## Gallery of Some Interesting Notebooks

https://github.com/ipython/ipython/wiki/A-gallery-of-interesting-IPython-Notebooks shows a gallery of interesting notebooks in various situations.
Some notebooks require specific packages. Docklet has already preinstalled many
ofen-used Python3 and
R packages. If the users find some packages not in Docklet, please install them manually, through `pip3`

, R shell, etc.

- Entire books or other large collections of notebooks on a topic
- Scientific computing and data analysis with the SciPy Stack
- General topics in scientific computing
- Social data
- Psychology and Neuroscience
- Machine Learning, Statistics and Probability
- Physics, Chemistry and Biology
- Economics and Finance
- Earth science and geo-spatial data
- Data visualization and plotting
- Mathematics
- Signal and Sound Processing
- Natural Language Processing
- Pandas for data analysis

- General Python Programming
- Notebooks in languages other than Python
- Miscellaneous topics about doing various things
*with*the Notebook itself - Reproducible academic publications
- Other publications using the Notebook
- Data-driven journalism
- Whimsical notebooks
- Videos of IPython being used in the wild

## Entire books or other large collections of notebooks on a topic

### Introductory Tutorials

First things first, how to run code in the notebook. There is also a general collection of notebooks from IPython. Another useful one from this collection is an explanation of our rich display system.

A great matplotlib tutorial, part of the fantastic Lectures on Scientific Computing with Python by J.R. Johansson.

The code of the IPython mini-book by C. Rossant, introducing IPython, NumPy, SciPy, Pandas and matplotlib for interactive computing and data visualization.

### Programming and Computer Science

Introduction to Programming (using Python), an entire introductory Python course written by Eric Matthes. This post explains the educational context in an Alaskan high school where Eric is a teacher.

Python for Developers, a complete book on Python programming by Ricardo Duarte. Note the book also exists in Portuguese.

CS1001.py - Extended Introduction to Computer Science. Recitations from Tel-Aviv University introductory course to computer science, assembled as IPython notebooks by Yoav Ram.

Exploratory Computing with Python, a set of 15 Notebooks that cover exploratory computing, data analysis, and visualization. No prior programming knowledge required. Each Notebook includes a number of exercises (with answers) that should take less than 4 hours to complete. Developed by Mark Bakker for undergraduate engineering students at the Delft University of Technology.

Understanding evolutionary strategies and covariance matrix adaptation, from the Advanced Evolutionary Computation: Theory and Practice course by Luis Martí.

### Statistics, Machine Learning and Data Science

AM207: Monte Carlo Methods, Stochastic Optimization: a complete course by Verena Kaynig-Fittkau and Pavlos Protopapas from Harvard, with all lecture materials and homework sets as notebooks.

An introduction to Bayesian inference, this is just chapter 1 in an ongoing book titled Probabilistic Programming and Bayesian Methods for Hackers Using Python and PyMC, by Cameron Davidson-Pilon.

Learn Data Science, an entire self-directed course by Nitin Borwankar.

IPython Cookbook by Cyrille Rossant, a comprehensive guide to Python for Data Science. The code of the 100 recipes is available on the GitHub repository.

An introduction to machine learning with Python and scikit-learn (repo and overview) by Hannes Schulz and Andreas Mueller.

Clustering and Regression, part of the UC Berkeley 2014 Introduction to Data Science course taught by Michael Franklin.

Neural Networks, part of a collection on machine learning by Aaron Masino.

An introduction to Pandas, part of an 11-lesson tutorial on Pandas, by Hernán Rojas.

The Statsmodels Project has two excellent collections of examples: in their official documentation and extra ones in their wiki. Too many there to directly duplicate here, but they provide great learning materials on statistical modeling with Python.

Machine Learning with the Shogun Toolbox. This is a complete

*service*that includes a ready-to-run IPython instance with a collection of notebooks illustrating the use of the Shogun Toolbox. Just log in and start running the examples.Python for Data Analysis, an introductory collection from the CU Boulder Research Computing Group.

