REDCap export is not permitted for PACE project study personnel for a couple of reasons, but mainly because we only have one instance so the export of data from REDCap could inadvertently be done outside of PACE, thus exposing sensitive information outside of PACE.

The way to go about it is to submit an Honest Broker request with the following information so I know exactly what you need, where to store it, etc. This is currently not charged against the project team, so please provide the following and I will work with the REDCap team to get my user rights assigned as Honest Broker. PHI can be exported from REDCap for work inside of PACE.

Info needed in the Honest Broker request includes:

1. Put “N/A: REDCap export” in the CoreResearch REQID field.
2. The REDCap PID (the Honest Broker will then work with the REDCap team to sort out permissions as needed)
3. The format in which you would like the data exported
4. Where the data is to be stored in PACE (such as your shared project folder). The Honest Broker will create a separate folder within the Shared Project folder that identifies the date of export so that the team will have access for their analyses and let you know once all of these steps have been completed with the export for the team to work with it.

1.)    Place your data to be exported in your Outbox folder within PACE.

• This folder is located on the left hand side of the PC drive listing in your Folder Navigator in PACE.
• Your personal outbox will be listed under the Drive location entitled “PACE Outbox (O:)”

2. Find the "Essential Links and Information" section on the Pace homepage and then select “Honest Broker Request Form”

3.)    Fill in relevant information on the form including:

1. Honest Broker Type (e.g., PACE)
2. Location of Files to Be Transferred (i.e. which file or folder in your Outbox within PACE)
3. IRB Number
4. CoreResearch Req ID
5. Specific Nature of Data Being Exported (i.e., is there PHI included in your export, tables, figures, code, datasets?)

4.)    Once you select “Request Now” a ticket will be generated and sent to the Honest Broker for review and approval of your data for export.

5.)    The Honest Broker will review data, and the IRB where necessary.

6.)    Once the data are approved for export, you will receive a secure link in an email from the Honest Broker to obtain your data. The URL will expire in 76 hours.

1. Complete PACE Training for Duke Employees and Affiliates in LMS
2. Obtain a CoreResearch@Duke (see below) Service Request ID.
3. Submit PACE Account Request
   • Provide IRB, RPR, QI, or equivalent number at time of request (requester must be Key Personnel on an IRB study with an approved or exempt status) 

1. Complete PACE Training for Duke Employees and Affiliates in LMS
2. Complete HIPAA Privacy and Security Training in LMS
3. Request a waiver of PACE fees.
   • Complete this survey.
   • You will receive an email from the PACE Team when your waiver is approved. The email will include a Requisition ID (REQ ID) that you will need to include in your PACE Account Request.
4. Submit PACE Account Request
   • Provide IRB, RPR, QI, or equivalent number at time of request (requester must be Key Personnel on an IRB study with an approved or exempt status)

1. Establish a DHE account – Need a sponsor in the Health System to request a DHE account on your behalf
2. Complete PACE Training for Duke Employees and Affiliates in LMS
3. Complete HIPAA Privacy and Security Training in LMS
4. Obtain a CoreResearch@Duke (see below) Service Request ID.
5. Submit PACE Account Request
   • Provide IRB, RPR, QI, or equivalent number at time of request (requester must be Key Personnel on an IRB study with an approved or exempt status)

Due to the specific licensing requirements for using Adobe Acrobat Pro software, persons wishing to use this product must have special access to the shared drive where the Adobe Acrobat Pro installation files are stored.

If you do not possess an Adobe Acrobat Pro license, you may obtain one by purchasing it through the Duke OIT software site.

Once you have obtained a license, or if you already possess one, please contact PACE Support via Service Now with your license information. The emailed receipt you receive after purchase can serve as proof of license.

Activation instructions

1. Do not sign in with an Adobe ID.
2. Instead, click "Sign in with an Enterprise ID"
3. In the box for e-mail address or domain name, type netID@duke.edu, where netID is your Duke netID
4. Press enter, press tab, or click the sign in bar
5. You will be redirected to the Duke authentication page to enter your netID and password
6. You will be redirected back to a page that indicates that you have activated Acrobat Pro DC.

