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 Fall 2017 short courses!
● 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.
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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 bokeh).
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. We will cover sample preparation, tandem mass spectrometry, protein identification, quantitation and modification analysis. Students will need to bring their own laptops.
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. Students will be required to establish a TACC account and can do so by visiting this link.
Version control can be thought of lab notebook of the digital world. Version control is really important and useful, but the tools for doing so often have a steep learning curve. This course will introduce you to the core concepts to getting you started on the path to version control and open science. In this course, we will cover: 1) what is version control and how is it useful, 2) tracking changes and exploring history with git 3) collaborating with GitHub, and 4) open science.
Students will need their own laptops for this course, and preinstall Git.
ABOUT THE INSTRUCTOR: Rayna Harris is a graduate student in Hans Hofmann lab. She uses RNA-sequencing to understand molecular changes that happen in the brain when animals learn.
Please visit our Spring 2016 archive here for past courses.