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FNT 1.104

Introduction to TACC

Member for

2 years 10 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This course provides a gentle introduction to the many resources available at TACC - the Texas Advanced Computing Center. Topics include account setup, requesting an allocation, TACC’s different compute and storage clusters, file system structures and protocols, how to find available software, and working with the TACC batch system. We focus on typical bioinformatics workflow patterns, which are different from those of standard High Performance Computing (HPC), and we provide some useful scripts for bioinformatics analysis support.

Prerequisites:
There are no prerequisites for taking this course.

CB27011
Instructor

Anna Battenhouse (Bioinformatics Consultant and Biomedical Research Computing Facility Director)

Anna Battenhouse is a research scientist in the lab of Dr. Edward Marcotte, is a Bioinformatics Consultant, and leads the Biomedical Research Computing Facility in its mission to support the computational needs of the UT Austin biomedical research community. She has extensive experience working with NGS data, develops and maintains analysis scripts for the Bioinformatics Consulting Group, and teaches the Introduction to NGS Tools course in the Big Data in Biology Summer School as well as several other CBRS short courses.

Status
Open
Location
Modality
Hybrid (In-person or Zoom)
Course Closes
Wed, Nov 11
Procard Disclaimer

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).

Course Semester
Fall 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Wed, Nov 18
Start Date
9:30 am - 12:30 pm

$50

Data Visualization Using R

Member for

2 years 10 months
Full name
Gary Chiang
Submitted by Gary Chiang on

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.

Prerequisites:
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.

CB27010
Instructor

Dennis Wylie (Co-Director, Bioinformatics Consulting Group, CBRS)

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.

Status
Open
Location
Modality
Hybrid, but in-person encouraged
Course Closes
Wed, Nov 11
Procard Disclaimer

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).

Course Semester
Fall 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Fri, Nov 13
Start Date
9:30 am - 12:30 pm

$50

Introduction to R

Member for

2 years 10 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This course will introduce the fundamentals of programming in R. The basic syntax and internal logic of working in R will be covered, with some coverage of Tidyverse tools, if time permits. Topics will include data types, functions, coding style, 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 with R in RStudio.

Prerequisites:
Students must bring their own laptop with an ability to connect to the UT WiFi network. No prior knowledge of R programming is required.

CB27009
Instructor

Matt Bramble (Bioinformatician, Bioinformatics Consulting Group, CBRS)

Matt Bramble has recently joined the CBRS team after six years at MD Anderson Cancer Center analyzing a wide range of NGS data in epigenomics. His areas of expertise include: Hi-C (chromatin conformation) analysis, mouse somatic variant analysis, and single cell RNAseq analysis. He has 10 years of experience with R and Python, and Master’s degrees from UT in Molecular Biology and Statistics.

Status
Open
Location
Modality
Hybrid, but in-person encouraged
Course Closes
Wed, Nov 04
Procard Disclaimer

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).

Course Semester
Fall 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Wed, Nov 11
Start Date
9:30 am - 12:30 pm

$50

Overview of the Biological Mass Spectrometry Facility

Member for

2 years 10 months
Full name
Gary Chiang
Submitted by Gary Chiang on

The class will be an overview of the Biological Mass Spectrometry Facility covering staff, equipment, services, and collaborative opportunities. Recent acquisitions, new services and opportunities for proteomics and metabolomics experiments will be highlighted.

Prerequisites:
There are no prerequisites for taking this course.

CB27008
Instructor

Maria Person (Facility Director)

Maria Person obtained her Ph.D. in molecular dynamics. She has been working in the field of biological mass spectrometry since 2000, specializing in proteomics and antibody sequencing. She has been the director of the facility since 2003.

Status
Open
Location
Modality
Hybrid (In-person or Zoom)
Course Closes
Wed, Oct 28
Procard Disclaimer

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).

Course Semester
Fall 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Wed, Nov 04
Start Date
10:00 am - 11:00 am

Free

Introduction to RNA seq

Member for

2 years 10 months
Full name
Gary Chiang
Submitted by Gary Chiang on

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.

Prerequisites:
There are no prerequisites for taking this course.

CB27007
Instructor

Dhivya Arasappan (Co-Director, Bioinformatics Consulting Group, CBRS)

Dhivya Arasappan has 15 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.

Status
Open
Location
Modality
Hybrid (In-person or Zoom)
Course Closes
Wed, Oct 14
Procard Disclaimer

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).

Course Semester
Fall 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Wed, Oct 21
Start Date
9:30 am - 12:30 pm

$50

Improving Rigor and Reproducibility in Mouse Research

Member for

2 years 10 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This class covers best practices for maintaining mouse colonies to promote rigor and reproducibility in experimental research. It is intended for lab staff, graduate students, postdocs, and undergraduates working on mouse projects.

The topics to be covered include:

  • Importance of genetic background
  • Reproduction, breeding, and genotyping
  • Sizing mouse colonies
  • Recordkeeping
  • Genetic drift
  • Tips
  • Resources

Preferred or Prerequisite Skills:
No prerequisites, although an understanding of basic genetics is presumed.

