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FNT 1.104

Introduction to RNA-seq

Member for

2 years 6 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.

CB26007
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 22
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 2025
Course Type
Short Courses in Bioinformatics and Biocomputing
Mon, Oct 27
Start Date
9:30 am - 12:30 pm

$50

Introduction to Next Generation Sequencing

Member for

2 years 6 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.

CB26005
Instructor

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

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 IT and 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 CBRS short courses.

Status
Open
Location
Modality
Hybrid (In-person or Zoom)
Course Closes
Wed, Oct 15
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 2025
Course Type
Short Courses in Bioinformatics and Biocomputing
Mon, Oct 20
Start Date
9:00 am - 1:00 pm

$50

Python for Machine Learning/AI

Member for

2 years 6 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.

CB26004
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
Mon, Oct 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
Fall 2025
Course Type
Short Courses in Bioinformatics and Biocomputing
Fri, Oct 17
Start Date
9:30 am - 12:30 pm

$50

Python for Data Science

Member for

2 years 6 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.

CB26003
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 08
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 2025
Course Type
Short Courses in Bioinformatics and Biocomputing
Mon, Oct 13
Start Date
9:30 am - 12:30 pm

$50

Intermediate Python

Member for

2 years 6 months
Full name
Gary Chiang
Submitted by Gary Chiang on

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.

CB26002
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
Mon, Oct 06
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 2025
Course Type
Short Courses in Bioinformatics and Biocomputing
Fri, Oct 10
Start Date
9:30 am - 12:30 pm

$50

Introduction to Python

Member for

2 years 6 months
Full name
Gary Chiang
Submitted by Gary Chiang on

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.

CB26001
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 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
Fall 2025
Course Type
Short Courses in Bioinformatics and Biocomputing
Mon, Oct 06
Start Date
9:30 am - 12:30 pm

$50

Introduction to Statistical Modeling

Member for

2 years 6 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This course is a hands-on introduction to building and interpreting statistical models in R, with a focus on real-world applications. We will cover key concepts in hypothesis testing, multiple linear regression, and logistic regression. You will learn how to choose appropriate modeling approaches, fit models using R, check assumptions, interpret results, and clearly communicate your findings. Each topic will include a brief introduction to foundational concepts, a demonstration of analysis in R, and guided practice through interactive coding exercises. Emphasis will be placed on using statistical modeling to answer research questions within reproducible workflows. By the end of the course, the goal is for you to be able to apply statistical modeling to your own data.

Preferred or Prerequisite Skills:
This course is recommended for students with some prior knowledge of R (in particular, we recommend taking the “Introduction to R for Biologists” summer school course offered above).

Computer Requirement:
Participants are expected to provide their own laptops.

CB25035
Instructor

Layla Guyot

Layla Guyot is a data analyst, educator, and researcher, who joined the department of Statistics and Data Sciences at UT Austin in Fall 2020. She studied mathematics and physics as an undergraduate before completing an M.S. in Applied Probability and Statistics, just by chance. After gaining experience as a biostatistician, she combined her interests in teaching, statistics, and research to complete her Ph.D. in Mathematics Education at Texas State University. Layla has over a decade of experience coding in R and brings that expertise to explore real-world applications, emphasizing hands-on, active learning in her courses.

Status
Closed
Location
Modality
Hybrid, but in-person encouraged
Course Closes
Wed, May 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
Summer 2025
Course Type
Big Data in Biology Summer School
June 2 - June 6
Start Date
1:30 pm - 4:30 pm

See Registration and Payment

Principles of Machine Learning for Bioinformatics

Member for

2 years 6 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.

CB25038
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
Closed
Location
Modality
Hybrid
Course Closes
Thu, Jun 12
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 2025
Course Type
Big Data in Biology Summer School
June 16 - June 20 (no class on June 19)
Start Date
9:00 am - 12:00 pm

See Registration and Payment

Introduction to RNA-Seq

Member for

2 years 6 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This five-day course provides an introduction to methods for analysis of RNA-seq data. It assumes familiarity and comfort with Linux command line. 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:
Familiarity working in a UNIX environment. Consider taking the “Introduction to Biocomputing” or “Introduction to Core NGS Concepts and Tools” summer school course to refresh your UNIX skills.

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

CB25037
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, Jun 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
Summer 2025
Course Type
Big Data in Biology Summer School
June 9 - June 13
Start Date
1:00 pm - 4:00 pm

See Registration and Payment.

Introduction to Python

Member for

2 years 6 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.

CB25036
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
Closed
Location
Modality
In-person
Course Closes
Wed, Jun 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
Summer 2025
Course Type
Big Data in Biology Summer School
June 9 - June 13
Start Date
9:00 am - 12:00 pm

See Registration and Payment.

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