Fall 2020 Semester

All Short Courses will be going online via Zoom in an effort to address social distancing. Instructors will be in contact with their students for further instructions. No further registrations will be permitted less than 24 hours before course begins.


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 2020 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 30, 2020
Time
10:00 am - 1:00 pm
Location
ONLINE via Zoom
Instructor
Benni Goetz (Bioinformatics Consultant, CBRS)
Cost
$50.00

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.

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Introduction to TACC (THIS COURSE IS CLOSED)

Date
Wednesday, October 07, 2020
Time
10:00 am - 1:00 pm
Location
ONLINE via Zoom
Instructor
Benni Goetz (Bioinformatics Consultant, CBRS)
Cost
$50.00

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 the Lonestar 5 and Stampede 2 computing clusters, 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.

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Introduction to Next Generation Sequencing (THIS COURSE IS CLOSED)

Date
Wednesday, October 14, 2020
Time
9:00 am - 1:00 pm
Location
ONLINE via Zoom
Instructor
Anna Battenhouse (Bioinformatics Consultant, CBRS)
Cost
$50.00

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.

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Introduction to RNA-Seq (THIS COURSE IS CLOSED)

Date
Wednesday, October 21, 2020
Time
9:00 am - 12:00 pm
Location
ONLINE via Zoom
Instructor
Dhivya Arasappan (Bioinformatics Consultant, CBRS)
Cost
$50.00

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.

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Introduction to ChIP-Seq (THIS COURSE IS CLOSED)

Date
Friday, November 06, 2020
Time
9:00 am - 1:00 pm
Location
ONLINE via Zoom
Instructor
Anna Battenhouse (Bioinformatics Consultant, CBRS)
Cost
$50.00

This is an introductory theory course on considerations for performing and analyzing ChIP-seq experiments, focusing on best practices based on the Iyer lab’s extensive experience in this field. We will discuss experimental design, library prep options, quality assessment, peak calling, and the many issues involved in properly analyzing ChIP-seq data. This course is designed to give you an idea of what options are available when designing, sequencing and interpreting results from a ChIP-seq experiment.

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.

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Data Visualization (THIS COURSE IS CLOSED)

Date
Wednesday, November 11, 2020
Time
9:00 am - 12:00 pm
Location
ONLINE via Zoom
Instructor
Dennis Wylie (Bioinformatics Consultant, CBRS)
Cost
$50.00

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 both R and python will be presented. Students should bring their own laptops to the course. Installation of either R (with ggplot2 and pheatmap) or Python (with matplotlib, seaborn, plotline, and pandas).

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.

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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).