute node:
+ - **`/groups/`**: This path corresponds to the shared group directories associated with your PI's NetID.
+ - **`/home//`**: This path corresponds to your personal home directory under your NetID.
+
+By utilizing these file paths, you can efficiently access and manage your data within the Soteria environment.
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diff --git a/docs/hpc.md b/docs/access/access_hpc.md.old
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@@ -1,3 +1,5 @@
+# NOTE: THIS PAGE IS ONLY FOR BACKUP PURPOSES #
+
{width="340"}
{width="400"}
diff --git a/docs/access/access_mac.md b/docs/access/access_mac.md
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+{width="340"}
+
+---
+
+
+
+
+
+
+
+
+
Soteria Access User Manual (Mac)
+
+
+
+
+
+## Background
+
+Soteria is a secure and collaborative platform designed for health sciences research. It enables researchers to analyze personally identifiable and protected health information while adhering to compliance guidelines. By providing cutting-edge software and web-based applications, Soteria ensures data security throughout the research lifecycle, allowing multiple research groups to work together effectively while meeting regulatory requirements.
+
+
+## Request Access to Soteria
+
+1. Establish a primary PI or sponsoring faculty member and have them indicate that you are a team member on Soteria.
+2. Open and click **Request Access**.
+
+
+
+
+
+
+
+3. Fill out the form with your user and project information. Once submitted you will receive an automated email indicating completion of the request.
+4. Once approved, you will receive a secondary automated email, UA Soteria Access Request Approved indicating required trainings. Log into Edge Learning () to sign up and complete all of the required trainings.
+
+## Download and Set up Cisco VPN
+
+1. Download the VPN software by following the link () . You will be prompted to log in. Use the default connections. Enter your NetID, Password and NetID +Method (ex: "push").
+
+
+
+
+
+2. Follow the prompts to download and install Cisco AnyConnect VPN.
+
+
+
+
+
+
+
+
+
+3. Open Cisco AnyConnect VPN on your desktop.
+4. The first connection must be to: vpn.arizona.edu. Type into the pop-up and click **connect**.
+
+
+
+
+
+5. Sign in as before, using the default group. Enter your NetID, Password and NetID +Method (ex: "push").
+
+
+
+
+
+6. Click **Disconnect**
+
+
+
+
+
+You are now ready to connect to your Soteria VPN.
+
+## Connect to Soteria VPN
+
+1. If it does not auto-populate, connect to the Soteria VPN using: vpn.arizona.edu/soteria. Again, enter your NetID, Password and NetID +Method (ex: "push") to sign in.
+
+
+
+
+
+2. Accept the pop-up notification. The Cisco Icon in the system tray (bottom right) of your desktop, will now display a lock, indicating a successful connection.
diff --git a/docs/access/access_vpn.md b/docs/access/access_vpn.md
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+{width="340"}
+
+---
+
+# **Accessing Soteria via VPN**
+
+## Request Access to Soteria
+
+Access to Soteria is administrated by the [Controlled and Regulated Research Services Program (CRRSP) team](https://medicineit.arizona.edu/compliance-and-security/hipaa-phi/approved-phi-solutions#:~:text=of%20my%20emails%3F-,Controlled%20and%20Regulated%20Research%20Services%20Program%20(CRRSP),-%3A). Prior to being admitted permission to use the secure enclave, prospective users must request access to Soteria first. The following 4 steps will highlight the process.
+
+1. Establish a primary PI or sponsoring faculty member and have them indicate that you are a team member on Soteria.
+2. Navigate to [soteria.arizona.edu](https://soteria.arizona.edu/), and from the *Get Started* dropdown menu click **Request Access**. Alternatively, you can click **Request Access** on the top right of the screen.
+
+
+ [{ width="800"}](https://soteria.arizona.edu/)
+
+3. This will open the Request Access page. Click **Apply for Soteria Access** and Fill out the form with your user and project information. Once submitted you will receive an automated email indicating completion of the request.
+
+
+ [{ width="800"}](https://soteria.arizona.edu/get-started/request-access)
+
+4. Once approved, you will receive a secondary automated email (title: *UA Soteria Access Request Approved*) indicating that you've been approved access and the required trainings needed to use Soteria. Log into [Edge Learning](https://edgelearning.arizona.edu/) to sign up and complete all of the required trainings.
+
+ !!! Warning "Required Trainings"
+
+ The trainings that Soteria requires completion of are:
+
+ - HIPAA Essentials
+ - UA Information Security Awareness Training
+ - Insiders Threat Training
+
+ These can be accessed at [uaccess.arizona.edu](https://uaccess.arizona.edu/) or [edgelearning.arizona.edu](https://edgelearning.arizona.edu/).
+
+## Downloading Cisco VPN
+
+!!! Warning "In order to access the Cisco VPN download page and other University of Arizona services including Soteria, one must have a functional [UA NetID](https://netid-portal.iam.arizona.edu/) with Duo authentification enabled."
+
+??? Tip "First time using a VPN?"
