GRS 097: Fundamentals for Teaching Assistants

Fall 2023

Meeting time to be determined. CNS has partnered with the Graduate School and the Faculty Innovation Center (FIC) to develop this course to support Teaching Assistants who will be leading a lab or discussion section for the first time. In this research-based seminar on pedagogy, graduate students will learn strategies for effectively leading lab/discussion sections, and will receive personalized support and feedback designed to improve their confidence and skills as instructors. Dr. Molly Hatcher of the FIC will serve as its instructor of record.

Prerequisites: None. 

Any CNS graduate student in their first year of leading a lab/discussion session can apply for this course.

NSC TBA: Communicating Science and Public Policy

Spring 2024

This course will help student researchers to identify and articulate the relevance of their scientific scholarship to public policy. In addition the course will help students: 

• Understand the difference between using science as an advisor versus an advocate, and determine their personal position 
• Understand how policy audiences use science to inform their decision making, and where policy makers access their information
• Learn how to become a professional resource for the media or policy leaders 
• Determine how to provide advice to policy makers when scientific findings are uncertain
• Determine how to respond when your scientific findings are not being used or are being misused
• Determine how to share findings that may be controversial

NSC TBA: Professional Ethics and Social Responsibility in Research

Spring 2023

Scientists have responsibilities, both to the public and to their own professions and specific fields. The public are stakeholders in the outcomes of scientific research, and in its potential impact on policy and decisions affecting the community and the environment. The scientific community are stakeholders whose interests are best served by the maintenance of high standards of practice and conduct by all of its members. This course examines the ethical obligations scientists have to both groups of stakeholders. It also provides an intellectual space in which emerging scientists may consider the best ways to meet those obligations in the face of multiple other demands on them.

NSC 088L: Intro to Evidence Based Teaching

Fall 2023

F 3:00-4:30pm. These seven workshops are designed for graduate students, postdocs, and faculty who are interested in learning how to teach science effectively in their own courses. Topics include the principles of learning, backward design, assessment, active learning, and inclusive teaching strategies. Assignments require participants to reflect on classroom observations, read science-education research, and create a mini-lesson using backward design. Completion of this course meets Core Requirements 1 & 2 of the Concentration in Teaching and Mentoring. Interested graduate students should sign-up for the workshop version of this course during registration. Postdocs and faculty should contact Dr. Kristin Patterson (kpatterson@austin.utexas.edu) in TIDES to be added to the course.

Prerequisites: None

NSC 088C: Science Communication Seminar

Spring 2023

Meeting time to be determined. This seminar course is a professional development elective within the CNS Concentration in Communicating Science.  Students may take this course alone or in conjunction with the Practicum described below. Taught by Anthony Dudo from the Stan Richards School of Advertising and Public Relations in the Moody College of Communication, this seminar course will introduce students to topics chosen from the following: 

• Models of “public engagement with science” (deficit model, contextual model, public participation model)
• Public understanding of science, science literacy, and trust in science
• Sources of information about science (journalism, entertainment media, social media)
• Motivations and barriers to scientist communicators
• Communicating science strategically (choosing communication goals and styles, working with media/public information officers)
• Science communication case studies (climate change, genetic engineering) 

Prerequisites: None

NSC 088P: Leading People and Organizations

Spring 2022

Meets Tuesday evenings, 5:00-8:00. This course is a professional development elective within the CNS Concentration in Leadership and Project Management. Taught by Caroline Bartel from the Department of Management in the McCombs College of Business, this is a special section of a McCombs MBA course tailored for graduate students in STEM disciplines. This course will develop the knowledge and skills necessary for scientists to manage and lead effectively within organizations. Students may take this class on either a C/NC (low workload) or a full credit (higher workload) basis.

Prerequisites: None 

NSC 088S: Strategic Management

Fall 2022

This course is concerned with the job of the general manager, who has responsibility for the performance of an entire organization or a multi-functional unit of an organization. The primary task faced by such managers is that of developing and managing an overall strategy; hence, the name "strategic management." Accordingly, the objectives of the course are to (1) take the first steps in developing a "general management" orientation in all students, (2) develop the new skills and knowledge needed in such positions, and (3) synthesize the skills and knowledge students have obtained through prior work experience and course work. Among the topics covered in the course are the role of the general manager, formulating business and corporate-level strategy, managing strategic change, strategy implementation, and developing general managers. The objectives of the course will be accomplished primarily through a combination of readings and case discussions. Students will be evaluated based on the quality of their participation in in-class discussions and course papers. The participative nature of the course requires daily preparation and participation of the highest quality.Further topics in this concentration will be piloted in the 2018-19 academic year.

Prerequisites:  None

Introduction to Unix

January 2022

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.

Introduction to TACC

January 2023

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.

