Spring 2022 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 has 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.

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.

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

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. Additional topics will include how to prepare and submit samples for analysis, how data analysis is performed, and examples of data interpretation.

ABOUT THE INSTRUCTORS: Maria Person got her Ph.D. in molecular dynamics. She has been working in biological mass spectrometry for 25 years and has been director of the Proteomics Facility since 2003. Maria will be joined in this course by Peter Faull. Peter got his Ph.D. in protein mass spectrometry, has been working in proteomics core facilities since 2012, and joined the UT core facility in the Fall of 2021.

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) 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 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.

ABOUT THE INSTRUCTOR: Benni is a Bioinformatics Consultant in the Center for Biomedical Research Support. 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 provides an overview of how the Microscopy and Imaging Facility can help researchers answer their scientific questions. It will cover the instruments and services available at the MIF, including advanced fluorescence microscopes, electron microscopes, flow cytometers, and cell sorters, the types of experiments that could be conducted using our instruments, an introduction to our staff scientists, and details about how to access our resources.

ABOUT THE INSTRUCTOR: Before becoming director of the Microscopy and Imaging Facility in 2021, Anna Webb was the light microscopy specialist at the MIF for 5 years and has worked in light microscopy support in core facilities for 15 years. She believes in making complex research instrumentation accessible to all, and the MIF’s expert staff is eager to help researchers plan and execute experiments using our instruments.

This course will dive more into how the Microscopy and Imaging Facility’s instruments work and some best practices for using them. We will discuss the fundamentals of fluorescence, resolution in light and electron microscopy, sample preparation recommendations for getting the best results, and the principles and operation of flow cytometers, cell sorters, light microscopes, and electron microscopes.

ABOUT THE INSTRUCTORS: The course intro will be taught by Anna Webb, the Microscopy and Imaging Facility Director. The three main sections will be taught by the MIF’s technical staff: Paul Oliphint, light microscopy specialist; Richard Salinas, flow cytometry and cell sorting specialist; and Michelle Mikesh, electron microscopy specialist.

Cryogenic electron microscopy (cryoEM) is a versatile tool in the determination of high-resolution biomolecular structures. Recent technological advancements have enabled cryoEM to transform from “blobology” to an increasingly approachable technique 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: Axel Brilot 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. Axel received his Ph.D. from Brandeis University, where he worked on methods development in cryoEM before joining the lab of David Agard at UCSF. He has 12 years’ experience in the field of cryoEM, and joined the Sauer Structural Biology lab at UT Austin in August 2021.

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.

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 (bioluminescence).

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.

This class will provide a basic, theoretical, introduction to the various biomedical imaging modalities that can be performed in the BIC. No prior knowledge of the techniques is required, and we will cover Magnetic Resonance Imaging (MRI) and Spectroscopy (MRS), Positron Emission Tomography (PET), Computed Tomography) CT, and bioluminescence (optical imaging).

ABOUT THE INSTRUCTORS: Doug Befroy is the Facility Director of the BIC and 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. Don Nolting is the BIC Facility Manager with expertise in PET, CT and MRI, including the development of novel tracers and contrast agents for these modalities. Julie DiCarlo is the MRI Staff Scientist for the BIC with extensive experience in the applications for MRI to monitor healthy and pathological tissues.

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.