Training in computational and bioinformatics approaches to biological problems is an important part of the CCBB mission. Each semester, we offer a variety of short courses each semester in diverse topics for learning computational approaches to solving biological problems. This year, some courses will be $30, others will be offered free. All meet for one day, lasting between two to three hours per course.
Stay tuned for the 2018 CCBB Summer School Big Data in Biology!
● (FREE) Experimental Design and Library Preparation for Next-Generation Sequencing
This course is designed to serve as an entry level introduction to the services available to researchers through the Genomic Sequencing and Analysis Facility at UT. We will begin with an overview of the GSAF including where to get started, touch base on the platforms we have and review the many library preparation types the facility performs.
ABOUT THE INSTRUCTOR: Jessica Podnar has been at the GSAF for 7+ years growing with the facility as it has rapidly progressed in the world of NGS. She oversees all daily operations for the facility and meets with faculty and graduate students to help plan their sequencing projects.
● (FREE) Introduction to Microscopy Resources Available at UT
This course is designed to introduce students to the many microscopy resources available to them across UT Austin and Dell Medical School.
ABOUT THE INSTRUCTOR: Julie is the Director of the ICMB Microscopy Core Facility as well as the Director of the Dell Medical School Core facilities.
Please read this disclaimer if you are using the UT ProCard for payment!
This course introduces both principles and practice of scientific data visualization, especially as applied to large multivariate data sets. Will cover common methods of visually summarizing data and illustrating relationships between variables of various common types (continuous, categorical, etc.) as well as design concepts for increasing the clarity of quantitative graphical communication. Will introduce modern "grammar of graphics" ideas as foundation for thinking about, relating, and ultimately building new types of informative plots. Implementations of covered methods in both R and python will be presented.
Students should bring their own laptops to the course. Installation of either R (with ggplot2) or Python (with matplotlib, seaborn, and plotnine) prior to class is required.
ABOUT THE INSTRUCTOR: Dennis Wylie joined the CCBB 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.
Topics to be covered include: 1) Obtaining a transgenic mouse line - animal research protocols, pronuclear injection, ES cell gene targeting, using CRISPR for gene editing, and identifying International Mouse Consortium resources. 2) Maintaining your transgenic line - mouse reproductive biology, breeding strategies, and Cre-lox basics. 3) Analyzing your mice - prenatal lethality and post-natal effects.
ABOUT THE INSTRUCTOR: William received his Ph.D. at Baylor College of Medicine, did Post-doctoral work at UT MD Anderson Cancer Center. He’s served as Assistant Professor at the University of Minnesota, a Senior Scientist at Texas A&M Institute for Genomic Medicine. His research focus is on cell lineage determination and embryo patterning during mammalian development.
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.
Learn the basics of using UNIX from the command line. Introductory topics include the filesystem, the shell, permissions, and text files. 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.
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. Familiarity with a unix command line is a prerequisite. Students must also establish a TACC account and can do so by visiting this link..
Please visit our Spring 2017 archive here for past courses.