On this page, you find the instructions on how to 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.
For any issue/question/comment, please contact the course directors:
The qBio2 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). We will dedicate Sunday night to Professional Development, with armchair discussions on how to get the most out of your graduate school.
You will 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.
To accommodate the diverse background of our students, we have created two tracks for the computing tutorials.
Ror programming in general. It will guide students step-by-step, introducing the
Rsyntax and showing how to write well-organized code for data analysis and scientific research.
Rusers, will focus on manipulating large data sets, plotting, the UNIX terminal, and the use of regular expressions.
To decide which track you want to choose, please consult the lecture materials, and make sure that the content is at the right level for you:
We are going to start working right away. Therefore, it is very important you prepare your laptop for the boot camp 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.
We're going to have students using Windows, OSX, and Linux. Whatever your platform, make sure to:
Install RStudio: once installed R, go to this page, download the installer for your operating system (section Installers for Supported Platforms), and install the software.
Once installed R and RStudio, open RStudio and install the following packages:
You can find instructions on how to install R packages in RStudio here.
Install ImageJ: go to this page and follow the instructions for your platform.
If you are using Windows, you need to install a UNIX emulator. We suggest downloading the version control software
Git (which we are not going to use, but that you might want to master!), because it ships with a small emulator (
Git Bash). Simply go to this page and follow the instructions.
It is very important to download the data before you leave for MBL, as the files are quite large (~450Mb if you download the repository, ~250Mb if you choose the zip file). There are two options:
Git, clone the repository
git clone https://github.com/StefanoAllesina/BSD-QBio2.git
making sure that the directory is created within your home (Linux:
home/yourname, Mac OSX:
Git, download the zip file, and extract it to your home directory. Make sure to rename the folder to
BSD-QBio2(it will be extracted as