+
+ If this is your first time using a VPN, we suggest reading [this general guide on connecting and using the VPN service](https://cbc.arizona.edu/vpn-instructions) from the UA Chemistry & Biochemistry Department or watching this short video from the Nursing department:
+
+
+
+
+
+
+!!! Info "Operating Systems"
+ These instructions are applicable to **macOS** and **Windows** Operating Systems as Cisco will automatically detect your hardware. If you are using a Linux machine, please refer to the official [Cisco AnyConnect documentation](https://www.cisco.com/c/en/us/support/docs/smb/routers/cisco-rv-series-small-business-routers/kmgmt-2597-Installing-AnyConnect-Linux-Ubuntu-desktop-User-Interface.html) on the topic. Although obtaining the software and intallation instructions might differ, connecting will follow the same method.
+
+If you have not done so yet, go to the download page of the the Cisco VPN software at [vpn.arizona.edu](https://vpn.arizona.edu/). Log in using your UA NetID information and download the VPN according to your Operating System. Download and install Cisco VPN.
+
+
+ [{ width="800"}](https://vpn.arizona.edu/)
+
+
+## Connecting to the Soteria Enclave
+
+When opening Cisco VPN you will be greeted with the following log in window.
+
+
+ 
+
+
+The typable field will allow you to type any VPN host associated to the University of Arizona. By default, you should be able to select *UA SSL VPN*. However, in order to connect to the Soteria VPN, you will need to insert the following URL: **vpn.arizona.edu/soteria**. In the future, the field should autopopulate to **Soteria**. Upon clicking **Connect** a second window will open, where you can insert your UA NetID, Password and NetID +Method (e.g.,: "push") to sign in.
+
+
+ 
+
+
+??? Tip "First time connecting to Soteria and having trouble? You may have to connect to the UA VPN."
+
+ In the typable field, type **vpn.arizona.edu** and Connect. Follow the connection instructions and establish connection first. Then disconnect from the UA VPN, and then connect to the Soteria VPN. Cisco *might* need to establish the connection first.
+
+When you see the following popup, **accept** the message and you will be connected to the Soteria enclave.
+
+
+ 
+
+
+The Cisco VPN icon will show a lock in front, meaning that the connection is working, secured and metered. You can now proceed to using he various services within the safe Soteria enclave!
+
+
+ 
+
diff --git a/docs/access/access_win.md b/docs/access/access_win.md
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--- /dev/null
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+{width="340"}
+
+---
+
+
+
+
+
+
+
+
+
Soteria Access User Manual (Windows)
+
+
+
+
+
+## Background
+
+Soteria is a secure and collaborative platform designed for researchers to analyze personally identifiable and protected health information while adhering to compliance guidelines. By providing cutting-edge software and web-based applications, Soteria ensures data security throughout the research lifecycle, allowing multiple research groups to work together effectively while meeting regulatory requirements.
+
+
+## Request Access to Soteria
+
+1. Establish a primary PI or sponsoring faculty member and have them indicate that you are a team member on Soteria.
+2. Open and click **Request Access**.
+
+
+
+
+
+
+
+3. Fill out the form with your user and project information. Once the form has been submitted, you will receive an automated email indicating completion of the request.
+4. Once approved, you will receive a secondary automated email, UA Soteria Access Request Approved indicating required trainings. Log into Edge Learning () to sign up and complete all of the required trainings.
+
+## Download and Set up Cisco VPN
+
+1. Download the VPN software by following the link () . You will be prompted to log in. Use the default connections. Enter your NetID, Password and NetID +Method (ex: "push").
+
+
+
+
+
+2. Follow the prompts to download and install Cisco AnyConnect VPN.
+
+
+
+
+
+
+
+
+
+3. Open Cisco AnyConnect VPN on your desktop.
+4. The first connection must be to: vpn.arizona.edu. Type into the pop-up and click **connect**.
+
+
+
+
+
+5. Sign in as before, using the default group. Enter your NetID, Password and NetID +Method (ex: "push").
+
+
+
+
+
+6. Click **Disconnect**
+
+
+
+
+
+You are now ready to connect to your Soteria VPN.
+
+## Connect to Soteria VPN
+
+1. If it does not auto-populate, connect to the Soteria VPN using: vpn.arizona.edu/soteria. Again, enter your NetID, Password and NetID +Method (ex: "push") to sign in.
+
+
+
+
+
+2. Accept the pop-up notification. The Cisco Icon in the system tray (bottom right) of your desktop, will now display a lock, indicating a successful connection.
diff --git a/docs/access/index.md b/docs/access/index.md
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+{width="340"}
+
+---
+
+# **Loggin in & Access Guides**
+
+Due to the objectives and nature of Soteria, here are guides that will help you connect with the secure Soteria services.
+
+## Access Guides
+
+
+
+- [:simple-cisco::material-security-network: **VPN Access**](access_vpn.md) - Learn how to get access to Soteria using the UA Cisco VPN (Win/macOS).
+- [:fontawesome-solid-computer::material-server: **UA HPC**](access_hpc.md) – A guide to connect and use the Soteria UA HPC enclave.
