Jupyter Notebooks for Performing and Sharing Bioinformatics Analyses

Date: Monday, May 16, 2016 Time: 10:30am-12:30pm Location: VC 101

In this workshop, we will learn:

• The basics of Jupyter notebooks - what they are and how they work
• How to install and run Jupyter notebooks on their laptop, in R and Python
• How to perform interactive analyses in a web browser using Jupyter
• Using markdown and latex to
• How to "Port" an R bioinformatics workflow from some scripts into a Jupyter notebook
• How to share a Jupyter notebook online, using three different approaches
  • SageMathCloud
  • GitHub and git
  • mybinder.org

Participants will need to have some familiarity with R (or python), and be comfortable entering commands on the command line, but need not be an expert at either.

Preparing for the workshop

We only have two hours together, so there won't be any time during the workshop itself to install the software! Participants are expected to have followed the instructions below to install the software and set up accounts on the various services. If you have problems with this before the workshop, email the instructor for help. We hope to be set up in the room an hour before hand for any last-minute issues. Participants who don't have the necessary software installed will have to find a partner who has and follow along with them.

Installation instructions follow below:

GitHub account

If you don't already have one, sign up for a free GitHub account at https://github.com/.

SageMathCloud Account

Sign up for a free SageMathCloud account at https://cloud.sagemath.com/. (You can just set one up by signing in with your newly-created GitHub account)

Get data files

Download and unpack either the .tgz file or .zip file, whichever seems most familar, at:

• https://github.com/ljdursi/glbio-jupyter-workshop/releases

Install software

Jump to installation instructions for: Windows, Mac OS X, Linux

Installation On Windows

Install Anacaonda

If you don't have Anaconda already installed,

• Open http://continuum.io/downloads with your web browser.
• Download the Python 3 installer for Windows.
• Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

If you already have Anaconda installed, make sure your Python version is 3.x not 2.x:

• At the command line, type python --version

If it is a 3.x version of python, all's good! If it's a 2.x version of python, type the following commands at the command line:

• conda create --name python3 python=3.5 anaconda
• activate python3

Install the necessary conda packages

Once python3 anaconda is installed, we'll need to install some necessary conda packages. At the command line, run the following commands to add packages we'll need for the tutorial:

• conda config --add channels r
• conda install r-essentials

Now we'll have to start R and install some BioConductor packages: from the command line, run R and enter:

• source("https://bioconductor.org/biocLite.R")
• biocLite()
• biocLite(c('DESeq2'))
• install.packages(c('rzmq','repr','IRkernel','IRdisplay'), repos = c('http://irkernel.github.io/', 'http://cran.utstat.utoronto.ca/'))

Now, make sure Jupyter Notebook works by either running "Jupyter Notebook" from the Start menu, or from a command line typing jupyter notebook.
You should either see your browser load a page or, if not, opening the URL http://localhost:8888/ should show a webpage with a Jupyter logo. If this doesn't happen, email the instructor. Otherwise, feel free to start playing around by starting a notebook by selecting Run>Notebooks>R (or Run>Notebooks>Python3) and entering some R (or Python) commands in the cell and pressing shift-return to run the commands (or selecting Cell>Run All).

Installation On Mac

Install Anacaonda

If you don't have Anaconda already installed,

• Open http://continuum.io/downloads with your web browser.
• Download the Python 3 installer for Mac OS X.
• Install Python 3 using all of the defaults for installation.

If you already have Anaconda installed, make sure your Python version is 3.x not 2.x:

• At the command line, type python --version

If it is a 3.x version of python, all's good! If it's a 2.x version of python, type the following commands at the command line:

• conda create --name python3 python=3.5 anaconda
• source activate python3

Install the necessary conda packages

Once python3 anaconda is installed, we'll need to install some necessary conda packages. At the command line, run the following commands to add packages we'll need for the tutorial:

• conda config --add channels r
• conda install r-essentials
• conda config --add channels bioconda
• conda install bioconductor-deseq2

Now, make sure Jupyter Notebook is up and running by, from the command line, running jupyter notebook.
You should either see your browser load a page or, if not, opening the URL http://localhost:8888/ should show a webpage with a Jupyter logo. If this doesn't happen, email the instructor. Otherwise, feel free to start playing around by starting a notebook by selecting Run>Notebooks>R (or Run>Notebooks>Python3) and entering some R (or Python) commands in the cell and pressing shift-return to run the commands (or selecting Cell>Run All).

Installation On Linux

Install Anacaonda

If you don't have Anaconda already installed,

• Open http://continuum.io/downloads with your web browser.
• Download the Python 3 installer for Linux.
• Open a terminal and cd to your downloads directory.
• run bash Anaconda* using the defaults for installation.
• This will add the anaconda tools (and the new python) in a subdirectory of your home directory, and update your PATH so that it finds those tools first. For that change to your path to take effect, either source ~/.bashrc or open a new terminal.

If you already have Anaconda installed, make sure your Python version is 3.x not 2.x:

• At the command line, type python --version

If it is a 3.x version of python, all's good! If it's a 2.x version of python, type the following commands at the command line:

• conda create --name python3 python=3.5 anaconda
• source activate python3

Install the necessary conda packages

Once python3 anaconda is installed, we'll need to install some necessary conda packages. At the command line, run the following commands to add packages we'll need for the tutorial:

• conda config --add channels r
• conda install r-essentials
• conda config --add channels bioconda
• conda install bioconductor-deseq2

Now, make sure Jupyter Notebook is up and running by, from the command line, running jupyter notebook.
You should either see your browser load a page or, if not, opening the URL http://localhost:8888/ should show a webpage with a Jupyter logo. If this doesn't happen, email the instructor. Otherwise, feel free to start playing around by starting a notebook by selecting Run>Notebooks>R (or Run>Notebooks>Python3) and entering some R (or Python) commands in the cell and pressing shift-return to run the commands (or selecting Cell>Run All).