{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# The [scikit-bio](http://scikit-bio.org) cookbook: delicious and nutritious bioinformatics recipes" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "
\n", "\n", "This series of Jupyter Notebooks contains executable \"recipes\" for bioinformatics workflows using [scikit-bio](http://scikit-bio.org).\n", "\n", "Readers interested in gaining more background information on bioinformatics may want to start with [An Introduction to Applied Bioinformatics](http://readiab.org/), which makes extensive use of scikit-bio to teach concepts in bioinformatics.\n", "\n", "**This is not the main scikit-bio documentation.** You can find the latest scikit-bio API documentation [here](http://scikit-bio.org/docs/latest/).\n", "\n", "These notebooks are only tested to work with **scikit-bio 0.5.0**, which **requires Python 3.4 or later**. The notebooks may not work with other versions of scikit-bio. Click [here](http://scikit-bio.org/docs/0.5.0/index.html) to view scikit-bio 0.5.0 API documentation." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Reading the scikit-bio cookbook" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "There are two ways to read the scikit-bio cookbook. \n", "\n", "The **easiest way** is to read the [static online version](http://nbviewer.jupyter.org/github/biocore/scikit-bio-cookbook/blob/master/Index.ipynb).\n", "\n", "The **recommended way** is to install the interactive version and read it locally. This will let you exectute and experiment with the recipes from within your web browser. To view and interact with the notebooks, you'll need Python 3.4 or later, scikit-bio 0.5.0, and the Jupyter Notebook installed.\n", "\n", "The easiest and recommended way to install these dependencies is via the ``conda`` package manager available in [Anaconda](http://continuum.io/downloads) or [miniconda](http://conda.pydata.org/miniconda.html). Once you have ``conda`` installed, create a new environment with the following packages:\n", "\n", " conda create -c https://conda.anaconda.org/biocore -n scikit-bio-cookbook python=3.5 scikit-bio=0.5.0 jupyter requests\n", "\n", "Activate the environment:\n", "\n", " source activate scikit-bio-cookbook\n", " \n", "Install extra (non-conda) dependencies needed for recipes:\n", "\n", " pip install ete3 qiime-default-reference\n", " \n", "Next, you'll need to download the scikit-bio cookbook. We recommend pulling the latest version from GitHub (you may need to install ``git`` first), and then changing to the new directory that is created:\n", "\n", " git clone https://github.com/biocore/scikit-bio-cookbook.git\n", " cd scikit-bio-cookbook\n", "\n", "Finally, start the Jupyter Notebook server:\n", "\n", " jupyter notebook Index.ipynb" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "data": { "text/html": [ "

Table of Contents

\n", "

  • Alignment viewing and filtering
    • \n", "
  • Alignments and phylogenetic reconstruction
    • \n", "
  • Computing pairwise sequence identity
    • \n", "
  • Creating a region-specific reference collection from full-length reference sequences
    • \n", "
  • Exploring microbial community diversity
    • \n", "
  • Finding PCR primers in sequencing products
    • \n", "
  • Finding the longest stretch of specific characters in a DNA sequence
    • \n", "
  • Phylogenetic diversity calculations
    • \n", "
  • Progressive multiple sequence alignment
    • \n", "
  • Reading and writing files
    • \n", "
  • Six-frame translation of nucleotide sequences
    • \n", "
  • Using the workflow to automate remote database queries
    • " ], "text/plain": [ "" ] }, "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Ignore this code, it is necessary to display the table of contents below.\n", "from skbiocookbook import cookbook_toc\n", "from IPython.display import HTML\n", "HTML(cookbook_toc())" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.5.1" } }, "nbformat": 4, "nbformat_minor": 0 }