\ No newline at end of file
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+{width="340"}
+
+---
+
+# **Transferring Data Using Globus**
+
+Welcome to the Globus Data Transfer with GridFTP, specifically tailored for the Soteria environment. Within Soteria's UA HPC HIPAA Filesystems, data movement becomes a breeze with the powerful capabilities of Globus and GridFTP.
+
+In this manual, we'll explore how GridFTP, an extension of the standard File Transfer Protocol (FTP), elevates data transfer to new heights. Its focus on high-speed, reliable, and secure transmission perfectly complements the demands of Soteria's environment. With Globus as your platform of choice, you'll find endpoints to be the key to effortless data transfers.
+
+Whether you're involved in research, data analysis, or IT management, understanding the benefits of GridFTP through Globus will empower you to handle large-scale data transfers with ease. Say goodbye to complex transfer processes and embrace a seamless approach to sharing data across all clusters in the shared storage.
+
+## Accessing Globus and Globus Connect Personal
+
+!!! Warning "Visit the [UA official documentation](https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75989646/Globus) for a detailed step by step guide to access Globus. This will take you through the standard university WebAuth login process. Once you successfully log in, you will be placed in a File Manager window. The various steps for setting up endpoints, initiating transfers, and viewing a transfer's progress can be found in the sections below."
+
+To transfer files to/from your personal computer with Globus, you'll need to have a local endpoint set up. In case of Soteria, the endpoint is **`UA HPC HIPAA Filesystems`**.
+
+This can be achieved using **Globus Connect Personal**. Official documentation on how to install the relevant software and configure a local endpoint can be found in [Globus' offical how-to documentation](https://docs.globus.org/how-to/). An overview is shown [here](https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75989646/Globus#:~:text=the%20sections%20below.-,Globus%20Connect%20Personal,-To%20transfer%20files) for Mac, Linux, and Windows.
+
+### Accessing HPC Storage Endpoint
+
+To access the HPC Storage Endpoint in the Soteria environment, follow these steps:
+
+- **Step 1:** Locate the Collections Tab After logging into Globus, navigate to the "Collections" tab.
+- **Step 2:** Search for UA HPC Filesystems In the search field, type "UA HPC Filesystems" and select the relevant result.
+
+ {width="650"}
+
+- **Step 3:** Open the HPC Storage Endpoint Click "Open in File Manager" to access your HPC files. The default location will be your "/home" on HPC.
+
+ {width="650"}
+
+- **Step 4:** Navigating HPC Files Navigate through directories by double-clicking on folders or by entering a full path in the Path search bar and hitting "Enter." This method allows access to any `/xdisk` or `/groups` directories you have permissions for.
+
+ {width="650"}
+
+
+## Making Data Transfers
+
+To initiate data transfers between endpoints using the File Manager window, follow these steps:
+
+- **Step 1:** Access the File Manager Tab Go to the "File Manager" tab in the Globus web application. Ensure you have dual-panel mode enabled (click the upper right-hand corner with the red arrow) to open two endpoints simultaneously.
+
+ {width="650"}
+
+- **Step 2:** Open the First Endpoint Click the Search bar on the left-hand side and search for your first endpoint (e.g., UA HPC Filesystems). Click the result to open it.
+
+ {width="650"}
+
+- **Step 3:** Open the Second Endpoint To open a second connection, click the Search bar on the right-hand side. Search for your next endpoint (e.g., a personal endpoint) or access recently used endpoints and collections under the "Recent" and "Your Collections" tabs. Click the result to open the second endpoint.
+
+ {width="650"}
+
+
+ {width="650"}
+
+- **Step 4:** Start the Transfer Select the item(s) you want to transfer from the first endpoint, then click the "Start" button to initiate the transfer to the second endpoint.
+
+ {width="650"}
+
+
+## Monitoring Your Transfers
+
+After initiating a transfer, a green box will appear confirming the request. To monitor your transfers:
+
+- **Step 1:** Access the Activity Panel On the left-hand side of the page, access the "Activity" panel. This will display active and past transfers along with their status.
+
+ {width="650"}
+
+- **Step 2:** View Transfer Details To view additional details about your transfers, click the "\>" symbol next to the target task on the right-hand side. This will provide more information about the ongoing or completed transfer.
+<
+ {width="650"}
+
+- **Step 3:** Cancel a Transfer If needed, you can cancel a transfer by clicking the "×" symbol on the right.
+- **Step 4:** Receive Transfer Status Email Once your transfer is completed, you will receive an email with its status.
+
+Congratulations! You have now learned how to access the HPC Storage Endpoint and perform data transfers using Globus. With this powerful tool, managing data within the Soteria environment becomes efficient and straightforward. Happy data transferring!
diff --git a/docs/data_transfer/index.md b/docs/data_transfer/index.md
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--- /dev/null
+++ b/docs/data_transfer/index.md
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+{width="340"}
+
+---
+
+# **Data Transfer & Management**
+
+Learn how to transfer data to Soteria and CyVerse Health.
+
+## Data Transfer Tutorials
+
+
+
+- [{: style="height:14px"}:material-play-network:
+ **Globus**](globus.md) - Connecting to Soteria and transferring using Globus.
