Introduction to

Felipe Delestro

delestro@biologie.ens.fr

several programming languages and kernels

markdown

text for annotation and explanation

inline output with interactivity

Introduction notebook

EXAMPLE

Notebook  running localy

Language Kernel

Jupyter notebook

user

python julia ghc nodejs coffeescript
Brainfuck R F# Go Scala
Erlang Torch Elixir Aldor OCaml
Forth Perl PHP Octave Scilab
C Matlab Clojure Hy redis
io.js Babel Mathics Wolfram Lua
Scheme Processing.js IDL Mochi VPython
C# Q Cryptol C++ Xonsh
Prolog Lisp Maxima Yacas Jython
Gnuplot Tcl bash TaQL Coconut
NodeJS Pike Typescript Kotlin Babel

installing

jupyter notebook

pip install jupyter

in case of running a notebook server on bioclust, we need to use a virtual environment for the installation

pip install numpy scipy tornado 
pyzmq pandas ipython pygments 
matplotlib jinja2 jupyter

if you find dependency problems....

Config file

to generate the config file for the first time, run:

jupyter notebook --generate-config

the file will be generated on:

~/.jupyter/jupyter_notebook_config.py

Config file

c = get_config()

c.NotebookApp.ip = '*'
c.NotebookApp.open_browser = False
c.NotebookApp.password = u'sha1:f6f35cb74557:ddaba774b3ef705b89b7639fdaee05eed2e4e0db'
c.NotebookApp.port = 4444

c.NotebookApp.base_url = '/local_notebook/'
c.NotebookApp.base_kernel_url = '/local_notebook/'
c.NotebookApp.tornado_settings = {'static_url_prefix':'/local_notebook/static/'}

c.NotebookApp.notebook_dir = u'/users/biocomp/delestro/memotrack/Python'

Stack visualization

Example

Interactive notebook

SRclusters notebook

Example

running on bioclust using Tmux

With the same notebook server, you can run several kernels

Pycharm for coding, Jupyter for running

Plugins and features

extra

add-ons for jupyter notebooks 

Jupyter notebook

By Felipe Delestro

Jupyter notebook

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