TNBGGA: The No Bullshit Guide to Genetic Analysis

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start [2024/09/01 22:12] – mikestart [2024/09/16 15:32] (current) – mike
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-If you don't care about any of this stuff, go to the [[Table_of_Contents|TNBGGA Table of Contents]] to get started. +If you don't care about any of this stuff, click on any of the links in the Sidebar to the left to get started. 
  
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-The **No Bullshit Guide to Genetic Analysis** (**TNBGGA**) was developed from a genetics course taught at [[http://csusb.edu|California State University San Bernardino]] in Fall 2020, at the height of the COVID-19 pandemic. The pandemic presented challenges to people of all walks of life. In education, the pandemic highlighted inequities in educational opportunities and access to educational resources. Educators across the world scrambled to adapt and rise to the challenge. One of the challenges was finding textbooks that were readily available and accessible to students that were stuck at home. I utilized [[https://ocw.mit.edu|OpenCourseWare]] [[https://ocw.mit.edu/courses/7-03-genetics-fall-2004/|Genetics 7.03]] course notes from the [[https://mit.edu|Massachusetts Institute of Technology]]. In addition to these notes being high quality and freely available, I found that I identified strongly with the ethos of information wanting (and needing) to be Free (Free as in freedom ("//libre//"), as well as free as in beer ("//gratis//"). The "No Bullshit" part of the title is not referring to the perceived quality of the work, but rather the lack of university bookstore and textbook publisher shenanigans. +The **No Bullshit Guide to Genetic Analysis** (**TNBGGA**) was developed from a genetics course taught at [[http://csusb.edu|California State University San Bernardino]] in Fall 2020, at the height of the COVID-19 pandemic. The pandemic presented challenges to people of all walks of life. In education, the pandemic highlighted inequities in educational opportunities and access to educational resources. Educators across the world scrambled to adapt and rise to the challenge. One of the challenges was finding textbooks that were readily available and accessible to students that were stuck at home. I utilized [[https://ocw.mit.edu|OpenCourseWare]] [[https://ocw.mit.edu/courses/7-03-genetics-fall-2004/|Genetics 7.03]] course notes from the [[https://mit.edu|Massachusetts Institute of Technology]]. In addition to these notes being high quality and freely available, I found that I identified strongly with the ethos of information wanting (and needing) to be Free (Free as in freedom ("//libre//"), as well as free as in beer ("//gratis//"). The notes did need a substantial remix to use as an actual "textbook" of sorts, and this was the genesis of this project. The "No Bullshit" part of the title is not referring to the perceived quality of the work, but rather the lack of university bookstore and textbook publisher shenanigans. 
  
 As a substantial remix of the original OpenCourseWare notes, this book is also bound by the Creative Commons licensing agreement that ensures it too will remain Free to future users. I find myself not just in compliance with the letter of the law, but also fully in compliance with the spirit of the law.  As a substantial remix of the original OpenCourseWare notes, this book is also bound by the Creative Commons licensing agreement that ensures it too will remain Free to future users. I find myself not just in compliance with the letter of the law, but also fully in compliance with the spirit of the law. 
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   * Conversion to fully online using [[https://dokuwiki.org|Dokuwiki]] - print version will be depreciated.    * Conversion to fully online using [[https://dokuwiki.org|Dokuwiki]] - print version will be depreciated. 
   * Minor rewrites for clarity and internal consistency.    * Minor rewrites for clarity and internal consistency. 
-  * Converting to using $\LaTeX$ instead of MathML from Microsoft Equation Editor for various equations and pseudo-equations. +  * Converting to using $\LaTeX$ formatting (via [[https://mathjax.org|MathJax]]) instead of MathML from Microsoft Equation Editor for various equations and pseudo-equations. I should have learned $\LaTeX$ years ago; MathML sucks. 
   * Added a glossary.   * Added a glossary.
 +  * Added Part 4 on population genetics (in progress). 
  
 Some general differences between ver. 1.x and the original OpenCourseWare notes include: Some general differences between ver. 1.x and the original OpenCourseWare notes include:
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   * Most content has been remixed and edited for readability in book form, rather than as a collection of notes. For instance, more context has been added for some topics. Also, notes from some lectures have been merged into a single chapter.    * Most content has been remixed and edited for readability in book form, rather than as a collection of notes. For instance, more context has been added for some topics. Also, notes from some lectures have been merged into a single chapter. 
   * Some figures were redrawn for more clarity, developed from scratch, or replaced with images that have public %%domain%% or Creative Commons licensing. In rare instances, images were used with non-Free licensing agreements that stipulated free use for educational purposes.   * Some figures were redrawn for more clarity, developed from scratch, or replaced with images that have public %%domain%% or Creative Commons licensing. In rare instances, images were used with non-Free licensing agreements that stipulated free use for educational purposes.
-  * As the original OpenCourseWare notes were from 2004, some of the content has been updated.  +  * As the original OpenCourseWare notes were from 2004, some of the content has been updated (e.g., %%NGS%% technologies).  
-  * The new content that I contributed includes various Exercises and Discussion Boxes in the chapters. Chapters 1 and 17 are also new content, and Appendix A is compiled from my own lecture notes. +  * The new content that I contributed includes various Exercises and Discussion Boxes in the chapters. Chapters 1 and 17 are also completely new content, and Appendix A is compiled from my own lecture notes. 
  
 TNBGGA reflects my own personal interests and biases, as well as those of the original authors of the OpenCourseWare notes at MIT. As I was trained as an experimental biologist on model genetic organisms, I do not include any chapters on population genetics - this is a shortcoming, and I invite those knowledgeable in this area to add chapters on population genetics, either using the original OpenCourseWare notes (they have a lecture on pop-gen!) or contribute original content. TNBGGA reflects my own personal interests and biases, as well as those of the original authors of the OpenCourseWare notes at MIT. As I was trained as an experimental biologist on model genetic organisms, I do not include any chapters on population genetics - this is a shortcoming, and I invite those knowledgeable in this area to add chapters on population genetics, either using the original OpenCourseWare notes (they have a lecture on pop-gen!) or contribute original content.
  
-Mike Chao ([[mailto:mchao@csusb.edu|mchao@csusb.edu]])\\ +Mike Chao\\ 
-[[https://csusb.edi/biology|CSUSB Dept. of Biology]]+[[mailto:mchao@csusb.edu|mchao@csusb.edu]]\\ 
 +[[https://csusb.edu|California State University San Bernardino]]\\ 
 +[[https://csusb.edi/biology|Dept. of Biology]]
  
start.1725253961.txt.gz · Last modified: 2024/09/01 22:12 by mike