+- {: style="height:14px"}:simple-go: **CyVerse GoCommands** - CyVerse GoCommands support to be released soon.
diff --git a/docs/index.md b/docs/index.md
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--- a/docs/index.md
+++ b/docs/index.md
@@ -1,13 +1,35 @@
-{width="340"}
+{width="340"}
-## Background
+---
-Soteria is a secure and collaborative platform designed for health sciences research. It enables researchers to analyze personally identifiable and protected health information while adhering to compliance guidelines. By providing cutting-edge software and web-based applications, Soteria ensures data security throughout the research lifecycle, allowing multiple research groups to work together effectively while meeting regulatory requirements.
+# **Soteria Documentation Home**
+
+
+ { width="500" }
+ Mosaic of [Soteria](https://en.wikipedia.org/wiki/Soteria_(mythology)) (circa 5 CE), goddess of safety and salvation, in display at the Hatay Archaeology Museum, Antakya.
+
+
+**Soteria** is a secure and collaborative platform designed for health sciences research. It enables researchers to analyze personally identifiable and protected health information while adhering to compliance guidelines. By providing cutting-edge software and web-based applications, Soteria ensures data security throughout the research lifecycle, allowing multiple research groups to work together effectively while meeting regulatory requirements.
+
+## Soteria: A Comprehensive Overview
+
+Soteria stands as a pivotal innovation in secure data analysis, providing a robust platform specifically designed for research involving [Personally Identifiable Information (PII)](https://www.dol.gov/general/ppii) and [Protected Health Information (PHI)](https://www.ncbi.nlm.nih.gov/books/NBK553131/). Recognizing the critical importance of privacy and security, Soteria offers a specialized enclave that champions compliance, control, and confidentiality throughout the research process.
+
+Key features of Soteria include its stringent access protocols, ensuring that only authorized researchers can engage with the sensitive data within. This is overseen by the [Soteria Access & Governance Committee](https://arizona.box.com/s/cyjgo0evur1bjlo44iz2ne6py0srys58) (UA ID required to access the document), a dedicated body ensuring adherence to legal and ethical standards. The platform's unique blend of resources and tools, including the cutting-edge Soteria HPC, External Data Transfer, and Posit Connect Health, are customized to meet the demands of secure, efficient, and collaborative research.
+
+By encapsulating all these features, Soteria emerges as more than just a platform; it's a safeguard for sensitive information, a facilitator of interdisciplinary research, and a beacon of trust in the realm of data security.
## Guides
-**Access & Logging in**
+### [Logging in & Access](access/index.md)
+
+- [Virtual Private Network (VPN)](access/access_vpn.md)
+- [High Performance Computing (UA HPC)](access/access_hpc.md)
+
+### [Data Transfer & Management](data_transfer/index.md)
+- [Globus File Transfer](data_transfer/globus.md)
+
+### [Training Modules & Tutorials](usage_guides/index.md)
+- [CyVerse Health](usage_guides/CyVerse_Health.md)
+- [Posit Connect Health Startup Tutorial](https://ua-data7.github.io/rsconnect-tutorial/)
-- [Mac OS X](mac.md)
-- [Windows OS](windows.md)
-- [High Performance Computing (HPC)](hpc.md)
\ No newline at end of file
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+++ b/docs/stylesheets/custom.css
@@ -24,7 +24,6 @@ body {
}
.md-header__button.md-logo img, .md-header__button.md-logo svg {
- width: 110px;
height: 35px;
}
@@ -78,4 +77,8 @@ body {
.spacing
{
margin-right: 50px;
-}
\ No newline at end of file
+}
+
+.inline-block {
+ display: inline-block;
+ }
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diff --git a/docs/usage_guides/CyVerse_Health.md b/docs/usage_guides/CyVerse_Health.md
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+{width="340"}
+
+
+
+
+
+
+
+# **CyVerse Health User Manual Overview**
+
+---
+
+## CyVerse Health: Spotlight on Functionality
+
+Within the secure perimeters of Soteria lies CyVerse Health, a specialized web workbench designed for data science teams navigating the complex landscapes of PII and PHI. This component amplifies Soteria’s functionalities, providing a space where collaboration, customization, and control converge.
+
+Key features of CyVerse Health include:
+
+**Collaborative Workbench:** CyVerse Health offers a dynamic space where research teams can manage data and share customized workflows securely. This feature is instrumental in fostering collaboration and ensuring consistency across projects.
+
+**Reproducible Research:** With its emphasis on containerization technology, CyVerse Health enables users to create reproducible workflows, a cornerstone in promoting transparency and verifiability in scientific discoveries.
+
+**Secure Data Access:** It maintains a controlled environment where access to specific data sets is regulated, ensuring that only authorized individuals can view or manipulate sensitive information.
+
+CyVerse Health therefore supports researchers by providing a secure, collaborative platform equipped with tools designed for in-depth data exploration and analysis, all within the secure ecosystem provided by Soteria.
+
+## Synergy: How CyVerse Health Complements Soteria
+
+CyVerse Health is an integral part of the Soteria platform, designed to extend the capabilities provided by Soteria into more specialized areas of data management and analysis. It leverages Soteria’s foundational security infrastructure, providing a space where researchers can perform more nuanced tasks with an assurance of data protection.
