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Summer 2025

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.

Introduction to Biocomputing: from files to functions to plots

Member for

2 years 6 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 engage with some more complex data analysis methods in R. The course will finish up with tidyverse tools and methods for visualizing data using ggplot2.

Preferred or Prerequisite Skills:
Some general familiarity with a programming language is assumed. Introductory topics in R will be covered, but at a relatively fast pace.

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.

CB25033
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
Closed
Location
Modality
Hybrid
Course Closes
Thu, May 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
Summer 2025
Course Type
Big Data in Biology Summer School
May 27 - May 30
Start Date
1:30 pm - 4:30 pm

See Registration and Payment.

Introduction to Core NGS Concepts and Tools

Member for

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

This five-day course provides an introduction to the concepts and vocabulary of Next Generation Sequencing (NGS) with an emphasis on common protocols, tools and file formats used in NGS data analysis. Subjects covered include quality assessment and manipulation of raw NGS sequences (FastQC, cutadapt), read mapping (bwa, bowtie2), the Sequence Alignment Map (SAM) format, and tools for manipulating BAM files (samtools, bedtools). Participants will gain hands-on experience using these and other NGS tools in the Linux command line environment at TACC, as well as exposure to the many bioinformatics resources TACC makes available.

Preferred or Prerequisite Skills:
None. UNIX/Linux command line experience is not required, and becoming familiar with how to use the command line for NGS analysis will be a major focus of this course. However, to get a head start on developing this important skill you can register for our Introductory UNIX short courses.

Computer Requirement:
In order to participate fully in the hands-on exercises students should have their own laptop computer with an SSH client program. Macs have SSH available in the Terminal application. Recent Windows versions have an SSH client built into its PowerShell and Command Prompt programs, or PuTTy can be used if SSH is not available. A TACC Account and UT EID are also required. To obtain a UT EID, go here. To sign up for a TACC account, go here.

CB25034
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, but in-person recommended
Course Closes
Thu, May 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
Summer 2025
Course Type
Big Data in Biology Summer School
June 2 - June 6
Start Date
9:00 am - 12:00 pm

See Registration and Payment.

Introduction to R for Biologists

Member for

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

This four-day course will introduce how to use the R programming language to analyze and visualize biological data on small and large scales. We will focus on the practical tools you need to quickly import your data, clean it up, analyze it, and then generate publication-quality plots. Along the way we’ll briefly address best practices for coding in R and how to effectively find help online. The structure of the course is “learn one, see one, do one”–for each topic (e.g., data manipulation or visualization), there will be a brief lecture on the basic principles, then a demonstration of the code in R, and then you will complete a similar problem in a coding worksheet. This course primarily uses the tidyverse ecosystem of R packages, and upon completion you’ll have used dplyr, tidyr, ggplot2, tidygraph, and more.

Preferred or Prerequisite Skills:
No previous programming experience is required.

Computer Requirement:
Students must have their own laptops that are able to connect to the utexas network. Prior installation of R and RStudio is not necessary but will be covered in this course.

CB25032
Instructor

Alexandra Lukasiewicz

Dr. Alexandra Lukasiewicz is a current post-doctoral researcher in the lab of Dr. Lydia Contreras, with extensive research experience in computational biology and bioinformatics. Their research focuses on biophysical systems modeling of protein-RNA interactions in bacteria. They have 6 years of experience programming in R, Python, and Unix/ Bash, as well as assisting in instruction of introductory programming courses.

Status
Closed
Location
Modality
In-person
Course Closes
Thu, May 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
Summer 2025
Course Type
Big Data in Biology Summer School
May 20 - May 23
Start Date
1:30 pm - 4:30 pm

See Registration and Payment.

Subscribe to Summer 2025