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<!DOCTYPE html>
<html class="html">
<head>
<meta http-equiv="Content-type" content="text/html;charset=UTF-8"/>
<meta name="generator" content="7.3.5.244"/>
<title>Programming</title>
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<link rel="stylesheet" type="text/css" href="css/site_global.css?3983832653"/>
<link rel="stylesheet" type="text/css" href="css/master_a-master.css?535769800"/>
<link rel="stylesheet" type="text/css" href="css/programming.css?459688718" id="pagesheet"/>
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<script type="text/javascript">
document.documentElement.className += ' js';
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<body class="museBGSize">
<div class="clearfix" id="page"><!-- column -->
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<div class="clearfix colelem" id="pu430-38"><!-- group -->
<div class="clearfix grpelem" id="u430-38"><!-- content -->
<p id="u430"> </p>
<p id="u430-3">Why I program</p>
<p id="u430-5">Programing has become my most commonly used tool in my research even though I am not trained as a computer scientist. My working tools are R, Python, and Linux. I work in Ubuntu most of the time which makes things easier than working in Windows and more importantly it is free. Although nothing replaces Excel, nothing.</p>
<p id="u430-6"> </p>
<p id="u430-8">Best practices</p>
<p id="u430-13">I have learn about coding best practices through painful experiences and also through reading PLOS Computational Biology and have created these <a class="nonblock" href="https://github.com/MohnLab/Lab_Code_Standards_And_Resources/blob/master/README.md">guidelines</a> (With the help of Lee Bergstrand and Roli Wilhelm). The guideline are based on these three articles:</p>
<p id="u430-14"> </p>
<p id="u430-18">Best Practices for Scientific Computing (<a class="nonblock" href="assets/best-practices-for-scientific-computing.pdf">download)</a></p>
<p id="u430-22">Ten Simple Rules for Reproducible Computational Research <a class="nonblock" href="assets/ten-simple-rules-for-reproducible-computational-research.pdf">(download)</a></p>
<p id="u430-26">Ten Simple Rules for the Open Development of Scientific Software<a class="nonblock" href="assets/ten-simple-rules-for-the-open-development-of-scientific-software.pdf"> (download)</a></p>
<p id="u430-27"> </p>
<p id="u430-29">My codes</p>
<p id="u430-34">The codes I use are freely available in this Github <a class="nonblock" href="https://github.com/carden24">repository</a>.</p>
<p id="u430-35"> </p>
<p id="u430-36"> </p>
</div>
<div class="clearfix grpelem" id="u1497-42"><!-- content -->
<p id="u1497"> </p>
<p id="u1497-6">R is a powerful language and and environment to do statistical analysis and graphical displays. Get it <a class="nonblock" href="http://www.r-project.org/%E2%80%8E">here.</a></p>
<p id="u1497-7"> </p>
<p id="u1497-12">I recommend using Rstudio, which is an alternative graphi user interface (GUI) for R that is more informative and more organized than the native R GUI. Get it <a class="nonblock" href="https://www.rstudio.com/">here</a>.</p>
<p id="u1497-13"> </p>
<p id="u1497-18">If you like visualization you can also try <a class="nonblock" href="http://ggplot2.org/">ggplot2</a>, a plotting system for R that can make easy to produce complex and beautiful graphs.</p>
<p id="u1497-19"> </p>
<p id="u1497-24">For coding in Windows I used Notepad++, a light but powerful plain text editor. It understands the grammar rules for different programming languages and can help you by pointing mistakes in indentation, closing parenthesis, etc. Get it <a class="nonblock" href="http://notepad-plus-plus.org/">here</a></p>
<p id="u1497-25"> </p>
<p id="u1497-29">To learn about basic programming in Unix, and version control go to <a class="nonblock" href="http://software-carpentry.org/index.html"><span id="u1497-27">Software Carpentry</span></a></p>
<p id="u1497-30"> </p>
<p id="u1497-32">Do you want to learn how to do assembly, mapping and all the basic bioinformatics tool? go to:</p>
<p id="u1497-35"><a class="nonblock" href="http://ged.msu.edu/angus/index.html"><span id="u1497-33">Titus Brown tutorial at Michigan State</span></a></p>
<p id="u1497-36"> </p>
<p id="u1497-40">Question in Bioinformatics? Try <a class="nonblock" href="https://www.biostars.org/">Biostar</a></p>
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