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FNT 1.104

Introduction to Python

Member for

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

Python is a popular programming language that is useful for a wide variety of tasks. This course is a basic introduction to scripting using Python. Skills taught will include data structures, loops, conditional statements, function definitions, and file input and output. This course is taught at an introductory level and is appropriate for students with no programming experience. However, the course is designed to include subjects and techniques that will be helpful to moderately experienced programmers new to Python.

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

CB27001
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, Sep 30
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 07
Start Date
9:30 am - 12:30 pm

$50

Introduction to RNA-Seq

Member for

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

This four-day course provides an introduction to methods for analysis of RNA-seq data. A typical RNA-seq workflow will be featured, starting from quality assessment of raw data, mapping (bwa, kallisto), differential expression analysis (DESeq2), and downstream analyses and visualization. The course also describes analysis methods for dealing with single-cell RNA-Seq data. Participants will gain hands-on experience using these tools in a Linux command line environment.

Preferred or Prerequisite Skills:
None

Computer Requirement:
Students should have their own laptop computer. UT EID is required for wireless access on campus. Please be sure you know both your UT EID when you come to class. To obtain a UT EID, go here.

CB26034
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, May 20
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
Summer 2026
Course Type
Big Data in Biology Summer School
Tue, May 26 - Fri, May 29
Start Date
1:00 pm - 4:00 pm

See Fees and Registration

Introduction to Biocomputing: Working in Unix and R

Member for

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

This course will cover the Unix command line and data analysis in R within the context of biocomputing. We will start at the Unix command line and cover command line tools for manipulating data files, before transitioning to RStudio to cover introductory topics and engage with data analysis methods in R. The course will finish up with tidyverse tools and methods for visualizing data using ggplot2.

Preferred or Prerequisite Skills:
None

Computer Requirement:
Students should have their own laptop computer. A UT EID is required for wireless access on campus. Please be sure you know both your UT EID when you come to class. To obtain a UT EID, go here.

CB26032
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, May 27
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
Summer 2026
Course Type
Big Data in Biology Summer School
Mon, Jun 1 - Fri, Jun 5
Start Date
9:00 am - 12:00 pm

See Fees and Registration

Introduction to Python

Member for

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

This five-day course will introduce students to basic concepts in programming using the Python language, establishing a foundation for scientific computing. Trainees will learn introductory topics such as data structures, control flow, functions, file input/output, and data parsing. The class will work with SciPy libraries like Pandas. Trainees will have full access to the teacher’s course book and course content (datasets, scripts, and jupyter notebooks).

Preferred or Prerequisite Skills:
None

Computer Requirement:
This class is offered in-person. Students must provide laptops able to connect to the internet, and a Firefox or Chrome browser. UT EID is required for wireless access. Please be sure you know your UT EID when you come to class. To obtain a UT EID, go here.

CB26035
Instructor

James Derry (Senior Systems Administrator)

James Derry is a senior systems administrator and has taught a semester-long introduction to programming course each long semester for the last 14 years.

Status
Open
Location
Modality
In-person
Course Closes
Wed, May 27
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
Summer 2026
Course Type
Big Data in Biology Summer School
Mon, Jun 1 - Fri, Jun 5
Start Date
1:00 pm - 4:00 pm

See Fees and Registration

Principles of Machine Learning for Bioinformatics

Member for

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

This four-day course will introduce a selection of machine learning methods used in bioinformatic analyses with a focus on RNA-seq gene expression data. We will cover unsupervised learning, dimensionality reduction and clustering; feature selection and extraction; and supervised learning methods for classification (e.g., random forests, SVM, LDA, kNN, etc.) and regression (with an emphasis on regularization methods appropriate for high-dimensional problems). Participants will have the opportunity to apply these methods as implemented in R and python to publicly available data.

Preferred or Prerequisite Skills:
This course is recommended for students with some prior knowledge of either R or python. Participants are expected to provide their own laptops with recent versions of R and/or python installed. Students will be instructed to download several free software packages (including R packages and python libraries including pandas and sklearn).

Computer Requirement:
Students should have their own laptop computer. UT EID is required for wireless access. Please be sure you know your UT EID when you come to class. To obtain a UT EID, go here.

CB26037
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
Course Closes
Wed, Jun 10
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
Summer 2026
Course Type
Big Data in Biology Summer School
Mon, Jun 15 - Thu, Jun 18
Start Date
9:00 am - 12:00 pm

See Fees and Registration

Practical Guide for Designing Genetically Engineered Mice

Member for

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

The class will cover strategies for designing genetically engineered mice. The allele types to be covered include null alleles, point mutations, conditional alleles, and reporter knock-ins.

CB26031
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, Apr 29
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
Spring 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Mon, May 4
Start Date
9:00 am - 12:00 pm

Free

Advanced Bash Scripting

Member for

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

This is a two-part course, with substantial hands-on experience in a shared computing environment. The 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 utilities such as awk and grep, as well as subtleties of UNIX streams and text manipulation.

Prerequisites:
Intermediate Unix or equivalent experience. Students wishing to participate in the hands-on portions should bring their own laptop.

CB26024
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
In-person. Zoom access available upon request.
Course Closes
Fri, May 01
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
Spring 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Wed, May 06 and Fri, May 08
Start Date
9:00 am - 12:00 pm

$50 (includes both days)

Intermediate Unix

Member for

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

This is a two-part course, with substantial hands-on practice in a shared computing environment. Topics will build on those in the introductory course, including more on the filesystem, the Bash shell, and text processing on the command line. The course will emphasize manipulating text using standard Linux utilities and stringing commands together using pipes. We’ll also introduce some of the powerful Linux utilities such as cut, sort, grep and awk, with the goal of continuing the climb up the steep Linux learning curve.

Prerequisites:
Introduction to Unix or equivalent experience. Students wishing to participate in the hands-on portions should bring their own laptop.

CB26023
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
In-person. Zoom access available upon request.
Course Closes
Fri, Apr 24
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
Spring 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Wed, Apr 29 and Fri, May 01
Start Date
9:00 am - 12:00 pm

$50 (includes both days)

Introduction to Unix

Member for

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

This is a two-part course, with substantial hands-on practice in a shared computing environment. Participants will learn the basics of using UNIX from the command line. Introductory topics include 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.

Prerequisites:
Students wishing to participate in the hands-on portions should bring their own laptop.

CB26022
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
In-person. Zoom access available upon request.
Course Closes
Fri, Apr 17
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
Spring 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Wed, Apr 22 and Fri, April 24
Start Date
9:00 am - 12:00 pm

$50 (includes both days)

Introduction to Light Microscopy

Member for

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

Light microscopy allows scientists to visualize and analyze the structure and function of biological and material samples. In this class, Quinn will cover the fundamentals of fluorescence and image resolution; the theory behind a variety of microscopy techniques, including confocal, spinning disk confocal, TIRF, multiphoton, and super-resolution microscopes; applications of these techniques; and best practices for imaging experiments.

CB26030
Instructor

Quinn Lee (Light Microscopy Specialist)

Quinn Lee has over 8 years of experience with advanced microscopy techniques. She joined the Microscopy and Flow Cytometry Facility as Light Microscopy Specialist after earning her PhD at the University of Illinois at Chicago.

Status
Open
Location
Modality
Hybrid
Course Closes
Mon, Apr 13
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
Spring 2026
Course Type
Short Courses in Bioinformatics and Biocomputing
Fri, Apr 17
Start Date
10:00 am - 12:00 pm

$20

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