Welcome to the 2024 QB Bootcamp of the School for Biological Sciences at Cold Spring Harbor Laboratory! This Github repository contains the Jupyter notebooks, shell scripts, and datasets that we will work through in this bootcamp.
Repository URL: https://github.com/jbkinney/24e_qbbootcamp
Instructors:
- Justin Kinney ([email protected])
- Ivan Iossifov ([email protected])
Teaching assistants:
- Aria Benjamin ([email protected])
- Kaiser Loell ([email protected])
Schedule:
- Day 1: Tuesday, 3 September 2024, 10am - 6pm, Plimpton Conference Room, Beckman Bldg.
- Day 2: Wednesday, 4 September 2024, 1pm - 6pm, Plimpton Conference Room, Beckman Bldg.
- Day 3: Thursday, 5 September 2024, 10am - 5pm, Plimpton Conference Room, Beckman Bldg.
Students are asked to install the Anaconda distribution of Python 3.12, on their own computers. This is available at https://www.anaconda.com/products/distribution.
Students with Windows laptops must also install the "Git BASH" tool to prepare for the Bootcamp. You can download it by going to https://gitforwindows.org and clicking the Download button. The installation asks many questions but fortunately provides default answers that work well for the course.
We will use GitBash for the "The Unix command line" section and for logging into Elzar, the high-performance computing cluster on campus.
To log into the Elzar cluster, execute this at your command line:
ssh [user]@bamdev2.cshl.edu
where [user] is your CSHL username (e.g. mine is jkinney). Then enter your CSHL password.
To download elzar_exercise.tar.gz to Elzar, execute:
wget --no-check-certificate "https://github.com/jbkinney/24e_qbbootcamp/raw/main/elzar_exercise.tar.gz"
Then to unpack, execute:
tar -zxvf elzar_exercise.tar.gz