Julin Maloof
Lecture 01
Instructor: Julin Maloof jnmaloof@ucdavis.edu
Teaching Assistant: Matt Davis mtdavis@ucdavis.edu
The goal of this course is to introduce you to the tools and thinking required for bioinformatics analysis.
This is a computer-based class. No bench work.
At the end of this course you should be able to:
“Every student deserves the opportunity to learn computer programming. Coding can unlock creativity and open doors for an entire generation of American students. We need more coders — not just in the tech industry, but in every industry.” – Mark Pincus, CEO and Founder, Zynga
“Coding is engaging and empowering. It’s a necessary 21st Century skill.” – Jan Cuny, Program Officer, National Science Foundation
“Code has become the 4th literacy. Everyone needs to know how our digital world works, not just engineers.” – Mark Surman, Executive Director, The Mozilla Foundation
“If you can program a computer, you can achieve your dreams. A computer doesn’t care about your family background, your gender, just that you know how to code. But we’re only teaching it in a small handful of schools, why?” – Dick Costolo, Former CEO, Twitter
Secrets for success:
Developing code is an interactive process. Both your friends and the web can be excellent resources.
However Any direct copying of text or code from any person (in this class or on the web, etc) is considered plagiarism in the context of this course.
If you receive inspiration or ideas from an external source give attribution
Main website: http://jnmaloof.github.io/BIS180L_web/
Canvas
Author: Vince Buffalo
This is an excellent book that covers much of the material that is covered in lab.
You can use this to help with ideas that are not clear from class, or for more in depth coverage of the material.
I particularly recommend reading it in depth for anyone planning to build on the skills learned in this class.
It is available online for free, through UCD library. See links on course website.
Authors: Hadley Wickham and Garrett Grolemund
This is another excellent book that more generally covers data manipulation and analysis in R.
The author, Hadley Wickham, has built some very nice additions to R that we will make use of in this class.
Available online for free
Image by Ruben Alexander, CC BY 2.0 license.
Quick demo of VNC and SSH
As detailed in the lab notes for today:
Markdown is a text-based formatting system for quickly and easily generating nicely formatted output.
This presentation as well as the entire BIS180L website was written in markdown.
It helps achieve three guiding principles:
What is we want to produce this:
The markdown file that generates it is
What is we want to produce this:
The word file that generates it is
We will work through a tutorial developed by Ian Korf.
You are learning a new language; treat it as such.
command [options] [file-path]
Slack is our main tool for communication (other than lecture and one-on-one lab time).
There are two UC Davis Slack channels that I have added you to: