2024 Summer School

IMPORTANT REGISTRATION NOTICE:

Incognito (private) mode, clearing web browser cache, or switching browsers might be necessary to complete course registration if cart remains empty.

Do NOT use someone else’s PIN number during the registration process, or your registration will not be complete. Use your own unique PIN number assigned to you during registration if you are new, or the same PIN number you have used for earlier registrations.

Also, if you are registering on behalf of someone else, PLEASE DO NOT use your name, contact information, or EID at any point in the process. You MUST use the information as it pertains to the student, or they will not be included on the course roster properly and could miss out on crucial course communication. Ask that the student you are registering email you the receipt when they receive it via their email.

Course Listings

Introduction to R for Biologists

Date
May 28 - May 31
Time
1:30 pm - 4:30 pm
Location
FNT 1.104
Instructor
Alexandra Lukasiewicz

Modality: In-person

Description: 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.

Instructor Bio: Alexandra Lukasiewicz is a current Cell and Molecular Biology PhD student in the lab of Dr. Lydia Contreras, with a degree focus 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.

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.

If using a UT Procard, read this disclaimer.

Back to top

Introduction to Core NGS Concepts and Tools

Date
June 3 - June 7
Time
9:00 am - 12:00 pm
Location
FNT 1.104
Instructor
Anna Battenhouse (Associate Research Scientist and Bioinformatics Consultant, CBRS)

Modality: Hybrid, but in-person recommended

Description: 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.

Instructor Bio: Anna Battenhouse is a research scientist in the lab of Dr. Edward Marcotte, is a member of UT Austin’s Bioinformatics Consulting Group, and leads the Biomedical Research Computing Facility’s mission to support IT and computational needs of the biological sciences community. She has extensive experience working with NGS data over the last 15 years, and develops and maintains NGS analysis scripts for UT’s BioITeam. Anna received a B.A. in English Literature from Carleton College in 1978. After a long career in commercial software development Anna began her “retirement career” at UT Austin in 2007, and obtained a B.S. in Biochemistry in 2013.

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 half-day short courses by clicking here.

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.

If using a UT Procard, read this disclaimer.

Back to top

Introduction to Biocomputing: from files to functions to plots

Date
June 3 - June 7
Time
1:00 pm - 4:00 pm
Location
FNT 1.104
Instructor
Nolan Bentley

Modality: Hybrid, but in-person recommended

Description: An introduction to the Unix command line and R. Unix basics will include file navigation, pipes, and core utilities. R basics will cover data types, loops, conditionals, and objects. After the basics are covered, the focus will turn to bioinformatics applications. No previous programming experience is assumed.

Instructor Bio: Nolan Bentley is an Assistant Professor of Instruction in the Department of Integrative Biology at UT Austin where he teaches the “Principles of Computational Biology” (BIO321G) course where he focuses on introducing students to R and computational analyses in biology. In his research, he conducts genomic analyses in various agricultural crops to facilitate breeding efforts R, Unix / Bash, and various other programs to do genomic analyses.

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

Computer Requirement: In order to participate fully in the hands-on exercises students should have their own laptop computer with an SSH client program and a web browser for accessing the cloud based RStudio server. 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.

If using a UT Procard, read this disclaimer.

Back to top

Introduction to Python

Date
June 10 - June 14
Time
9:00 am - 12:00 pm
Location
FNT 1.104
Instructor
James Derry, Senior Systems Administrator

Modality: Hybrid, but in-person recommended

Description: 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.

Instructor Bio: James Derry is a Systems Administrator for CNS. He has been teaching researchers how to program in Perl and Python in semester-long classes since 2011.

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.

If using a UT Procard, read this disclaimer.

Back to top

Introduction to RNA-Seq

Date
June 10 - June 14
Time
1:00 pm - 4:00 pm
Location
FNT 1.104
Instructor
Dhivya Arasappan (Assistant Professor of Practice and Co-director, Bioinformatics Consulting Group, CBRS)

Modality: Hybrid, but in-person recommended

Description: This five-day course provides an introduction to methods for analysis of RNA-seq data. It assumes familiarity and comfort with Linux command line and TACC. 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 at TACC.

Instructor Bio: Dhivya Arasappan has over 10 years experience analyzing NGS data from multiple platforms. Her areas of expertise include RNA-Seq analysis (specifically involving large-scale brain expression datasets and coexpression network analysis), de novo genome assembly (particularly using hybrid sequencing data) and benchmarking of bioinformatics tools. She is the research educator for the Big Data in Biology Freshman Research Initiative stream.

Preferred or Prerequisite Skills: Familiarity working in a UNIX environment. Consider taking the Introduction to Biocomputing summer school course to refresh your UNIX skills.

Computer Requirement: Students should have their own laptop computer. TACC Account and UT EID are required. Please be sure you know both your UT EID and your TACC username when you come to class. To obtain a UT EID, go here. To sign up for a TACC account, go here.

If using a UT Procard, read this disclaimer.

Back to top

Principles of Machine Learning for Bioinformatics

Date
June 17 - June 21 (no class on June 19)
Time
9:00 am - 12:00 pm
Location
FNT 1.104
Instructor
Dennis Wylie (Research Scientist and Bioinformatics Consultant, CBRS)

Modality: Hybrid, but in-person recommended

Description: 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.

Instructor Bio: 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 in immunology, did postdoctoral work modeling the transmission of infectious disease, and spent six years as a bioinformatician in industry.

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.

If using a UT Procard, read this disclaimer.

Back to top

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).