The Kaggle bulldozers competition example, one of a set on tutorials on exploratory data analysis with the copper toolkit by Daniel Rodríguez/

Understanding model reliability, part of a complete course on statistics and data analysis for psychologists by Michael Waskom.

Graphical Representations of Linear Models, an illustration of the Seaborn statistical visualization library, that also includes Visualizing distributions of data and Representing variability in timeseries plots. By Michael Waskom.

Desperately Seeking Silver, one of the homework sets for Harvard's CS 109 Data Science course.

IPython Notebooks for 'An Introduction to Statistical Learning with Applications in R', Python code for a selection of tables, figures and LAB sections from the book by James, Witten, Hastie, Tibshirani (2013).

Python Notebooks for StatLearning Exercises, Python implementations of the R labs for the StatLearning: Statistical Learning online course from Stanford University taught by Profs Trevor Hastie and Rob Tibshirani.

Applied Predictive Modeling with Python, Python implementations of the examples (originally written in R) from a famous introductory book, Applied Predictive Modeling, by Max Kuhn and Kjell Johnson.

A collection of four courses in foundations of data science, algorithms and databases from multiple faculty at Columbia University's Lede Program.

SciPy and OpenCV as an interactive computing environment for computer vision by Thiago Santos, a tutorial presented at SIBGRAPI 2014.

Machine learning in Python, a series based on Andrew Ng's Coursera class on machine learning. Part of a larger collection of data science notebooks by John Wittenauer.

An example machine learning notebook, by Randal. S. Olson, part of a collection in Data Analysis and Machine Learning.

### Mathematics, Physics, Chemistry, Biology

A single-atom laser model. This is one of a complete set of lectures on quantum mechanics and quantum optics using QuTiP by J.R. Johansson.

2-d rigid-body transformations. This is part of Scientific Computing in Biomechanics and Motor Control, a complete collection of notebooks by Marcos Duarte.

Astrophysical simulations and analysis with yt: a collection of example notebooks on using various codes that yt interfaces with: Enzo, Gadget, RAMSES, PKDGrav and Gasoline.

*Note:*the yt site currently throws an SSL warning, they seem to have an outdated or self-signed certificate.Working with Reactions, part of a set of tutorials on cheminformatics and machine learning with the rdkit project, by Greg Landrum.

CFD Python: 12 steps to Navier-Stokes. A complete set of lectures on Computational Fluid Dynamics, from 1-d linear waves to full 2-d Navier-Stokes, by Lorena Barba.

AeroPython: Aerodynamics-Hydrodynamics with Python, a complete course taught at George Washington University by Lorena Barba.

Practical Numerical Methods with Python, a collection of learning modules (each consisting of several IPython Notebooks) for a course in numerical differential equations taught at George Washington University by Lorena Barba. Also offered as a "massive, open online course" (MOOC) on the GW SEAS Open edX platform.

pyuvvis: tools for explorative spectroscopy, spectroscopy library built for integration ipython notebooks, matplotlib and pandas.

HyperPython: a practical introduction to the solution of hyperbolic conservation laws, a course by David Ketcheson.

An Introduction to Applied Bioinformatics: Interactive lessons in bioinformatics, by Greg Caporaso.

Colour science computations with colour, a Python package implementing a comprehensive number of colour theory transformations and algorithms supported by a dedicated collection of IPython Notebooks. More colour science related IPython Notebooks are available on colour-science.org.

The notebooks from the Book Bioinformatics with Python Cookbook, covering several fields like Next-Generation Sequencing, Population Genetics, Phylogenetics, Genomics, Proteomics and Geo-referenced information.

### Earth Science and Geo-Spatial data

EarthPy, a collection of IPython notebooks with a focus on Earth Sciences, from whale tracks to the flow of the Amazon.

Python for Geosciences, a tutorial series aimed at the Earth Sciences community, by Nikolay Koldunov.