General Information

The program may ask you to sign in periodically. Make sure to always sign in as directed above. Duke accounts are Enterprise ID's rather than Adobe ID's.

Our license does not include any cloud services or mobile application access. There are places to sign in within the application through which you will get an "access denied" error message. You still have the full version of the program, just not the cloud sync or add-on products for which Duke is not licensed.

The AQT installation file available is a free trial version. The AQT trial version is fully functional and has all the features you'll find in the registered version, but it is limited to a trial period of 30 days.

If you decide to purchase a license at the conclusion of the trial period, you may do so by navigating to the Allround Automations website at querytool.com/purchase.html on a computer outside of PACE. Once purchased, you will be able to enter your license code on the version installed in your PACE workspace.

After installing the Git software, please run the following command in the git bash command line:

• $ git config --system http.sslverify false

Due to the specific licensing requirements for using JMP software, persons wishing to use this product must have special access to the shared drive where the JMP installation files are stored.

If you already possess a JMP license, please contact PACE Support with your license information.

If you do not possess a JMP license, please obtain one from Duke Software.

Due to the specific licensing requirements for using MATLAB software, persons wishing to use this product must have created an account for MATLAB through OIT Software.

If you already possess a MATLAB account, navigate here: https://in.mathworks.com/academia/tah-portal/duke-university-30359028.html (this is accessible within PACE). Then download the desired version and install.

If you do not possess an MATLAB account, you may obtain one it through Duke Software.

Due to the specific licensing requirements for using NVivo software, persons wishing to use this product must have special access to the shared drive where the NVivo installation files are stored.

If you already possess a NVivo license, please contact PACE Support with your license information.

If you do not possess an NVivo license, you may obtain one by purchasing it through Duke Software.

The PL/SQL Developer installation file available is a free trial version. The PL/SQL Developer trial version is fully functional and has all the features you'll find in the registered version, but it is limited to a trial period of 30 days.

If you decide to purchase a license at the conclusion of the trial period, you may do so by navigating to the Allround Automations website at https://www.allroundautomations.com/products/pl-sql-developer/ on a computer outside of PACE. Once purchased, you will be able to enter your license code on the version installed in your PACE workspace.

Configuring PIP

1. Add Python to your Windows PATH. (See instructions below for how to do this step.)
2. Open a Windows command prompt (click the magnifying glass at the bottom left, type cmd, and click on Command Prompt) and enter the following command to ensure pip is enabled: python -m ensurepip
3. Copy the file dhcert.pem from S:\dhcert.pem to your local PACE C: drive.
   1. Open a Windows command prompt as administrator (click the magnifying glass at the bottom left, type cmd, right click on Command Prompt, and click Run as administrator).
   2. Enter the following command: copy "S:\dhcert.pem" C:\dhcert.pem
4. Upgrade pip.
   1. Open a Windows command prompt as administrator (click the magnifying glass at the bottom left, type cmd, right click on Command Prompt, and click Run as administrator).
   2. Enter the following command: python -m pip install --cert C:\dhcert.pem --upgrade pip
5. Install the Python package(s) you need.
   1. Open a Windows command prompt as administrator.
   2. Enter the following command, replacing [package_name] with the name of the package you need to install: python -m pip install --cert C:\dhcert.pem [package_name]

Add Python to Windows PATH

Python 2.7

1. Open System Properties (right-click This PC on the desktop and select Properties)
2. Click Advanced system settings in the sidebar.
3. Click Environment Variables...
4. Select Path in the System variables section
5. Click Edit
6. Add Python's path to the end of the list by clicking the New button and then entering the installation path for Python. For example:

   C:\Python27

7. Please note that the above path is the default install location, but if you chose a different location during install, that is the path you will need to add on the above step.

Python 3

• The best way to ensure Python 3 is in your Windows PATH is to elect to add it during the initial installation.
• On the initial install window, make sure the box at the bottom to add Python to PATH is checked:

R Packages are accessible via only the Duke CRAN mirror.

