{ "cells": [ { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "
\n", "

Introduction to Jupyter Notebooks

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" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "## Why use Jupyter?" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "subslide" } }, "source": [ "### Bridge the gap between biology and code\n", "\n", "
“We used to speak two different languages. I would talk about the biology and she would talk about coding. Now we have common ground; we can communicate to each other better. This accelerates our research,”
\n", "\n", "* Shen, Helen. \"[Interactive notebooks: Sharing the code.](http://doi.org/10.1038/515151a)\" Nature 515.7525 (2014): 151." ] }, { "cell_type": "markdown", "metadata": { "collapsed": true, "slideshow": { "slide_type": "subslide" } }, "source": [ "### Use your favorite languages\n", "\n", "* [Python](https://www.python.org/)\n", "* [R](https://irkernel.github.io/)\n", "* [MATLAB](http://nbviewer.jupyter.org/github/Calysto/matlab_kernel/blob/master/matlab_kernel.ipynb)\n", "* [Groovy](https://beakerx.com) – scripting on the JVM\n", "* [Many others](https://github.com/jupyter/jupyter/wiki/Jupyter-kernels)" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "subslide" } }, "source": [ "### Run in the cloud, free, reproducible\n", "\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "subslide" } }, "source": [ "### Here to stay\n", "
\n", " \n", "* [JULY 7, 2015 - Project Jupyter gets $6M to expand collaborative data-science software](http://news.berkeley.edu/2015/07/07/jupyter-project/)\n", "" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "subslide" } }, "source": [ "### Any notebook can be a presentation\n", "\n", "[Reveal.js](https://revealjs.com/) is an HTML presentation framework.\n", "\n", "The [RISE extension for Jupyter](https://damianavila.github.io/RISE/) makes any Jupyter notebook into a LIVE reveal.js presentation.\n", "\n", "Like this one! 🤩" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Example notebooks" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "subslide" } }, "source": [ "* The [gallery of interesting Jupyter notebooks](https://github.com/jupyter/jupyter/wiki/A-gallery-of-interesting-Jupyter-Notebooks) spans a broad range of scientific disciplines including Computer Science, Statistics, Machine Learning, Data Science, Mathematics, Physics, Chemistry, Biology, Earth Science and Geo-Spatial, Linguistics and Text Mining, Signal Processing and more.\n", "\n", " In particular, see the [reproducible academic publications](https://github.com/jupyter/jupyter/wiki/A-gallery-of-interesting-Jupyter-Notebooks#reproducible-academic-publications) section." ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "subslide" } }, "source": [ "* The ImageJ Tutorial Notebooks demonstrate how to use ImageJ in a notebook with either the BeakerX Groovy kernel or with the Python 3 kernel.\n", "\n", "
" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "subslide" } }, "source": [ "Finally, ___an awesome walkthrough___ of the Python data analysis pipeline from start to finish:\n", "\n", "* [An example machine learning notebook](https://github.com/rhiever/Data-Analysis-and-Machine-Learning-Projects/blob/master/example-data-science-notebook/Example%20Machine%20Learning%20Notebook.ipynb)" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Added new repo: imagej.public\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "", "version_major": 2, "version_minor": 0 }, "method": "display_data" }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "e35c04e2-9bee-4bc2-a774-aeff8445223e", "version_major": 2, "version_minor": 0 }, "method": "display_data" }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "[INFO] Populating metadata\n", "[INFO] Populating metadata\n" ] }, { "data": { "text/html": [ "" ] }, "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ "%classpath config resolver imagej.public https://maven.imagej.net/content/groups/public\n", "%classpath add mvn net.imagej imagej 2.0.0-rc-71\n", "ij = new net.imagej.ImageJ()\n", "ij.io().open(\"https://imagej.net/images/FluorescentCells.jpg\")" ] } ], "metadata": { "celltoolbar": "Slideshow", "kernelspec": { "display_name": "Groovy", "language": "groovy", "name": "groovy" }, "language_info": { "codemirror_mode": "groovy", "file_extension": ".groovy", "mimetype": "", "name": "Groovy", "nbconverter_exporter": "", "version": "2.4.3" }, "toc": { "base_numbering": 1, "nav_menu": {}, "number_sections": true, "sideBar": true, "skip_h1_title": true, "title_cell": "Table of Contents", "title_sidebar": "Contents", "toc_cell": false, "toc_position": { "height": "calc(100% - 180px)", "left": "10px", "top": "150px", "width": "307px" }, "toc_section_display": true, "toc_window_display": true } }, "nbformat": 4, "nbformat_minor": 1 }