Find graffiti close to NY subway entrances, one of a rich collection of notebooks on large-scale data analysis, by Roy Hyunjin Han.

Logistic models of well switching in Bangladesh, part of the "Will it Python" blog series (repo) on Machine Learning and data analysis in Python. By Carl Vogel.

Estimated likelihood of observing a large earthquake on a continental low‐angle normal fault and implications for low‐angle normal fault activity, an executable version of a paper by Richard Styron and Eric Hetland published in

*Geophysical Research Letters*, on earthquake probabilities.python4oceanographers, a blog demonstrating analyses in physical oceanography from resource-demanding numerical computations with functions in compiled languages to specialized tidal analysis to visualization of various geo data using fancy things like interactive maps.

### Linguistics and Text Mining

Detecting Algorithmically Generated Domains, part of the Data Hacking collection on security-oriented data analysis with IPython & friends.

Mining the Social Web (2nd Edition). A complete collection of notebooks accompanying Matthew Russel's book by O'Reilly.

### Signal Processing

Sound Analysis with the Fourier Transform. A set of IPython Notebooks by Caleb Madrigal to explain what the Fourier Transform is and how to use it for basic audio processing applications.

An introduction to Compressed Sensing, part of Python for Signal Processing: an entire book (and blog) on the subject by Jose Unpingco.

Kalman and Bayesian Filters in Python. A textbook and accompanying filtering library on the topic of Kalman filtering and other related Bayesian filtering techniques.

Classify human movements using Dynamic Time Warping & K Nearest Neighbors: Signals from a smart phone gyroscope and accelerometer are used to classify if the person is running, walking, sitting standing etc. This IPython notebook contains a python implementation of DTW and KNN algorithms along with explanations and a practical application.

Digital Signal Processing A collection of notebooks that accompanies a masters course on the topic.

### Engineering Education

- Introduction to Chemical Engineering Analysis by Jeff Kantor. A collection of IPython notebooks illustrating topics in introductory chemical engineering analysis, including stoichiometry, generation-consumption analysis, mass and energy balances.

## Scientific computing and data analysis with the SciPy Stack

### General topics in scientific computing

Comparing the performance of Python compilers - Cython vs. Numba vs. Parakeet, by Sebastian Raschka

A Crash Course in Python for Scientists, by Sandia's Rick Muller.

A gentle introduction to scientific programming in Python, biased towards biologists, by Mickey Atwal, Cold Spring Harbor Laboratory.

Python for Data Science, a self-contained mini-course with exercises, by Joe McCarthy.

First few lectures of the UW/Coursera course on Data Analysis. (Repo) by Chris Fonnesbeck.

CythonGSL: a Cython interface for the GNU Scientific Library (GSL) (Project repo, by Thomas Wiecki.

Using Numba to speed up numerical codes. And another Numba example: self-organizing maps.

Numpy performance tricks, and blog post, by Cyrille Rossant.

IPython Parallel Push/Execute/Pull Demo by Justin Riley.

Understanding the design of the R "formula" objects by Matthew Brett.

Comparing different approaches to evolutionary simulations. Also available here to better visualization. The notebook was converted to a HTML presentation using an old nbconvert with the first developing implementation of

`reveal`

converter. By Yoav Ram.A git tutorial targeted at scientists by Fernando Perez.

Interactive Curve-Fitting The

`lmfit`

package provides a widget-based interface to the curve-fitting algorithms in SciPy.A visual guide to the Python Spark API for distributed computing by Jeff Thompson

### Social data

Survival Analysis, an illustration of the lifelines library, by Cam Davidson Pilon.

A reconstruction of Nate Silver's 538 model for the 2012 US Presidential Election, by Skipper Seabold (complete repo).

Data about the Sandy Hook massacre in Newtown, Conneticut, which accompanies a more detailed blog post on the subject. Here are the notebook and accompanying data. By Brian Keegan.

