Fall 2021 Semester

All Short Courses will be taught online via Zoom.


Training in computational and bioinformatics approaches to biological problems is an important part of the CBRS mission. Each semester, we offer a variety of short courses in diverse topics for learning computational approaches to solving biological problems. Courses are $50.00. All meet for one day, lasting between three to four hours per course.

Fall 2021 Semester Courses

IMPORTANT REGISTRATION NOTICE: If you are registering on behalf of someone else, PLEASE DO NOT use your name, contact information, or EID at any point in the process. You MUST use the information as it pertains to the student, or they will not be included on the course roster properly and could miss out on crucial course communication. Ask that the student you are registering email you the receipt when they receive it via their email.

Introduction to Unix (THIS COURSE IS CLOSED)

Date
Wednesday, September 29, 2021
Time
10:00 am - 1:00 pm
Location
ONLINE via Zoom
Instructor
Benni Goetz (Bioinformatics Consultant, CBRS)
Cost
$50

Learn the basics of using UNIX from the command line. Introductory topics include the filesystem, the shell, and text files. The course will touch on manipulating text files using standard UNIX utilities, how to string utilities together, and how to output the results to files. The goal of the course is to develop some basic comfort at the command line, get a sense of what’s possible, and learn how to find help.

ABOUT THE INSTRUCTOR: Benni is a Bioinformatics Consultant in the Center for Biomedical Research Support. Python, Bash, and huge computing clusters are some of his favorite things. In a previous life Benni studied pure math, differential geometry in particular.

If using a UT Procard, read this disclaimer.

Back to top

Introduction to TACC (THIS COURSE IS CLOSED)

Date
Wednesday, October 06, 2021
Time
10:00 am - 1:00 pm
Location
ONLINE via Zoom
Instructor
Benni Goetz (Bioinformatics Consultant, CBRS)
Cost
$50

Students in the course will learn what a cluster is and how to use the world-class clusters available at the Texas Advanced Computing Center (TACC). The course will discuss the basic architecture of TACC’s high-performance computing facilities, and how they compare to a regular computer. It will touch on job launchers and job scheduling, and how to submit your own jobs to TACC. Custom tools by the Bioinformatics Consulting Group for job submission will be emphasized. Students will be required to establish a TACC account and can do so by visiting this link.

ABOUT THE INSTRUCTOR: Benni is a Bioinformatics Consultant in the Center for Biomedical Research Support. Python, Bash, and huge computing clusters are some of his favorite things. In a previous life Benni studied pure math, differential geometry in particular.

If using a UT Procard, read this disclaimer.

Back to top

Introduction to Next Generation Sequencing (THIS COURSE IS CLOSED)

Date
Wednesday, October 13, 2021
Time
9:00 am - 1:00 pm
Location
ONLINE via Zoom
Instructor
Anna Battenhouse
Cost
$50

This course provides a high-level introduction to concepts and best practices for next generation sequencing analysis (NGS). Participants will gain familiarity with NGS vocabulary and file formats as well as popular tools commonly used in early processing. We will touch on the main skills and resources you need to get started, and hope this course will help you better understand what it takes to bridge the bench-scientist to bioinformatician divide.

ABOUT THE INSTRUCTOR: Anna Battenhouse is a research scientist in the labs of Drs. Edward Marcotte and Vishy Iyer, is a Bioinformatics Consultant, and leads the Biomedical Research Support Facility in its mission to support the IT and computational needs of the UT Austin biomedical research community. She has extensive experience working with NGS data, and teaches the Introduction to NGS Tools course in the Big Data in Biology Summer School as well as several CBRS short courses.

If using a UT Procard, read this disclaimer.

Back to top

Introduction to RNA-Seq (THIS COURSE IS CLOSED)

Date
Wednesday, October 20, 2021
Time
9:00 am - 12:00 pm
Location
ONLINE via Zoom
Instructor
Dhivya Arasappan
Cost
$50

This is a theory course that will introduce some basics (both in experimental design and bioinformatics) that need to be considered when doing an RNA-Seq experiment. We will discuss library prep options, quality assessment, and bioinformatics analysis pipelines. We will also talk about analysis of single-cell and 3′ targeted RNA-Seq data. This course is designed to give you an idea of the options that are available when designing an RNA-Seq study or analyzing an RNA-Seq data set.

ABOUT THE INSTRUCTOR: Dhivya Arasappan has 11 years experience analyzing NGS data from multiple platforms: Illumina, PacBio and SOLiD. Her areas of expertise include: de novo genome assembly, particularly using hybrid sequencing data, RNA-Seq analysis, exome analysis, and benchmarking of bioinformatics tools. She is the research educator for the Big Data in Biology Freshman Research Initiative stream and teaches an RNA-Seq course as part of the Summer School for Big Data in Biology.

If using a UT Procard, read this disclaimer.

Back to top

Advanced Bash Scripting (THIS COURSE IS CLOSED)

Date
Wednesday, October 27, 2021
Time
9:00 am - 1:00 pm
Location
ONLINE via Zoom
Instructor
Anna Battenhouse
Cost
$50

This course will cover advanced topics in writing Bash shell scripts, providing tips, examples and best practices for creating robust “pipeline scripts” that execute multiple processing steps. Topics include defining functions, argument processing and defaulting, error checking, effective use of awk, grep and sed, as well as subtleties of UNIX stream and text manipulation.

PREREQUISITE: This is not an introductory course. Students must be comfortable performing basic tasks on the Linux command line. Suggested minimum background is completion of the “Intro to UNIX Command Line” short course and/or substantial command-line experience. Students can use their own laptops to access coding examples in a shared computing environment (Windows users should install an SSH client such as Putty).

