Spring 2021 Semester

This course will offer an introduction into the services provided by the Genomic Sequencing and Analysis Facility available to researchers at the University of Texas. The course will cover the platforms and services available, best practices and how to submit samples to the core.

ABOUT THE INSTRUCTOR: Jessica Podnar joined the GSAF in 2010, prior to UT she worked at a biotech company focused on drug discovery and telomere biology. She has 15 years experience in cell and molecular biology and been part of the rapidly changing field of Next Generation Sequencing for most of her career. She is familiar with an assortment of NGS technologies and is always ready to support new projects.

The class will provide an introduction to mass spectrometry-based proteomics and the resources available at the proteomics facility that can be used to facilitate research.

ABOUT THE INSTRUCTOR: Maria Person got her Ph.D. in molecular dynamics. She has been working in biological mass spectrometry for 20 years and has been director of the Proteomics Facility since 2003.

This course provides an introduction to the bioinformatics analysis of single-cell RNA-seq (scRNA-seq) data, with a particular focus on methods especially appropriate for analysis of 10X Genomics data. Differences between bulk RNA-seq and scRNA-seq will be discussed in order to develop understanding of both what new methods are required versus what established RNA-seq analysis methods can be retained. Students interested in following along in class should bring their own laptops to the course with R (with Seurat, https://cran.r-project.org/web/packages/Seurat/index.html) installed.

ABOUT THE INSTRUCTOR: 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 Ph.D. 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.

This course is designed to introduce researchers to the many microscopy resources available to them across UT Austin, including resources at Dell Medical School. We will cover laser scanning confocal, spinning disk confocal, multiphoton, super resolution microscopy (STORM, TIRF, SIM), transmission electron microscopy (TEM), scanning electron microscopy (SEM), cryo-EM, a wide variety of compound fluorescent microscopes, cell sorting and flow cytometry.

ABOUT THE INSTRUCTORS: Julie is the Director of the Microscopy and Flow Cytometry Core Facility as well as the Associate Director of the CBRS. Julie developed a passion for microscopy during her years as a developmental biologist. She is an advocate of microscopy as a means to obtain beautiful, data-rich images that shed light on fascinating research questions. Anna Webb is the light microscopy specialist at the Microscopy and Imaging Core facility and will teach a section of the course on light microscopes. Richard Salinas is the flow cytometry and cell sorting specialist and will teach the section on flow cytometry and cell sorting resources. Michelle Mikesh is the electron microscopy specialist and will teach the section on TEM, SEM and the many accessories available to support electron microscopy at the core facility.

Tag Seq is a method of sequencing the 3′ ends of mRNA in order to identify differential gene expression using a significantly cost-effective method. This course is an introduction to this Tag Seq method as well as the bioinformatics involved in analyzing a Tag Seq dataset. We will discuss library prep, quality assessment, read mapping, gene quantification, differential expression analysis and downstream analysis. There are no prerequisites for taking this course.

ABOUT THE INSTRUCTOR: Dhivya Arasappan has 10 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.

Cryogenic electron microscopy (cryoEM) is poised to supersede X-ray crystallography as the primary method for biomolecular structure determination. The immense growth in its popularity is primarily due to technological advancements made in the past decade which have enabled cryoEM to transform from “blobology” to a high-resolution method capable of generating atomic structures. In this course, we will discuss both the basic principles of single particle cryoEM along with what our core offers users. We will also discuss the practical applications of cryoEM and what a user will need to perform a successful experiment.

ABOUT THE INSTRUCTOR: Sasha Dickinson is the facility manager for the Sauer Structural Biology Lab at UT Austin which houses two state-of-the-art electron microscopes for biomolecular structure determination. Sasha received his B.S. in chemistry from University of Washington and his Ph.D. from UCSF where he used single particle cryoEM to determine structures of voltage-gated ion channels and polyketide synthases.

Learn the basics of using UNIX from the command line. Introductory topics include the filesystem, the shell, and basic text processing. The course will touch on 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.

ABOUT THE INSTRUCTOR: Benni is a Bioinformatics Consultant in the CCBB. Python, Bash, and huge computing clusters are some of his favorite things. In a previous life Benni studied pure math, differential geometry in particular.

This 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 awk, grep and sed, as well as subtleties of UNIX stream and text manipulation.

PRE-REQUISITES: This is not an introductory course. Students must be comfortable performing basic tasks on the Linux command line. Suggested minimum background is completion of the “Intro to UNIX Command Line” short course and/or substantial command-line experience. Students can use their own laptops to access coding examples in a shared computing environment (Windows users should install an SSH client such as Putty).

ABOUT THE INSTRUCTOR: Anna Battenhouse is a research scientist in the lab of Dr. Edward Marcotte as well as leading the Biomedical Research Support Facility in its mission to support the IT and computational needs of the UT Austin biological sciences community. She has extensive experience writing pipeline scripts to process Next Generation Sequencing data and perform other functions.

Students in the course will learn what a cluster is and how to use the world-class clusters available at the Texas Advanced Computing Center (TACC). The course will discuss the basic architecture of the Lonestar and Stampede computing clusters, how they compare to a regular computer, job launchers and job scheduling, and how to submit your own jobs to TACC. Custom tools by the Bioinformatics Consulting Group for job submission will be emphasized. Comfort at a UNIX command line is a prerequisite.

ABOUT THE INSTRUCTOR: Benni is a Bioinformatics Consultant in the CCBB. Python, Bash, and huge computing clusters are some of his favorite things. In a previous life Benni studied pure math, differential geometry in particular.

This class will provide an introduction to the resources and support available for clinical and preclinical imaging studies at the BIC, including Magnetic Resonance Imaging (MRI) and Spectroscopy (MRS), Positron Emission Tomography (PET), Computed Tomography) CT and optical imaging.

ABOUT THE INSTRUCTOR: Doug Befroy has over 20 years of experience in biomedical imaging with a particular focus on the research applications of MRI and MRS in health and disease spanning both academia and industry. He joined the BIC as Facility Director in January 2021.