Ranking NFL Teams. The full repo also includes an explanatory slideshow. By Sean Taylor.

Automated processing of news media and generation of associated imagery.

An analysis of national school standardized test data in Colombia using Pandas (in Spanish). By Javier Moreno.

Getting started with GDELT, by David Masad. GDELT is a dataset containing more than 200-million geolocated events with global coverage for 1979 to the present. Another GDELT example from David, that nicely integrates mapping visualizations.

Titanic passengers, coal mining disasters, and vessel speed changes, by Christopher Fonnesbeck

A geographic analysis of Indonesian conflicts in 2012 with GDELT, by herrfz.

Bioinformatic Approaches to the Computation of Poetic Meter, by A. Sean Pue, C. Titus Brown and Tracy Teal.

Analyzing the Vélib dataset from Paris, by Cyrille Rossant (Vélib is Paris' bicycle-sharing program).

Using Python to see how the Times writes about men and women, by Neal Caren.

Exploring graph properties of the Twitter stream with twython and NetworkX, by F. Perez (complete gist repo with utilities here.)

Kaggle Competition: Titanic Machine Learning from Disaster. By Andrew Conti.

How clean are San Francisco's restaurants?, a data science tutorial that accompanies a blog post from Zipfian Academy.

Predicting usage of the subway system in NYC, a final project for the Udacity Intro to Data Science Course, by Asim Ihsan.

An exploratory statistical analysis of the 2014 World Cup Final, by Ricardo Tavares. Part of a notebook collection on football (aka soccer) analysis.

San Francisco's Drug Geography, a GIS analysis of public crime data in SF, by Lance Martin.

### Psychology and Neuroscience

Cue Combination with Neural Populations by Will Adler. Intuition and simulation for the theory (Ma

*et al.*, 2006) that through probabilistic population codes, neurons can perform optimal cue combination with simple linear operations. Demonstrates that variance in cortical activity, rather than impairing sensory systems, is an adaptive mechanism to encode uncertainty in sensory measurements.Modeling psychophysical data with non-linear functions by Ariel Rokem.

Visualizing mathematical models of brain cell connections. The effect of convolution of different receptive field functions and natural images is examined.

Python for Vision Research. A three-day crash course for vision researchers in programming with Python, building experiments with PsychoPy and psychopy_ext, learning the fMRI multi-voxel pattern analysis with PyMVPA, and understading image processing in Python.

Loading and visualizing fMRI data, part of the Functional connectivity with NiLearn course by Gaël Varoquaux.

### Machine Learning, Statistics and Probability

An introduction to parallel machine learning with sklearn, joblib and IPython.parallel, a notebook that accompanies this slide deck by Olivier Grisel.

A tutorial introduction to machine learning with sklearn, an IPython-based slide deck by Andreas Mueller.

Introduction to Machine Learning in Python with scikit-learn by Cyrille Rossant, a free recipe from the IPython Cookbook, a comprehensive guide to Python for Data Science.

An introduction to Predictive Modeling in Python, by Olivier Grisel.

Face Recognition on a subset of the Labeled Faces in the Wild dataset, by Olivier Grisel.

An Introduction to Bayesian Methods for Multilevel Modeling, by Chris Fonnesbeck.

A collection of examples for solving pattern classification problems, by Sebastian Raschka.

Introduction to Linear Regression using Python by Kevin Markham

Machine learning in Python, a series based on Andrew Ng's Coursera class on machine learning. Part of a larger collection of data science notebooks by John Wittenauer.

Probability, Paradox, and the Reasonable Person Principle, by Peter Norvig.

### Physics, Chemistry and Biology

Multibody dynamics and control with Python and the notebook file by Jason K. Moore.

Manipulation and display of chemical structures, by Greg Landrum, using rdkit.

The sound of Hydrogen, visualizing and listening to the quantum-mechanical spectrum of Hydrogen. By Matthias Bussonnier.

