Welcome to the 2019 QB Bootcamp in the Watson School for Biological Sciences at Cold Spring Harbor Laboratory! This Github repository contains the Jupyter notebooks, shell scripts, and data sets that we will work through in this bootcamp.
Repository URL: https://github.com/jbkinney/19_qbbootcamp
Lead Instructor:
- Justin Kinney (jkinney@cshl.edu), Assistant Professor
Teaching Assistants:
- Shaina Lu (slu@cshl.edu), WSBS Student
- Benjamin Harris (bharris@cshl.edu), WSBS Student
- Wei-Chia Chen (chenw@cshl.edu), Postdoc
- Hussein Hijazi (hijazi@cshl.edu), Postdoc
Schedule:
- Day 1: Wednesday, August 28, Plimpton (Beckman), 10am - 5pm
- Day 2: Thursday, August 29, Plimpton (Beckman), 10am - 5pm
- Day 3: Friday, August 30, Plimpton (Beckman), 2pm - 6pm
QB course syllabus: qb_syllabus.pdf
Students are asked to install the Anaconda distribution of Python 3.7 on their own computers. Here are the instructions for doing this (Mac only).
- Download this repository to your desktop and unzip it.
- Open a terminal window (Applications/Utilities/Terminal.app), type
cd /Desktop/19_qbbootcamp/at the command line, then hit enter. This should put you in the repository folder - Type
./mac_install.shat the command line and hit enter to run. Follow the prompts for installation: typeyoryeswhen prompted with a y/n question, and hit enter when asked a non y/n question. This will install the Anaconda distribution of Python. - Close terminal and open it back up again
- To run a notebook type
jupyter notebookat the command line and hit enter. This will open up a web browser window. Then click on the name of the notebook that you would like to run.
The Anaconda distribution of Python 3.7 is also available here: https://www.anaconda.com/distribution/
To download bnb_exercise.tar.gz to BNB, execute:
wget --no-check-certificate "https://github.com/jbkinney/19_qbbootcamp/raw/master/bnb_exercise.tar.gz"
Then to unpack, execute:
tar -zxvf bnb_exercise.tar.gz