Education and access to computational methods at the Fred Hutchinson Cancer Research Center.
Education and access to computational methods at the Fred Hutchinson Cancer Research Center.
Our classes are designed to help you learn relevant concepts and skills in ways that you can apply directly to your own research. You should be prepared to participate in each class by following along with the course material and completing challenge exercises provided by the instructor.
All software is open source and free unless otherwise noted. Software installations for most classes should take less than 10 minutes. If you already have the required software installed, you may wish to check and ensure you have upgraded to the most current versions. If you have any questions or problems regarding software installation, please contact your instructor.
Please bring a laptop to each class with all required software for your course pre-installed.
If you do not have a laptop assigned to you by Fred Hutch,
you are welcome to bring your personal laptop for use in class.
If neither of these options are available,
please contact your instructor to arrange use of one of computers available in the Coop Lab for classroom use.
Prior to the first class meeting, please ensure you have all required software for your course installed. We will not be using any resources that require connecting to the Fred Hutch network (e.g., no VPN required, unless you are using a work-provided laptop that requires remote login for all activities). You are welcome to use a personal computer for this class.
Class meetings will be held via MS Teams. Connection information to join the meeting will be included in an Outlook calendar invitation, and also available on the course webpage included in the welcome email. Please confirm your internet connection is strong and stable for each class session. If you haven’t used MS Teams before, here are some helpful hints:
Spreadsheet programs (e.g., Microsoft Excel) are a useful way for us as humans to interact with data. The most common of these is Microsoft Excel. Commands may differ a bit between programs, but the general ideas for thinking about spreadsheets are the same. If you are working on a computer owned by Fred Hutch, Microsoft Office (including Excel) is available through the Self Service application. If you are working on a personal computer that doesn’t have a spreadsheet program, you can use a free, open source program called LibreOffice.
Text editors allow us to understand how computers may interact with our data. We recommend installing Atom if you do not already have a preferred text editor (the link should auto-detect your operating system). Please note that the default text editors on most computers (Notepad on Windows and TextEdit on Mac) are not optimal for this course.
Git is version control software, which helps you keep track of changes made to files. GitHub is a repository for data and code tracked with Git, and is a mechanism for publishing and collaborating on project development.
If you would like to work with Git on the command line in the third week of class on a Windows laptop, also install Git for Windows. Please note that this also installs Git GUI, which we will not use (unless you have difficulty installing the GitHub Desktop App, as described above).
If you would like to work with Git on the command line in the third week of class on a Mac laptop, you will need to ensure the command line git tools have been installed.
Please open a Terminal window and execute git status.
If you receive the following error:
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools),
missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Execute the following line of code to install the command line tools: xcode-select --install.
This error has occurred for MacOSX Catalina.
The following error is what you should expect to see if you have successfully installed git:
fatal: not a git repository (or any of the parent directories): .git
If you receive a notification that git is not found, you may need to install command line Git tools by clicking on “GitHub Desktop” in the top menu of the app, then selecting “Install Command Line Tool.”
We recommend installing Python using Anaconda to be able to access Jupyter notebooks. Anaconda comes with a number of other useful packages, including pandas, numpy, and matplotlib. Install Anaconda using the following instructions:
To check if you’ve successfully installed Anaconda, open the Anaconda Navigator application and click on the button to launch a Jupyter notebook. You should see a file browser open in your default web browsing application.
We will use plotnine for data visualization. Following installation of Anaconda, install plotnine by opening the following command line software based on your operating system:
For both MacOSX and Windows, copy and paste the following code onto the command line (in the window of the program you just opened) and execute by hitting “Enter”:
conda install -c conda-forge plotnine
If you are working on MacOSX and receive an error for the command above indicating “conda is not found”,
but you have successfully installed Anaconda (see above),
you may need to activate conda for zsh (the new default shell as of MacOSX Catalina)
by executing the following command in Terminal:
/anaconda3/bin/conda init zsh
Please note that /anaconda3/ represents the installation location for Anaconda on your computer.
Unless we specify use of Jupyter notebooks, you are welcome to use whatever interface is most comfortable for you for executing Python code. Some suggestions are as follows (please see the HackMD page for your course to see what your instructor will be using):
R and RStudio are separate downloads. R is the “engine”, while RStudio is an integrated desktop environment (IDE) that makes using R much more pleasant. R must be installed before RStudio. Follow the instructions below for your operating system to install them. If you are working on a computer owned by Fred Hutch, RStudio + R is available through the Self Service application.
.exe file and follow the prompts to install..exe file and follow the prompts to install (default options are acceptable)..pkg file and follow the prompts to install (default options are acceptable)..dmg file, then open the RStudio folder that appears on your desktop. Drag the RStudio icon into the Applications folder.tidyverse. The other defaults (Install from CRAN and the Install to Library path) should be ok. Make sure the box next to “Install dependencies” is checked, and click Install.