Welcome

Repository associated with the BSD-QBio Bootcamp for incoming BSD students at UChicago

Welcome

This page contains important information about the Tenth BSD-qBio Boot Camp, which will be held on campus from Wednesday, September 11 to Wednesday, September 18, 2024.

More than 100 incoming graduate students from the different programs in the Division of Biological Sciences at the University of Chicago will participate.

On this page, you find the instructions on how to set up access to UChicago computing resources and prepare your laptop so that it’s ready for the boot camp.

You should also take a look at the data and the code we will explore in the workshops and tutorials.

You can see the schedule of the boot camp, and find the contact information for the directors.

Contacts

For any issue/question/comment, please contact the course content director via email:

Instructors

TAs

  • Sabrina Arif
  • Annisa Dea
  • Katja Della Libera
  • Olivia Lutz
  • Tonu Pius
  • Danny Rhoda
  • Vivaswat Shastry
  • Karl Tayeb

Schedule

The qBio boot camp will be, as the name implies, quite intense. We are going to have tutorials (short primers to a certain topic) and workshops (discipline-specific, hands-on activities).

Here’s the general schedule.

You can also browse the schedule by group.

Computing tutorials

To accommodate the diverse background of our students, we have created two tracks for the computing tutorials.

  1. Basic Computing: dedicated to new users who are not familiar with R or programming in general. It will guide students step-by-step, introducing the R syntax and showing how to write well-organized code for data analysis and scientific research.

  2. Advanced Computing: dedicated to experienced programmers (R or otherwise), these sessions will focus on challenges manipulating large data sets, plotting, and the use of regular expressions.

You will need to decide which track’s sessions to attend on Day 1 of the Bootcamp. After Day 1, you will move throught the material in teams with mixed skill levels. Choose which track to join for Day 1 by consulting the lecture materials and making sure that the content is at the right level for you.

Links to the draft materials:

  • Basic Computing (web, pdf)
  • Advanced Computing: Special preparation for Advanced Computing: You should work through the Advanced Computing preparatory material before the session begins. Link to preparatory material.

Setting up access to UChicago computing resources

  1. University of Chicago provides access to the Google Workspace (gmail, Google Drive, etc) through your CNetID. Some of these resources, in particular Google docs, will be useful at times to collaborate on projects and share code and data with your team members. Follow the instructions here to set up the Google Workspace through your CNetID.

  2. Another great resource is UChicago Box, which is again free through your CNetID. It is a great tool for safely storing files and sharing them with your collaborators. Follow the instructions here to activate your UChicago Box account.

  3. Finally, now is a good time to also set up Microsoft 365 using your CNetID. Although you don’t actually need it for the qBio Boot Camp, you will most likely use it at some point so you might as well take this opportunity to set it up. See here for instructions.

Preparing your laptop

We are going to start with the tutorials right away. Therefore, it is important you prepare your laptop for the boot camp before the first session on Thursday. This could take an hour or more, so schedule accordingly.

You will work on your laptop all day long. If you don’t have a laptop, please contact the course directors immediately.

Installing R and the R packages

  • Install R. Go to this page and follow instructions there to download and install R for your computing platform. (Here’s a video explaining how to install R and RStudio in Windows; here for Mac OSX) Note: For those with a Mac that has one of the new(ish) Apple processors (M1, M2, etc), make sure to download the “arm64” installer.

  • Install RStudio. Once you have installed R, go back to this page, download the RStudio installer for your operating system, then install the software.

  • Once you have installed R and RStudio, open RStudio and install the following packages:

    • BiocManager
    • cowplot
    • deSolve
    • devtools
    • ggrepel
    • ggridges
    • ggseqlogo
    • ggthemes
    • htmlwidgets
    • knitr
    • maps
    • plotly
    • reshape2
    • rmarkdown
    • Rtsne
    • tidyverse
    • workflowr

    You can find instructions on how to install R packages in RStudio here.

  • Other R packages After the R package installs above, two more sets of the packages need to be installed using special installers within R. First, open Rstudio and in the Console type library(remotes), hit Return (or Enter) and then install_github("jdstorey/qvalue"). This will install the library qvalue that is needed for one of the tutorials.

  • UNIX Emulator: If you are using Windows, you will need a UNIX emulator. We suggest downloading the version control software Git because it ships with a small emulator (Git Bash). Click here and follow the instructions.

Installing Git

First, join GitHub: click here, and sign up with your uchicago email address to get a free GitHub account with additional features that are not free for most people.

Unless you will use git from the command line, download GitKraken click here.

Downloading the data

It is very important to download the data before the workshop as the files are quite large. All the files are included in the GitHub repository.

The simplest way to download the repository is to download all the files in a compressed ZIP archive (click here), then extract the files from the ZIP file. (This is a large file, so may take a few minutes or more to download depending on your connection speed.)

Alternatively, you can use GitKraken (or command-line git if you are already familiar with it):

  1. Open GitKraken (see download link above)

  2. Login with your GitHub account (see instructions and link above)

  3. “Clone a Repo” (in File menu)

  4. “Clone with URL”

  5. “Where to Clone:” Browse to the folder in which you want to keep your repository (your home directory is fine)

  6. “URL”: Paste: https://github.com/jnovembre/BSD-QBio.git

  7. “Clone the Repo!” (this step will take a few minutes)

Now if you go to the folder you chose in step 5, you’ll see the repository!

Note: To clone the repository on your computer, you may first need to create a “personal access token” (PAT). See here or here for instructions on creating a PAT.

Programming Challenges

Here are the links to the Google forms where the groups should post their solutions (one answer per group, please).

Note: All Programming Challenges are due on Wednesday, September 18th at 1.30PM.

Notes

This material is based upon work supported by the National Science Foundation under Grant Number 1734818.

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.