+
+This integration ensures that while researchers benefit from advanced tools and collaborative features specific to CyVerse Health, they remain within the overarching secure environment established by Soteria. This interconnectedness makes the combined platform a robust, comprehensive solution for conducting sensitive health-related research projects securely.
+
+---
+
+## Getting Started with CyVerse Health
+
+!!! Warning "Getting Soteria Access"
+ Before diving into the specific features and capabilities of CyVerse Health, users must first gain access to the overarching Soteria platform. Please refer to the [VPN Access page](../access/access_vpn.md) in the Logging in & Access section.
+
+### Accessing CyVerse Health
+
+!!! info " Although a [CyVerse](https://user.cyverse.org/) account is not needed, CyVerse Health requires an approved [University of Arizona NetID](https://netid-portal.iam.arizona.edu/)."
+
+Upon obtaining access to Soteria and connecting to the Soteria VPN, users can now access CyVerse Health at [**de.soteria.arizona.edu**](https://de.soteria.arizona.edu/).
+
+
+ 
+ CyVerse Health Home screen.
+
+
+Clicking the **Login** button will redirect you to the UA Web Authentication page. Insert your UA NetID and password, and you should be able to log in!
+
+
+ {width="700"}
+
+
+Logging in should give you additional information on your Home screen. Now you will be able to see the following features:
+
+- **Resource Usage**
+ - **Data Storage**: How much data you have uploaded/generated and stored in the CyVerse Health Data Store.
+ - **CPU Consumption**: All time [core hours](https://datascience.arizona.edu/research/cyverse#:~:text=*%20Compute%20units%20are%20normalized%20if%20jobs%20run%20on%20CPUs%2C%20GPUs%2C%20etc.%3B%201%20Compute%20Unit%20equals%201%20Core%20Hour%20on%20a%20CPU.)* consumed.
+- **Analysis Status**: All time analyses status (completed, cancelled, failed, submitted and running)
+- **Previous Analyes**: Shows previous results of completed analyses (non-depending of status).
+
+**\*** Compute units are normalized if jobs run on CPUs, GPUs, etc.; 1 Compute Unit equals 1 Core Hour on a CPU.
+
+
+ 
+ CyVerse Health Home screen post log in.
+
+
+### Working with CyVerse Health
+
+Once your account is set up, and you have access to the necessary services, you can start your projects on CyVerse. Utilize the Learning Center for helpful guides and tutorials on using different tools and services effectively. These resources are designed to assist you in understanding specific tasks or in-depth functionalities of CyVerse platforms.
+
+**Remember:** Keep your account details secure, and ensure you log out from shared or public computers to maintain the security of your data.
+
+## Getting Started with the Discovery Environment Interface
+
+### Exploring the Main Interface:
+
+Once logged in, take a moment to view the main dashboard. This central hub provides a snapshot of the tools and features at your disposal within the **Discovery Environment (DE)**.
+
+1. Locate the *Search Bar* positioned at the top of the page. Here, you have the ability to perform integrated searches across different data points:
+ 1. Click on the dropdown menu adjacent to the search bar to filter your search criteria by *Data*, *Apps*, or *Analyses*.
+ 2. Enter your query into the search field and press *Enter* to execute the search. Review the returned results, accessible by navigating through the tabs corresponding to the categories mentioned above.
+2. Familiarize yourself with the quick access icons, often found near the search bar:
+ 1. Look for a 'bag' or cart icon, symbolizing a space where you can aggregate items for download or sharing. It functions similarly to an online shopping cart, allowing you to organize data or apps you wish to further interact with.
+ 2. The 'notifications' bell icon is your go-to for updates on the platform. Clicking this will show you a history of your activities, including analysis statuses, data sharing updates, and general account activity.
+3. Navigating the Sidebar Menu:
+ 1. Shift your attention to the left-hand sidebar, known as the **DE Menu**. This is your primary navigation tool for the platform's various sections. If the sidebar is collapsed, you can expand it for more detailed descriptions by clicking the expand button (three line icon).
+4. Explore the following key areas by clicking on each respective icon or text:
+
+ {width="200", align=left}
+
+ - {width=20} **Home/Dashboard:** Your main control panel that may display summary widgets, quick links to recent activities, or educational content such as tutorials and webinars.
+ - {width=20} **Data:** This interface connects you to the Data Store. Here, you can manage your files, including uploading, downloading, organizing, and sharing data. You'll have access to your personal storage space and shared directories.
+ - {width=20} **Apps:** Discover various applications, including VICE (Visual Interactive Computing Environment) apps for interactive computing sessions. You can browse, search, and launch these applications based on your research needs.
+ - {width=20} **Analyses:** View and manage your computational tasks. This section logs your history of analysis jobs, allowing you to monitor current processes, review completed ones, and access resulting data.
+ - {width=20} **Cloud Shell:** Access a Linux shell environment directly within the DE. This feature enables advanced users to perform command-line operations without leaving the platform.