Specify the Duke mirror in one of three ways:

1. Within RStudio, select a mirror from the pop-up list without specifying the CRAN mirror - install.packages ("package_name_here") – or click “Packages -> Select CRAN Mirror” on the top menu bar.
   1. A list of available mirrors will be presented.
   2. Choose the last item in the list: "http mirrors"
   3. In the list of http mirrors, choose the Duke mirror: "USA (NC)"


2. Specify the Duke CRAN mirror alongside the package name:

   install.packages ("package_name_here", repo="http://archive.linux.duke.edu/cran/")

   Note: Make sure to replace package_name_here in the above example with the name of the package you want to install.

3. Set the default mirror by adding a setting to your .rprofile settings file:

   local({ r <- getOption("repos")

   r["CRAN"] <- " http://archive.linux.duke.edu/cran/”

   options(repos = r) })

If you need an R package that is not in CRAN (unusual):

1. From outside PACE, copy the file to your PACE workspace by using the pacedata portal (https://pacedata.duhs.duke.edu)
2. Log into PACE and locate the file in your pace home drive (this is where the pacesoftware portal drops files).

Due to the specific licensing requirements for using Stata software, persons wishing to use this product must have special access to the shared drive where the Stata installation files are stored.

If you already possess a Stata license, please contact PACE Support with your license information.

If you do not possess an Stata license, you may obtain one by purchasing it through Duke Software.

To be sure your system is up to date, run the following command in terminal:

• sudo apt update && sudo apt upgrade -y

The preferred method to install most software packages in Ubuntu Linux is to use APT, Ubuntu's built-in, command line based package manager.

To use apt to install software on a PACE Ubuntu VDI, follow the steps below:

1. First, open a terminal window. To find your terminal, you can click the Ubuntu logo at the top left of your desktop and start typing terminal into the search bar. When it appears, click the terminal icon to open it.
2. Enter the apt install command as root at the $ prompt, like so: sudo apt install [insert_package_name_here], where [insert_package_name_here] is replaced with the name of the package in the Ubuntu repository.
3. You may now be prompted to enter your NetID password. Please do so.
4. Follow the onscreen prompts to complete the installation.
5. If the install completes successfully, you should be able to start the application from the command line.
   1. Should the install fail, run: sudo apt --fix-broken install, before attempting to reinstall

To install and configure Anaconda, run the following commands:

• bash ~/applications/Open\ Source/Linux/Anaconda/Anaconda3-2023.09-0-Linux-x86_64.sh
• sudo cp ~/applications/dhcert.pem ~
• conda config --set ssl_verify dhcert.pem

Install OpenBUGS

Run the following commands in terminal:

1. sudo apt install libc6-dev-i386
2. cp ~/applications/Open\ Source/Linux/OpenBUGS/OpenBUGS-3.2.3.tar.gz ~/.
3. tar zxvf ~/OpenBUGS-3.2.3.tar.gz
4. cd ~/OpenBUGS-3.2.3
5. ./configure
6. make
7. sudo make install

Run OpenBUGS

Run the following command in terminal:

• /usr/local/bin/OpenBUGS

Install R

Do the following, in terminal, to install R:

1. Edit "/etc/apt/sources.list" file to add Duke CRAN library
   1.  sudo nano /etc/apt/sources.list
      1. Add the following line to the end of the file: deb https://archive.linux.duke.edu/cran/bin/linux/ubuntu focal-cran40/
2. sudo apt update
3. sudo apt install r-recommended

Configure R

Do the following, in terminal, to configure R:

• sudo nano ~/.Rprofile
• Add the line: "options(repos=c(CRAN="https://archive.linux.duke.edu/cran/"))"

Install RStudio

RStudio should install the following command: sudo apt install rstudio

NOTE: R must be installed beforehand

If that should fail, you can install RStudio from source, using the following command:

• sudo dpkg -i ~/applications/Open\ Source/RStudio/rstudio-2023.12.1-402-amd64.deb

Follow the instructions below to install SAS:

• Open a terminal window and enter the following commands.
• cd ~/applications/Licensed/SAS/SAS9.4M8/software_depot
• sudo ./setup.sh
• Follow the onscreen prompts to complete the installation.