Lectures on Informatics: An Introduction to Computers and Informatics in the Health Sciences

This lecture series will provide a practical introduction to computers, critical concepts in computing, and their application to informatics problems in the health sciences arena. My goal is for you to walk away from these sessions with a much deeper understanding of the internal workings of computers armed with an array of practical knowledge that you can apply to your everyday interactions with computer systems. I also intend for this material to lay the foundations necessary for entry into more detailed study on specialized computational topics such as DNA sequence analysis, genomics, and bioinformatics.

Directed by

Christopher Taylor, PhD
Associate Professor of Microbiology, Immunology, and Parasitology
Director of Bioinformatics, Biostatistics, and Computational Biology Core
Louisiana State University Health Sciences Center, New Orleans

Lecture 1: Introduction, Logistics and Philosophy: A Practical Approach

February 23, 2016

The first lecture will provide an introduction to the goals of this lecture series, what to expect, the logistics of participating in the lectures, and an explanation of the philosophy underlying my approach to teaching informatics.

Lecture 2: Basic Computer Architecture I: Bits, Bytes and Busses

March 1, 2016

We will provide an overview of the critical components of a computer system, hardware organization, operating systems concepts, the structure of data, data storage technologies, data caching, and data transit.

Lecture 3: Data Wrangling with Atom I: Basic Data Manipulation

March 8, 2016

We will introduce the free Atom advanced text editor. This is a powerful text editor that allows you to perform complex data manipulations easily and will become an essential tool for your data wrangling needs.

Lecture 4: Basic Computer Architecture II: Programming, Processes and Networking

March 15, 2016

This lecture will provide an overview of software architecture, computer programs, computer networks, network interconnects, network protocols, computer processes, and multiprogramming.

Lecture 5: The Markdown Language: Learning Markdown in Atom

March 22, 2016

Markdown provides an easy and intuitive way to organize your notes and is supported in many web forms for advanced text formatting. We will introduce the markdown language and provide tips and tricks for better note taking and documentation.

Lecture 6: Data Wrangling with Atom II: Advanced Data Manipulation

March 29, 2016

We will cover regular expressions using find and replace, complex data manipulations using advance selection features of Atom, and advance navigation features that will enhance and streamline your data wrangling.

Lecture 7: Keyboard Shortcuts: Giving Your Mouse a Vacation

April 5, 2016

The less you touch your mouse, the more productive you can be. Often times reaching for the mouse can break the flow of your work and learning useful keyboard shortcuts can allow you to enhance your productivity at the computer. We will cover a variety of keyboard shortcuts with tips and trick that allow you to perform common interface operations with the press of a few keys. We will primarily focus on operating system shortcuts that can be used while interacting with any program (or switching between programs) but will also cover several useful tricks within specific programs you may commonly use.

Lecture 8: Sequencing Intro: Common File Formats and Visualization Software

April 12, 2016

We will introduce common sequencing file formats including fasta, fastq, bed, sam and bam along with ways to interact with, visualize and manipulate sequencing data using a free genome browser. We will also discuss integrating publicly available data sets into visualization of your own sequencing data.

Lecture 9: Sequencing Application I: Sequencing of Microbiome Data

April 19, 2016

We will introduce 16S rDNA amplicon sequencing as a technique to assess the composition of bacteria in an environmental or clinical sample. The theory and practice behind this technique will be discussed and we will investigate an example dataset.

Lecture 10: Sequencing Application II: Analysis of Microbiome Data

April 26, 2016

We will introduce free and open source computing tools such as UPARSE and QIIME that can be used to perform the stages of analysis of microbiome data continuing the analysis of our example dataset.

Lecture 11: Sequencing Application III: Visualization of Microbiome Data

May 3, 2016

We will cover visualization of microbiome data using QIIME and other free tools to further explore our example data set.

Lecture 12: Sequencing Application IV: Discussion of Metagenomic Methods

May 10, 2016

Alternative methods to microbial community assessment such as metagenomic sequencing will be discussed along with benefits and drawbacks to employment of such techniques.


Google Groups Forum

You can join the Google Groups Forum to post any questions or comments you may have about the lecture series.

  • Christopher Taylor, PhD