+ - {width=20} **Teams:** Create and manage collaboration groups. Teams allow you to group together with other users for easier sharing of data, analyses, and other collaborative efforts.
+ - {width=20} **Collections:** Explore public collections of data and apps curated by other users or the CyVerse team. This resource can be invaluable for finding information relevant to your studies.
+ - {width=20} **Help:** Access various support materials, including FAQs, guides, and contact information for direct assistance from the CyVerse support team.
+
+
+## Data Management
+
+### CyVerse Data Store
+
+The CyVerse **Data Store (DS)** is an integrated data management solution, ensuring data remains FAIR - Findable, Accessible, Interoperable, Reusable. Access your files across all CyVerse platforms, utilizing features that maintain data integrity and value.
+
+Return to the {width=20} **Data** section from the DE Menu to explore further. Within this space, you'll interact with several specific areas:
+
+{width="200", align=left}
+
+ 1. :material-home: **Your Personal Folder:** Navigate to your home directory. Use this private space to store your data files and analyses. You can create sub-folders for better organization.
+ 2. :material-folder-account: **Shared With Me:** Click on this folder to view items that other users have shared with you. This collaboration feature is crucial for team projects and shared research initiatives.
+ 3. :octicons-people-16: **Community Data:** Explore data shared publicly by other CyVerse users. This repository can contain valuable resources for your research.
+ 4. :fontawesome-solid-trash: **Trash:** View recently deleted items. You may have the option to restore files from here if necessary.
+
+### Obtaining Data from the Community Data Folder
+
+{width="300", align=left}
+
+The **Community Data** folder is not only where you can find public data, more importantly, the **Community Data folder is where you are gonig to find data shared with you and your team from official sources such as [Banner Health](https://www.bannerhealth.com/patients/patient-resources/privacy), the [UArizona Cancer Center](https://cancercenter.arizona.edu/) and [UArizona's Center for Biomedical Informatics and Biostatistics (CB2)](https://cb2.uahs.arizona.edu/).**
+
+!!! warning "Data and folders originating from the above distributors (e.g., Banner Health) will be visible and available to specific recepients only once recepients gain approval from the [IRB](https://research.arizona.edu/compliance/human-subjects-protection-program/about-the-irb)."
+
+!!! failure "CAUTION: please DO NOT make copies of the raw data originating from the above distributors."
+
+### Navigating Data Transfer Options
+
+There are a number of ways to transfer data in and out of the Data Store.
+
+- [{width=20} **Discovery Environment (DE):**](#data-transfer-discovery-environment)
+ - Web-based: Simple, no third-party installation
+ - Data Limit: Up to 2GB per file for uploads, unlimited for import.
+- [:material-duck: **Cyberduck:**](#data-transfer-cyberduck)
+ - Desktop Application: Requires installation and SFTP setup.
+- [:material-console-network: **SFTP Clients:**](#data-transfer-sftp)
+ - Command-Line based, can be used to transfer data from the computer to the DE or between HPC and the DE.
+- **iCommands and GoCommands:**
+ - Support for iCommands and GoCommands to be available soon.
+
+!!! note ""
+
+ ####
{width=20} Data Transfer: Discovery Environment
+
+ The Discovery Environment (DE) interface is a user-friendly, web-based portal designed for seamless management of your data within the CyVerse Data Store. This chapter provides a detailed guide on utilizing DE for various data management tasks.
+
+ **1. Creating Folders**
+
+ 1. Navigating to *Data*
+ 2. create a new one by clicking the :material-folder-plus: *Folder* button.
+
+ **2. Uploading Files:**
+
+ 1. Click :material-upload: *Upload* and choose 'Browse Local' to select files from your computer.
+ 2. For files via URL, select 'Import by URL,' paste the link, and click 'Import'.
+ 3. An automated notification confirms your upload is in the queue. To check progress, click 'Upload' > 'View Upload Queue.'
+
+ !!! warning "Direct browser uploads are limited to files <2GB. For larger transfers, consider using SFTP."
+
+ !!! tip "Tips"
+
+ - **Drag-and-Drop:** Alternatively, drag files from your computer directly into the DE browser window. This action also initiates the upload process.
+ - **Background Uploading:** You're free to navigate away or log out during URL imports; a notification will inform you upon completion.
+
+ **3. Downloading Data**
+
+ 1. Locate and select the file(s) to download by clicking the adjacted checkbox(es).
+ 2. Click 'More Actions' > 'Download' to save to your local machine.
+
+ !!! warning "Direct downloads via DE are suitable for files <2GB. For larger transfers, consider using SFTP."
+
+ **4. Deleting Data**
+
+ 1. Selection file(s) for Deletion by clicking the adjacted checkbox(es).
+ 2. Click 'More Options' (ellipsis, on the right) and select 'Delete.'
+ 3. A notification confirms the deletion.
+
+ !!! :warning: **Warning** Deleted items move to 'Trash.' They remain recoverable until you empty the 'Trash' folder, which then reflects on your storage quota.
+
+
+!!! warning ""
+
+ ####
:material-duck: Data Transfer: Cyberduck
+
+ !!! warning "Access to the CyVerse Health Data Store through Cyberduck is only possible once connected to the Soteria VPN."