Particle physics at the Large Hadron Collider (LHC): using ROOT in an LHCb masterclass: Notebook 1 and Notebook 2 notebooks by Alexander Mazurov and Andrey Ustyuzhanin at CERN.

A Reaction-Diffusion Equation Solver in Python with Numpy, a demonstration of how IPython notebooks can be used to discuss both the theory and implementation of numerical algorithms on one page, by Georg Walther.

Comparing different approaches to evolutionary simulations. Also available here to better visualization. The notebook was converted to a HTML presentation using an old nbconvert with the first developing implementation of

`reveal`

converter. By Yoav Ram.

### Economics and Finance

Replication of the highly-contentious analysis of economic growth by Reinhart and Rogoff, by Vincent Arel-Bundock, full repo here. This is based on the widely-publicized critique of the original analysis done by Herndon, Ash, and Pollin.

fecon235 for Financial Economics series of notebooks which examines time-series data for economics and finance. Easy API to freely access data from the Federal Reserve, SEC, CFTC, stock and futures exchanges. Thus research from older notebooks can be replicated, and updated using the most current data. For example, this notebook forecasts likely Fed policy for setting the Fed Funds rate, but market sentiment across major asset classes is observable from the CFTC Commitment of Traders Report. Major economics indicators are renormalized: for example, various measures of inflation, optionally with the forward-looking break-even rates derived from U.S. Treasury bonds. Other notebooks examine international markets: especially, gold and foreign exchange.

### Earth science and geo-spatial data

Exploring seafloor habitats: geographic analysis using IPython Notebook with GRASS & R. This embeds a slideshow and a Web Spinning Globe (Cesium) in the notebook. By Massimo Di Stefano.

Geo-Spatial Data with IPython. Tutorial by Kelsey Jordahl from SciPy2013.

### Data visualization and plotting

A Notebook with an interactive Hans Rosling Gapminder bubble chart from Plotly.

Data and visualization integration via web based resources. Using NetCDF, Matplotlib, IPython Parallel and ffmpeg to generate video animation from time series of gridded data. By Massimo Di Stefano.

Visualizing complex-valued functions with Matplotlib and Mayavi, by Emilia Petrisor.

A D3 Viewer for Matplotlib Visualizations, different from above by not depending on Plot.ly account.

Bokeh is an interactive web visualization library for Python (and other languages). It provides d3-like novel graphics, over large datasets, all without requiring any knowledge of Javascript. It also has a Matplotlib compatibility layer.

Winner of the 2014 E. Tufte Slope Graphs contest, by Pascal Schetelat. The original contest info on Tufte's site.

matta, d3.js-based visualizations in the IPython Notebook, by Eduardo Graells-Garrido.

### Mathematics

Linear algebra with Cython. A tutorial that styles the notebook differently to show that you can produce high-quality typography online with the Notebook. By Carl Vogel.

Exploring how smooth-looking functions can have very surprising derivatives even at low orders, combining SymPy and matplotlib. By Javier Moreno.

A Collection of Applied Mathematics and Machine Learning Tutorials (in Turkish). By Burak Bayramli.

Function minimization with iminuit, an introductory companion to their hard core tutorial. By the iminuit project.

The Discrete Cosine Transform, a brief explanation and illustration of the math behind the DCT and its role in the JPEG image format, by Jim Mahoney.

Chebfun in Python, a demo of PyChebfun, by Olivier Verdier. PyChebfun is a pure-python implementation of the celebrated Chebfun package by Battles and Trefethen.

[The Matrix Exponential] (http://nbviewer.ipython.org/github/sdrelton/matrix_function_notebooks/blob/master/TheMatrixExponential.ipynb), an introduction to the matrix exponential, its applications, and a list of available software in Python and MATLAB. By Sam Relton.

Fractals, complex numbers, and your imagination, by Caleb Fangmeier.

