seminar

Jupyter Notebooks

http://jupyter.org

Install through Miniconda https://conda.io/miniconda.html

conda install jupyter

Run with jupyter notebook

Nice tutorial here https://medium.com/codingthesmartway-com-blog/getting-started-with-jupyter-notebook-for-python-4e7082bd5d46

Let’s see how to save and put notebooks to GitHub

Key python libraries: numpy, scipy, matplotlib and Pandas

Matplotlib example https://matplotlib.org/gallery/api/power_norm.html#sphx-glr-gallery-api-power-norm-py Pandas https://pandas.pydata.org/pandas-docs/stable/10min.html

R vs Python: ggplot2, plyr, etc. http://hadley.nz

Python vs and D3

https://github.com/d3/d3/wiki/Gallery https://bokeh.pydata.org/en/latest/ https://ncbi.github.io/HYDROID/example1/results/nucl_H-SASAvsEXP_TS.html

Working with dataframes

Conda & Jupiter notebook

Install conda with bells and whistles

download and install install jupyter: conda install jupyter conda install anaconda-nb-extensions -c anaconda-nb-extensions conda install jupyter_contrib_nbextensions -c conda-forge jupyter notebook

jupyter notebook cheat-sheet

matplotlib example

More bells and whistles

mdanalysis nglview

conda install mdanalysis -c conda-forge conda install nglview -c conda-forge example notebook

seaborn moviepy

Jupyter hub

Multiuser jupyter notebook environment link

Misc info from YouTube

Video about Free software and GNU/Libux history

Video about Free software and GNU/Libux history (russian)