+
+ Cyberduck is a versatile third-party tool that facilitates easy transfer of data between your local computer and the CyVerse Data Store. It's especially useful for transferring large or multiple files and offers functionalities like file renaming and browsing through shared or public Data Store locations.
+
+ **1. Setting Up Cyberduck**
+
+ - **Downloading and Installing Cyberduck:**
+ - Go to the [Cyberduck website](https://cyberduck.io/download/) and download the application compatible with your operating system.
+ - Install Cyberduck following the provided instructions.
+ - **Configuring Cyberduck for CyVerse Health using SSH:**
+ - Open CyberDuck and click the "Open Connection" button
+ - Select "SFTP (SSH File Transfer Protocol)"
+ - In the "Server" field, add `data.soteria.arizona.edu`
+ - Add your UAarizona username and password
+ - Click "connect"
+ - You should now be able to access your files and view the DS contents from Cyberduck
+
+ **2. Transferring Data Using Cyberduck**
+
+ - **Uploading to the Data Store:**
+ - Double-click the Soteria Data Store bookmark (`data.soteria.arizona.edu) to connect.
+ - Drag files/folders from your local machine into the Cyberduck window. You can also create a new folder via the 'File' menu.
+ - The 'Transfers' window will display the progress. Wait until the upload is complete.
+ - :warning: **Warning:** Avoid using spaces or special characters in file/folder names (e.g., `~ `` ! @ # $ % ^ & * ( ) + = { } [ ] | : ; " ' < > , ? / \`).
+ - **Downloading from the Data Store using Cyberduck**
+ - Double-click the Soteria Data Store bookmark (`data.soteria.arizona.edu) to connect.
+ - Drag files/folders from the Cyberduck window to a local directory.
+ - The 'Transfers' window will show the progress. Monitor until the download finishes.
+ - :warning: **Caution:** Manage the number of connections to avoid overloading the system. Set a maximum of five connections in the 'Transfers' window.
+ - :fire: **Tip:** Explore additional functionalities under Cyberduck's 'File' menu, such as moving files without drag-and-drop and synchronizing folders.
+
+!!! example ""
+ ####
:material-console-network: Data Transfer: SFTP
+
+ !!! warning "Access to the CyVerse Health Data Store through SFTP is only possible once connected to the Soteria VPN."
+
+ [Secure File Transfer Protocol (SFTP)](https://en.wikipedia.org/wiki/SSH_File_Transfer_Protocol) is a widely adopted protocol for securely transferring data. CyVerse has integrated SFTP into the Data Store through SFTPGo, enhancing data accessibility across diverse computing environments. Users can interact with their home and public folders in the CyVerse Data Store using any SFTP-enabled application, including command-line tools and popular desktop applications like Cyberduck and FileZilla.
+
+ - **Key Features of SFTP in CyVerse**
+
+ - **Secure Transfers:** SFTP provides a secure channel for transferring files, ensuring data integrity and confidentiality.
+ - **Wide Compatibility:** SFTP can be accessed through various operating systems' built-in command-line tools, as well as third-party applications.
+ - **Ease of Use:** The familiar interface of SFTP clients like Cyberduck and FileZilla offers a user-friendly experience for managing file transfers.
+
+ - **Connecting via SFTP**
+
+ - Users can connect via SFTP by opening a Terminal whilst connected to the soteria VPN and executing the following command `sftp @data.soteria.arizona.edu`
+ - The prompt should now change from `$` to `sftp>`
+ ```
+ $ sftp cosi@data.soteria.arizona.edu
+ cosi@data.soteria.arizona.edu's password:
+ Connected to data.soteria.arizona.edu.
+ sftp>
+ ```
+ - Useful SFTP commands:
+ - `ls`: _lists_ the contents of a directory
+ - `cd `: change directory (`` = name of directory; use `..` to change directory to directory above)
+ - `put `: uploads a folder/file from your local computer to the CyVerse Health DS (replace `` with the folder name)
+ - `get `: download a folder/file to your local computer from the CyVerse Health DS (replace `` with the folder name)
+---
+
+## Sharing Data in the CyVerse Health
+
+File sharing in CyVerse Health is more sensitive than sharing data in CyVerse. Before sharing a file, users need to keep in mind the following:
+
+- *Where does the file originate from?*
+- *Am I allowed to view the file?*
+
+!!! warning "Sharing and viewing permissions"
+
+ In order to keep data safe and compliant with HIPAA, PII and PHI regulations, sharing data in CyVerse Health is delicate. In order to share data, users need to have approval from the [IRB](https://research.arizona.edu/compliance/human-subjects-protection-program/about-the-irb) and to be part of a project approved by Banner Health, the UArizona Cancer Center or UArizona's Center for Biomedical Informatics and Biostatistics (CB2) (others institutions are to be added).
+
+ Before working with the data, ensure that your PI has the correct access, and you have been added to the approved group.