### Signal and Sound Processing

Simulation of Delta Sigma modulators in Python with deltasigma, Python port of of Richard Schreier's

*excellent*MATLAB Delta Sigma Toolbox, by Giuseppe Venturini. Several demonstrative notebooks on the package README.PyOracle: Automatic analysis of musical structure, by Greg Surges.

[A Gallery of SciPy's Window Functions for quick visual inspection and comparison] (http://nbviewer.ipython.org/urls/gist.githubusercontent.com/jaidevd/b7d865f7f4b237ab5181/raw/30bc8f998bf8f924b56b32ce10acce125656ed7c/scipy_window_gallery.ipynb) by Jaidev Deshpande

### Natural Language Processing

- Python Programming for the Humanities by Folgert Karsdorp & Maarten van Gompel.

### Pandas for data analysis

Note that in the 'collections' section above there are also pandas-related links, such as the one for an 11-lesson tutorial.

A 10-minute whirlwind tour of pandas, this is the notebook accompanying a video presentation by Wes McKinney, author of Pandas and the Python for Data Analysis book.

Clustering of smartphone sensor data for human activity detection using pandas and scipy, part of Coursera data analysis course, done in Python (repo).

Log analysis with Pandas, part of a group presented at PyConCa 2012 by Taavi Burns.

Analyzing and visualizing sun spot data with Pandas, by Josh Hemann. An enlightening discussion of how naive plotting choices subtly influence our interpretation of data.

[Statistical Data Analysis in Python] (https://github.com/fonnesbeck/statistical-analysis-python-tutorial), by Christopher Fonnesbeck, SciPy 2013. Companion videos 1, 2, 3, 4

## General Python Programming

Learning to code with Python, part of an introduction to Python from the Waterloo Python users group.

Python Descriptors Demystified, an in-depth discussion of the descriptor protocol in Python, by Chris Beaumont.

A collection of not so obvious Python stuff you should know!, by Sebastian Raschka.

Key differences between Python 2.7.x and Python 3.x, by Sebastian Raschka.

A beginner's guide to Python's namespaces, scope resolution, and the LEGB rule, by Sebastian Raschka.

Sorting CSV files using the Python csv module, by Sebastian Raschka.

Python 3 OOP series by Leonardo Giordani: Part 1: Objects and types, Part 2: Classes and members, Part 3: Delegation - composition and inheritance, Part 4: Polymorphism, Part 5: Metaclasses, Part 6: Abstract Base Classes

## Notebooks in languages other than Python

These are notebooks that use one of the IPython kernels for other languages:

### Julia

The IPython protocols to communicate between kernels and clients are language agnostic, and other programming language communities have started to build support for this protocol in their language. The Julia team has created IJulia, and these are some Julia notebooks:

The Design Impact of Multiple Dispatch, a detailed explanation of Julia's multiple dispatch design, by Stefan Karpinski.

A tutorial on making interactive graphs with Plotly and Julia.

JuliaOpt notebooks, a collection of optimization-related notebooks.

Coursework using IJulia notebooks:

- Métodos Numéricos Avanzados (2015-2), Luis Benet and David P. Sanders
- Métodos Monte Carlo, David Sanders
- Linear Partial Differential Equations: Analysis and Numerics, Steven G. Johnson
- Julia tutorial for Computational Molecular Biology, Younhun Kim and Matthew Reyna

Other collections of IJulia notebooks:

- Jiahao Chen
- Christoph Ortner
- Crossing Language Barriers with Julia, Scipy, and IPython, presented at EuroSciPy '14 by Steven G. Johnson.

### Haskell

There exists a Haskell kernel for IPython in the IHaskell project.

- IHaskell Demo Notebook
- Homophone reduction, a solution to a cute problem involving treating English letters as generators of a large group.
- Gradient descent typeclass, a look at how arbitrary gradient descent algorithms can be represented with a typeclass.

### OCaml

iocaml is an OCaml kernel for IPython

### Ruby

Similar to the Julia kernel there exists also a Ruby kernel for IPython.