Introduction to Python I

January 2022

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, input and output, loops, and if time permits, function definitions. 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 experience, but will contain material and techniques helpful to moderately experienced python programmers.Topics to be covered:

• Introduction 
• Control Flow 
• Lists 
• Input and Output 
• Strings 
• Functions 

Introduction to R, Part I

Currently unavailable

This course introduces R, a free and open-source software package used for statistical computing and graphics. We will cover navigating the free graphical user interface RStudio, importing and exporting data, combining (merging) data, creating and manipulating variables, basic data descriptives, and visualization. The course will introduce installation of R packages to leverage two popular workflows: the tidyverse and ggplot2.After completing this course, a new user should be able to:

• Navigate RStudio.
• Install and use R packages.
• Import/export data from/to external files.
• Create and manipulate new variables.
• Generate simple descriptive statistics to summarize data.
• Graphically display various types of data.
• Edit features of graphs (titles/labels, colors, shading, etc.).
• Make graphs using ggplot2.

Introduction to Data Visualization & SQL

Currently unavailable

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.

Working with SQL Databases

Currently unavailable

This is an introductory course on the basics of database technology using MySQL, including the structured query language (SQL) along with modes of database interaction specific for bioinformatics workflows. We begin with a hands-on introduction to databases and the MySQLWorkbench user interface, creating and populating a schema, followed by simple and more complex queries to manipulate different subsets of data. Finally, we discuss bulk loading of database tables and programmatic database access, for example from Python.

ABOUT THE INSTRUCTOR: Anna Battenhouse is a research scientist in the labs of Drs. Edward Marcotte and Vishy Iyer as well as leading the Biomedical Research Support Facility in its mission to support the IT and computational needs of the UT Austin biomedical research community. She has extensive experience working with NGS data, and teaches the Introduction to NGS Tools course in the Big Data in Biology Summer School as well as several CCBB short courses.

Introduction to R, Part II

Currently unavailable

This short course covers data analysis in R in greater depth than the introductory course.  For various statistical methods (see list below), participants will learn how to prepare a dataset, test relevant assumptions, and carry out the analyses. In addition, students will be introduced to the premise of reproducible research, and create RMarkdown objects. This hands-on course will teach participants how to use R to run different types of analysis, interpret the output, and reproducible documents.After completing this course, participants should be able to carry out:

• Correlation and simple linear regression analysis.
• Chi-squared tests.
• T-tests and one-way ANOVA.
• Multiple regression and multivariate ANOVA models.
• Logistic regression.
• Reproducible report creation in RStudio.

Machine Learning

August 2021

This course introduces a selection of machine learning methods for both unsupervised learning (dimensionality  reduction and clustering) and supervised learning (classification and regression). The phenomenon of model overfitting will be discussed along with techniques such as cross-validation for its assessment and quantification.

ABOUT THE INSTRUCTOR: Dennis Wylie has worked for the UT Center for Biomedical Research Support (CBRS) since 2015 focusing primarily on biological sequence data analysis and predictive modeling. Prior to UT, he earned a PhD in Biophysics from UC Berkely applying sthochastic simulation methods in immunology, did postdoctoral work modeling the transmission of infectious disease, and spent six years as a bioinformatician in industry.

Bash Scripts

August 2021

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.

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 need of the UT Austin biological sciences community. She has extensive experience writing pipeline scripts to process Next Generation Sequencing data and perform other functions.

GitHub and Code Management

August 2021

GitHub and Code Management is a hands-on workshop that will cover basic concepts and tools for version control and code management. In this course, you will learn Git and commands that are all you need for most day-to-day version control tasks. You'll also learn how to use GitHub to host your own Git repositories. More information about this course can be found at: https://alice-macqueen.github.io/2020-08-13-utexas/

ABOUT THE INSTRUCTOR: Alice MacQueen is a Research Associate in Integrative Biology where she studies the genetics of plant adaptation to the environment. She has learned how to use Git and GitHub just over a year ago in a course like this one. She finds Git and incredibly useful tool for making her research clearly documented and replicable, and for working with others and her past and future self.

Creating Publicaton Qulaity Graphics with ggplot2

Currently unavailable

ggplot2 is a plotting package in R that makes it simple to create complex plots from data in a data frame, allowing you to create and edit publication quality plots with minimal amounts of adjustments and tweaking. In this course, you will learn how to produce plots using ggplot2, set universal plot settings and themes, apply faceting in ggplot, and build and save complex and customized plots from data in a data frame.

ABOUT THE INSTRUCTOR: Alice MacQueen is a Research Associate in Integrative Biology where she studies the genetics of plant adaptation to the environment. She has learned how to use Git and GitHub just over a year ago in a course like this one. She finds Git and incredibly useful tool for making her research clearly documented and replicable, and for working with others and her past and future self.