ABOUT THE INSTRUCTOR: Anna Battenhouse is a research scientist in the lab of Dr. Edward Marcotte as well as leading the Biomedical Research Support Facility in its mission to support the IT and computational needs of the UT Austin biological sciences community. She has extensive experience writing pipeline scripts to process Next Generation Sequencing data and perform other functions.

If using a UT Procard, read this disclaimer.

Back to top

Introduction to R (THIS COURSE IS CLOSED)

Date
Wednesday, November 03, 2021
Time
9:00 am - 12:00 pm
Location
ONLINE via Zoom
Instructor
Rachael Cox
Cost
$50

This course will introduce the fundamentals of programming in R. Will touch on base R and R Markdown, but will mostly focus on the Tidyverse ecosystem. Topics include data types, functions, coding etiquette, reading/writing files and basic data manipulation. This course is designed for students with little to no programming experience (prior installation of R is not required). The goal of this course is to get comfortable working in an R environment.

ABOUT THE INSTRUCTOR: Rachael Cox is a PhD candidate in the Biochemistry PhD program. Previously, Rachael obtained a BS in Chemistry (Texas A&M, 2013) and spent several years designing and building continuous reaction systems at Eastman Chemical Company. Since then, she’s decided big molecules are much more interesting than small molecules, and now studies the evolution of protein complexes in Dr. Edward Marcotte’s lab. Rachael frequently works with multi-omics datasets using Bash, Python, and R.

If using a UT Procard, read this disclaimer.

Back to top

Introduction to Python (THIS COURSE IS CLOSED)

Date
Thursday, November 04, 2021
Time
10:00 am - 1:00 pm
Location
ONLINE via Zoom
Instructor
Benni Goetz (Bioinformatics Consultant, CBRS)
Cost
$50

Python is a simple and popular programming language that can be used across platforms, and is useful for a wide variety of tasks.

This short course is a basic introduction to scripting using Python. Skills taught will include data structures, loops, conditional statements, function definitions, and if time permits, file input and output. These tools will be useful for researchers in many fields for data management, automating tedious computational tasks, and handling “big data.” This course is taught at an introductory level and is appropriate for students with no programming experience, but will contain material and techniques helpful to moderately experienced programmers new to Python.

ABOUT THE INSTRUCTOR: Benni is a Bioinformatics Consultant in the Center for Biomedical Research Support. Python, Bash, and huge computing clusters are some of his favorite things. In a previous life Benni studied pure math, differential geometry in particular.

If using a UT Procard, read this disclaimer.

Back to top

Data Visualization Using R (THIS COURSE IS CLOSED)

Date
Wednesday, November 10, 2021
Time
9:00 am - 12:00 pm
Location
ONLINE via Zoom
Instructor
Dennis Wylie
Cost
$50

This course introduces both principles and practice of scientific data visualization, especially as applied to large multivariate data sets. Will cover common methods of visually summarizing data and illustrating relationships between variables of various common types (continuous, categorical, etc.) as well as design concepts for increasing the clarity of quantitative graphical communication. Will introduce modern “grammar of graphics” ideas as foundation for thinking about, relating, and ultimately building new types of informative plots. Implementations of covered methods in R will be presented. Students should bring their own laptops to the course with R and the associated packages dplyr, ggplot2 and pheatmap installed.

PREREQUISITE: Some prior knowledge of R is required to get the most out of this class. The “Introduction to R” class would be useful for those not already comfortable with R programming prior to this course.

ABOUT THE INSTRUCTOR: Dennis Wylie joined the Bioinformatics group in 2015. He has experience in NGS data analysis including variant calling and RNA-Seq-based biomarker discovery and predictive modeling (classification, regression, etc.). Prior to UT, he earned a PhD in Biophysics from UC Berkeley applying stochastic simulation methods to problems in immunology, did postdoctoral work modeling the transmission of infectious disease, and spent six years as a bioinformatician in industry.

If using a UT Procard, read this disclaimer.

Back to top

Intermediate Python (THIS COURSE IS CLOSED)

Date
Thursday, November 11, 2021
Time
10:00 am - 1:00 pm
Location
ONLINE via Zoom
Instructor
Benni Goetz (Bioinformatics Consultant, CBRS)
Cost
$50

This domain non-specific course is designed for Python programmers who have basic experience with the language. Learners are expected to be familiar with control flow and basic Python data structures (variable assignment, lists, dictionaries). This course will cover the knowledge to make code modular, readable and reproducible. A major focus will be object-oriented programming and Python’s implementation of the object-oriented paradigm.

ABOUT THE INSTRUCTOR: Benni is a Bioinformatics Consultant in the Center for Biomedical Research Support. Python, Bash, and huge computing clusters are some of his favorite things. In a previous life Benni studied pure math, differential geometry in particular.

If using a UT Procard, read this disclaimer.

Back to top

If you use the UT ProCard for payment of courses, please be aware that you can only charge ONCE per 24 hour period. Any attempts to charge more courses will fail, and you will not be registered.

For example, you may add one to many courses for one student into your shopping cart at any one time, and charge them to the ProCard, and you should receive a "registration successful!" page at the end. This is because you registered ONCE for ONE student. If you attempt to register and pay again, for example, for a different student, this will trigger the UT ProCard security system to stop payment, and your registration will not be successful. A page stating this fact will occur after you attempt to process payment. It looks a lot like the "registration was successful" page.

Ways to avoid this are: use the ProCard after 24 hours have passed, or the student may use their credit card and be reimbursed later through the usual UT accounting methods, or process the registration with an IDT, otherwise known as an Interdepartmental Transfer (talk to someone in your department that handles the accounts).