<commit_before><commit_msg>test push<commit_after>{"nbformat_minor": 0, "cells": [{"source": "<h1 align=\"center\"> Welcome to `EGRIN 2.0`</h1>\n<br>\n<img src=\"../header-photo.jpg\">", "cell_type": "markdown", "metadata": {}}, {"source": "<br>\nThese documents will introduce you to the `EGRIN 2.0` ensemble and all of its associated tools. \n\nGiven a little bit of your time and patience, you will learn how to:\n\n\n<br>\n\n<div align=\"center\" vertical-align=\"middle\">\n\n    <a style=\"color:black;text-decoration:none;\" title=\"Build\" href=\"./build_docs/build.ipynb\">\n        <img src=\"../css/iconmonstr-puzzle-icon-text.png\" height = \"150\" width = \"150\" style=\"display:inline\">\n    </a>\n    \n    <a style=\"color:black;text-decoration:none;\" title=\"Assemble\" href=\"./assemble_docs/assemble.ipynb\">\n        <img src=\"../css/iconmonstr-puzzle-17-icon-text.png\" height = \"150\" width = \"150\" style=\"display:inline\">\n    </a>\n\n\n    <a style=\"color:black;text-decoration:none;\" title=\"Query\" href=\"./query_docs/query.ipynb\">\n        <img src=\"../css/iconmonstr-flask-3-icon-text.png\" height = \"150\" width = \"150\" style=\"display:inline\">\n    </a>\n</div>\n\n\nan `EGRIN 2.0` ensemble. \n\n<h2> What is an `EGRIN 2.0` ensemble? </h2>\n\n`EGRIN 2.0` ensembles are predictive models of how and when genes are co-regulated in microorganisms. \n\nTo learn more about the underlying biological motivation for this type of model you can [read our paper](http://msb.embopress.org/content/10/7/740.long) or check out [our previous web resource.](http://egrin2.systemsbiology.net/)\n\n<h2> What's different here? </h2>\n\n*Good question.* We wanted to put you back in control. We wanted you to query the models in whatever way is appropriate for your biological question. That's what you can do here.\n\n<h2> System Requirements </h2>\n\n* Developed and tested with Python 2.7.6\n* biopython >= 1.65\n* colorbrewer >= 9172\n* joblib >= 0.7.1\n* matplotlib >= 1.3.1\n* numpy >= 1.8.2\n* pandas >= 0.15.2\n* plotly >= 1.6.6\n* pymongo >= 2.7.2\n* scipy >= 0.13.3\n* statsmodels >= 0.6.1\n\nThese can be installed easily using [pip](http://pip.pypa.io/en/latest/index.html).\n\nIn addition, to run the [ASSEMBLE](./assemble_docs/assemble.ipynb) code you must compile the `C++` code provided in the [src directory](http://github.com/scalefreegan/egrin2-tools/tree/master/src). Instructions for compiling this code are available [here](./assemble_docs/cpp_scripts.ipynb).\n\n<h2> About this wiki </h2>\n\nThis \"*Wiki*\" is an iPython notebook, which means that code, visualizations, and other neat stuff are directly embedded. The documents will teleport you to quick results and predictions or, if you need to go deeper, they will help guide you towards mastery. You can download these files or copy snippets of code, modify them, and run them on your machine to make them do what you want. Think of it as a living template.\n\n*Fancy.* I know.\n\n<h2> Credits </h2>\n\nMost of the tools were developed by [<NAME>](http://www.aaron-brooks.org/) with help from [<NAME>](http://www.systemsbiology.org/David-Reiss), [<NAME>](http://github.com/weiju), and [<NAME>](http://github.com/micheleenharris). \n\nComments and questions can be addressed to [Wei-ju Wu](https://github.com/weiju) or directed to the cMonkey2 [developer](http://groups.google.com/d/forum/cmonkey-dev) or [user](http://groups.google.com/d/forum/cmonkey-users) discussion groups.  \n\nHave fun!\n\n> [<NAME>](http://www.aaron-brooks.org/), Feb 2015", "cell_type": "markdown", "metadata": {}}, {"execution_count": null, "cell_type": "code", "source": "", "outputs": [], "metadata": {"collapsed": true, "trusted": false}}], "nbformat": 4, "metadata": {"kernelspec": {"display_name": "Python 2", "name": "python2", "language": "python"}, "language_info": {"mimetype": "text/x-python", "nbconvert_exporter": "python", "version": "2.7.6", "name": "python", "file_extension": ".py", "pygments_lexer": "ipython2", "codemirror_mode": {"version": 2, "name": "ipython"}}}}
{'fraction_non_alphanumeric': 0.1941508970262964, 'fraction_numerical': 0.024821823543868273, 'mean_word_length': 4.285714285714286, 'pattern_counts': {'":': 31, '<': 35, '<?xml version=': 0, '>': 46, 'https://': 1, 'lorem ipsum': 0, 'www.': 3, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2707551', 'n_tokens_mistral': 1459, 'n_tokens_neox': 1376, 'n_words': 392}