The interactive plotting library Nyaplot has some case studies using IRuby:

### Perl

- An example showcasing full use of the display protocol with the IPerl kernel.

## Miscellaneous topics about doing various things *with* the Notebook itself

Blogging With IPython in Blogger, also available in blog post form, full repo here. By Fernando Perez.

Blogging With IPython in Octopress, by Jake van der Plas and available as a blog post. Other notebooks by Jake contain many more great examples of doing interesting work with the scientific Python stack.

Blogging With IPython in Nikola, also available in blog post form by Damián Avila.

Custom CSS control of the notebook, this is part of a blog repo by Matthias Bussonnier.

IPython display hookery: tools to help display visual output from various sources, a gist by @deeplook.

## Reproducible academic publications

This section contains academic papers that have been published in the peer-reviewed literature or pre-print sites such as the ArXiv that include one or more notebooks that enable (even if only partially) readers to reproduce the results of the publication. If you include a publication here, please link to the journal article as well as providing the nbviewer notebook link (and any other relevant resources associated with the paper).

Reply to 'Influence of cosmic ray variability on the monsoon rainfall and temperature': a false-positive in the field of solar-terrestrial research by Benjamin Laken, 2015. Reviewed article will appear in JASTP. The IPython notebook reproduces the full analysis and figures exactly as they appear in the article, and is available on Github: link via figshare.

The probability of improvement in Fisher's geometric model: a probabilistic approach, by Yoav Ram and Lilach Hadany. (Theoretical Population Biology, 2014). An IPython notebook, allowing figure reproduction, was deposited as a supplementry file.

Stress-induced mutagenesis and complex adaptation, by Yoav Ram and Lilach Hadany (Proceedings B, 2014). An IPython notebook, allowing figures reproduction, was deposited as a supplementry file.

Automatic segmentation of odor maps in the mouse olfactory bulb using regularized non-negative matrix factorization, by J. Soelter et al. (Neuroimage 2014, Open Access). The notebook allows to reproduce most figures from the paper and provides a deeper look at the data. The full code repository is also available.

Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss, by A. Gross et al. (Nature Genetics 2014). The full collection of notebooks to replicate the results.

powerlaw: a Python package for analysis of heavy-tailed distributions, by J. Alstott et al.. Notebook of examples in manuscript, ArXiv link and project repository.

Collaborative cloud-enabled tools allow rapid, reproducible biological insights, by B. Ragan-Kelley et al.. The main notebook, the full collection of related notebooks and the companion site with the Amazon AMI information for reproducing the full paper.

A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data, by C.T. Brown et al.. Full notebook, ArXiv link and project repository.

The kinematics of the Local Group in a cosmological context by J.E. Forero-Romero et al.. The Full notebook and also all the data in a github repo.

Warming Ocean Threatens Sea Life, an article in Scientific American backed by a notebook for its main plot. By Roberto de Almeida from MarinExplore.

Extrapolating Weak Selection in Evolutionary Games, by Wu, García, Hauert and Traulsen. PLOS Comp Bio paper and Figshare link.

[Using neural networks to estimate redshift distributions. An application to CFHTLenS] (http://nbviewer.ipython.org/urls/bitbucket.org/christopher_bonnett/nn_notebook/raw/5e69b55193a229cb2076a2f18e43b45c56e317e0/T-800.ipynb) by Christopher Bonnett paper(submitted to MNRAS)

Mechanisms for stable, robust, and adaptive development of orientation maps in the primary visual cortex by Jean-Luc R. Stevens, Judith S. Law, Jan Antolik, and James A. Bednar. Journal of Neuroscience, 33:15747-15766, 2013. [Notebook1] (https://ioam.github.io/topographica/_static/gcal_notebook.html), Notebook2.

