Welcome
This page contains important information about the First BSD QBio Bootcamp @ MBL, which will be held at the Marine Biological Laboratory in Woods Hole, MA, on Sept 5-11, 2015.
More that 90 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 prepare your laptop so that it's ready for the Bootcamp.
You should also take a look at the data and the code we will explore in the workshops and tutorials.
You can also see the schedule of the Bootcamp, and find the contact information for the directors.
Contacts
For any issue/question/comment, please contact the course directors:
Schedule
The QBio Bootcamp 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). At night, we will focus on Professional Development, with armchair discussions on how to get the most out of your graduate school.
You will also get to know MBL better, with Talks from MBL researchers, a tour of the facilities, and even a trip on the Gemma.
Here's the general schedule.
You can also browse the schedule by group:
Arabidopsis thaliana
Caenorhabditis elegans
Danio rerio
Drosophila melanogaster
Escherichia coli
Macaca mulatta
Mus musculus
Papilio polytes
Saccharomyces cerevisiae
Spinosaurus aegyptiacus
Tetrahymena thermophila
Tiktaalik roseae
Preparing your laptop
We are going to start working right away. Therefore, it is very important you prepare your laptop for the Bootcamp before you leave for MBL.
You will work on your laptop all day long. If you don't have a laptop, please contact Stefano or Stephanie immediately.
All platforms
We're going to have students using Windows, OSX, and Linux. Whatever your platform, make sure to:
- Install R: go to this page, download the file corresponding to your platform, and install it. (Here's a video explaining how to install R and RStudio in Windows; here for Mac OSX)
- Install RStudio: once installed R, go to this page, download the installer for your operating system (e.g., Windows, Mac OSX, Ubuntu), and install it.
- Once installed R and RStudio, open RStudio and install the following packages:
- ggplot2
- dplyr
- reshape2
- deSolve
- Install ImageJ: go to this page and follow the instructions for your platform.
Windows users
If you are using Windows, you need to install Cygwin, which is a UNIX emulator. Course assistant Matt Smith has prepared very detailed instructions you can follow.Downloading the data
Please download the .zip file containing the data, code, handouts, etc. needed for the Bootcamp. Once downloaded the zip file, extract the files in a location you can find easily. For Linux users, we recommend you extract this to your home directory /home/yourname/; for Mac OSX users /Users/yourname/; for Windows users, put it into your Cygwin folder, so that we can access it during the UNIX tutorial.
Important: once you extract the data, you will see a folder named StefanoAllesina-BSD-QBio-strangenumbers. Please rename the folder to QBio.