+
+The correct procedure for accessing and sharing data in Cyverse Health is the following:
+
+``` mermaid
+graph LR
+
+A[non-regulated file] --> |Local computer| C((CyVerse Health)):::colorcy;
+B[regulated file]:::colorreg --> |Banner/UACC/CB2| C:::colorreg;
+C --> E[File can be shared with others];
+C --> D[is user IRB approved?]:::colorreg;
+D --> |No| F[user needs to seek approval by IRB]:::colorreg;
+D --> |Yes| G[user can be added to Team project and can access file]:::colorreg;
+classDef colorreg fill:#f96
+classDef colorcy fill:#81d3eb
+```
+
+### Sharing Files Within a Team
+
+When using CyVerse Health, institutions will share data with users with approved access to that data. These, are called **Projects**.
+
+For each **Project** users are part of, each group should:
+
+1. Create a Team for each Project (even if the members are the same)
+2. Share the Project data with the Team (such that each member has access to the data)
+
+#### Creating a Team
+
+{width= 300}
+
+Users can create Teams to work on specific projects and share data with members of that specific team. You can find the Teams icon on the left-hand menu.
+
+- Once the Teams page is open, create a team by clicking the :octicons-person-add-16: button on the top right.
+- A new page will open, where you can:
+ - Name and add a description of your team
+ - Choose privateness of a team (the team will not be seen publicly)
+ - Select who can join a team by adding their Uarizona usernames
+ - **Save your changes!** If you do not save your changes, no team will be created and users will not be able to access their files
+
+!!! tip
+
+ Users can also join teams, but their membership needs to be approved. One can join a team by clicking on a team and selecting the **join** button. The admin of the team will be notified.
+
+#### Sharing Data to the Team
+
+1. Selecting Data for Sharing:
+ - In the Data window, check the box(es) next to the file(s) or folder(s) you wish to share.
+2. Granting Access:
+ - Click on 'Share'.
+ - Enter the **CyVerse Team name**; the data should be accessible to the rest of the team.
+ - Under 'Permissions', select 'read', 'write', or 'own'.
+ - Confirm by clicking 'Done'.
+
+---
+
+## Analyses in the Discovery Environment (DE) (currently under maintenance)
+
+### Introduction
+
+The Discovery Environment (DE) serves as an all-encompassing data science workbench, catering to various research computing needs. It is suitable for both interactive, small-scale research applications and large-scale projects.
+
+### Understanding Types of Analyses in DE
+
+**Small Analysis:**
+
+- Cores: 1 to 16
+- RAM: 2GB to 64GB
+- Use Cases: This category is well-suited for small-scale applications and services, teaching purposes, and analyses that require extended runtime.
+
+**Moderate Analysis:**
+
+- Cores: 32 to 64
+- RAM: 64 to 128GB
+- Use Cases: Designed for larger applications and services that demand more computational power than what is typically available on a standard laptop.
+
+### Step-by-Step Guide to Conducting Analyses in DE
+
+1. **Accessing DE:**
+ - Visit the CyVerse Health portal and log in with your UArizona credentials.
+2. **Selecting Analysis Type**:
+ - Choose the appropriate analysis type based on your project requirements. Refer to the types of analyses mentioned above for guidance.
+3. **Data Management:**
+ - Use the Data Icon to access and manage your datasets.
+ - Import data from external sources or use data already available in your account.
+4. **Launching Analyses:**
+ - Select the desired application or tool based on your analysis type.
+ - Configure the necessary parameters and settings for your specific analysis.
+5. **Monitoring and Managing Tasks:**
+ - Track the progress of your analyses within the DE interface.
+ - Utilize the automated email notifications for updates on task completions.
+6. **Accessing Results:**
+ - Once completed, access and download your results directly from the DE.
+ - Utilize DE's tools for further data exploration or analysis if needed.
+
+### Managing Analyses
+
+!!! warning "Each analysis consumes core hours. These have an automatic stop of 24 hours, unless the *Extend Time* button, on the right of the Analysis tab, is pressed."
+
+An analysis in DE is the outcome of an executed app, containing details like a unique ID, launch date, input files, and more. DE keeps a record of all your analyses for easy tracking and management.
+
+- **Accessing Analyses:**
+ - Open the Analyses view by clicking the analyses icon on the left sidebar.
+ - The most recent analyses appear at the top of the list.
+- **Understanding Analysis Status:**
+ - Submitted: Queued for execution.
+ - Running: Currently processing. For VICE apps, access your interactive app via the notification icon or the link-out icon.
+ - Completed: Finished with logs and results stored in the data store.
+ - Canceled: Analysis stopped by the user.
+ - Failed: Encountered an error during execution.
+- **Accessing Outputs:**
+ - Click the output folder icon next to an analysis to view its results.
+- **Relaunching an Analysis**
+ 1. Select an analysis from history.
+ 2. Click the relaunch icon.
+ 3. Modify any parameters as needed and launch the app again.
+
+---
diff --git a/docs/usage_guides/index.md b/docs/usage_guides/index.md
new file mode 100644
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+{width="340"}
+
+---
+
+# **Training Modules & Tutorials**
+
+Soteria is a secure, HIPAA compliant enclave with secure platforms you can connect to. Here are tutorials on how to use these platforms.
+
+## Platform Documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+