Accelerated Randomized Benchmarking, by Christopher Granade, Christopher Ferrie and D. G. Cory. New Journal of Physics

**17**013042 (2015), arXiv, GitHub repo.Dynamics and associations of microbial community types across the human body, by Tao Ding & Patrick D. Schloss. Notebook replicating results.

Variations in submarine channel sinuosity as a function of latitude and slope, by Sylvester, Z., Pirmez, C., Cantelli, A., & Jobe, Z. R.

Frontoparietal representations of task context support the flexible control of goal directed cognition, by M.L. Waskom, D. Kumaran, A.M. Gordon, J. Rissman, & A.D. Wagner. Github repository | Main notebook

pyparty: Intuitive Particle Processing in Python, Adam Hughes Notebook to Generate the Published Figures | Also, check out the pyparty tutorial notebooks.

Indication of family-specific DNA methylation patterns in developing oysters, Claire E. Olson, Steven B. Roberts doi: http://dx.doi.org/10.1101/012831. Notebook to generate results in the paper.

Parallel Prefix Polymorphism Permits Parallelization, Presentation & Proof, Jiahao Chen and Alan Edelman, HPTCDL'14. Website and notebook

Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in

*SF3B1*-mutated Cancers by Christopher DeBoever et al. There are several notebooks to replicate results and make figures.A Workflow for Characterizing Nanoparticle Monolayers for Biosensors: Machine Learning on Real and Artificial SEM Images, Adam Hughes, Zhaowen Liu, Maryam Raftari, Mark. E Reeves. Notebooks are linked in Table 1 in the text.

AtomPy: An Open Atomic Data Curation Environment for Astrophysical Applications, by C. Mendoza, J. Boswell, D. Ajoku, M. Bautista.

Visualizing 4-Dimensional Asteroids, in Scientific American (by Jake VanderPlas)

Challenges and opportunities in understanding microbial communities with metagenome assembly, accompanied by IPython Notebook tutorial, by Adina Howe and Patrick Chain.

## Data-driven journalism

St. Louis County Segregation Analysis , analysis for the article The Ferguson Area Is Even More Segregated Than You Probably Guessed by Jeremy Singer-Vine.

## Whimsical notebooks

XKCD-styled plots created with Matplotlib. Here is the blog post version with discussion. By Jake van der Plas.

Van Gogh's Starry Night with ipythonblocks, part of Matt Davis' ipythonblocks. This is a teaching tool for use with the IPython notebook that provides visual elements to understand programming concepts.

Conway's Game of Life. Interesting use of convolution operation to calculate the next state of game board, instead of obvious find neighbors and filter the board for next state.

pynguins. Using jupyter notebook, python, and numpy to solve Board Game "Penguins on Ice".

"People plots", stick figures generated with matplotlib.

Reveal converter mini-tutorial, also available in blog post form. Do you want to make static html/css slideshow straight from the IPython notebook? OK, now you can do it with the

*reveal*converter (nbconvert). Demo by Damián Avila.[Personal IPython Weight Notebook] (http://nbviewer.ipython.org/gist/9769238). Plot your loss of weight with prognosis and motivation features.

Porque Charles Xavier debe cambiar a Cerebro por Python, a study in data and gender in the Marvel comics universe, by Mai Giménez and Angela Rivera.

Functional Geometry: a deconstruction of the MC Escher woodcut Square Limit, an IJulia notebook by Shashi Gowda.

## Videos of IPython being used in the wild

Of course the first thing you might try is searching for videos about IPython (1900 or so by last count on Youtube) but there are demonstrations of other applications using the power of IPython but are not mentioned is the descriptions. Below are a few such:

Video on how to learn Python featuring IPython as the platform of choice for learning!

This video shows IPython being used in the scikit-learn project

He doesn't show IPython in use but his IPython sticker is clear for the entire video: Planning and Tending the Garden: The Future of Early Childhood Python Education

Wes McKinney's speech on Python and data analysis features IPython as does his book Python for Data Analysis

This video shows Plotly and IPython in use at a Montreal Python meetup.