CB27006
Instructor

William Shawlot (Director, Mouse Genetic Engineering Facility, CBRS)

William Shawlot received his Ph.D. from Baylor College of Medicine and completed his postdoctoral training with Richard Behringer at the M.D. Anderson Cancer Center. He served as an Assistant Professor in the Department of Genetics, Cell Biology, and Development at the University of Minnesota before joining the Texas A&M Institute for Genomic Medicine (TIGM). He led TIGM’s knockout mouse production efforts as part of the International Knockout Mouse Consortium program. He has more than 30 years of experience in the transgenic mouse field and serves on the External Advisory Committee for the NIH’s Mutant Mouse Resource and Research Center program.

Status
Open
Location
Modality
In-person
Course Closes
Wed, Oct 21
Procard Disclaimer

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).

Course Semester
Fall 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Wed, Oct 28
Start Date
9:30 am - 12:30 pm

$10

Introduction to Next Generation Sequencing

Member for

2 years 10 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This course provides a high-level introduction to concepts and best practices for Next Generation Sequencing (NGS) analysis. 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 aim to help you better understand what it takes to bridge the bench-scientist-to-bioinformatician divide.

Preferred or Prerequisite Skills:
Basic familiarity with DNA and RNA.

CB27005
Instructor

Anna Battenhouse (Bioinformatics Consultant and Biomedical Research Computing Facility Director)

Anna Battenhouse is a research scientist in the lab of Dr. Edward Marcotte, is a Bioinformatics Consultant, and leads the Biomedical Research Computing Facility in its mission to support the computational needs of the UT Austin biomedical research community. She has extensive experience working with NGS data, develops and maintains analysis scripts for the Bioinformatics Consulting Group, and teaches the Introduction to NGS Tools course in the Big Data in Biology Summer School as well as several other CBRS short courses.

Status
Open
Location
Modality
Hybrid (In-person or Zoom)
Course Closes
Wed, Oct 07
Procard Disclaimer

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).

Course Semester
Fall 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Wed, Oct 14
Start Date
9:00 am - 1:00 pm

$50

Python for Machine Learning/AI

Member for

2 years 10 months
Full name
Gary Chiang
Submitted by Gary Chiang on

Building further on the concepts covered in the Introduction, Intermediate, and Data Science Python courses, we will introduce Python as a tool for training and testing machine learning (ML) models with a particular focus on deep learning approaches. Specific topics will include an introduction to the PyTorch software library and a brief survey of some of the basic model architectures which it implements. Some prior familiarity with the basic ideas of ML (underfitting vs. overfitting, use of training and test data sets, etc.) and/or linear algebra will be helpful for getting the most out of this course.

Prerequisites:
There are no prerequisites for taking this course.

CB27004
Instructor

Dennis Wylie (Co-Director, Bioinformatics Consulting Group, CBRS)

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.

Status
Open
Location
Modality
Hybrid (In-person or Zoom)
Course Closes
Wed, Oct 21
Procard Disclaimer

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).

Course Semester
Fall 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Fri, Oct 23
Start Date
9:30 am - 12:30 pm

$50

Python for Data Science

Member for

2 years 10 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This course will build up on the concepts covered in the Introduction to Python and Intermediate Python courses. We will introduce the use of Pandas Data frames to read in, subset, analyze and visualize RNA-Seq gene expression data.

Prerequisites:
There are no prerequisites for taking this course.

CB27003
Instructor

Dhivya Arasappan (Co-Director, Bioinformatics Consulting Group, CBRS)

Dhivya Arasappan has 15 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.

Status
Open
Location
Modality
Hybrid, but in-person encouraged
Course Closes
Wed, Oct 14
Procard Disclaimer

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).

Course Semester
Fall 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Fri, Oct 16
Start Date
9:30 am - 12:30 pm

$50

Intermediate Python

Member for

2 years 10 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This course is designed for Python programmers who have basic experience with the language or who have taken the introductory Python course. Learners should already have some basic knowledge of Python control flow and data structures (variables, lists, dictionaries). The course will focus on the syntax and structure of Python objects at a deeper level, and the use of functions, loops, and conditionals to produce code that is modular and readable.

Prerequisites:
Students must bring their own laptop with an ability to connect to the UT WiFi network and should already have some knowledge of Python control flow and basic data structures.

CB27002
Instructor

Matt Bramble (Bioinformatician, Bioinformatics Consulting Group, CBRS)

Matt Bramble has recently joined the CBRS team after six years at MD Anderson Cancer Center analyzing a wide range of NGS data in epigenomics. His areas of expertise include: Hi-C (chromatin conformation) analysis, mouse somatic variant analysis, and single cell RNAseq analysis. He has 10 years of experience with R and Python, and Master’s degrees from UT in Molecular Biology and Statistics.

Status
Open
Location
Modality
Hybrid, but in-person encouraged
Course Closes
Wed, Oct 07
Procard Disclaimer

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).

Course Semester
Fall 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Fri, Oct 09
Start Date
9:30 am - 12:30 pm

$50

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