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FNT 1.104

Overview of the Biological Mass Spectrometry Facility

Member for

2 years 9 months
Full name
Gary Chiang

The class will be an overview of the Biological Mass Spectrometry Facility covering staff, equipment, services, and collaborative opportunities. New equipment for proteomics and metabolomics will be highlighted.

CB26012
Instructor

Maria Person (Facility Director)

Maria Person obtained her Ph.D. in molecular dynamics and has been working in the field of biological mass spectrometry since 2000, specializing in protein post-translational modifications. She has been the director of the facility since 2003.

Status
Open
Modality
Hybrid (In-person or Zoom)
Course Closes
Wed, Oct 29
Procard Disclaimer

If you use the UT ProCard for payment of courses, please be aware that you can only charge ONCE per 24 hour period. Any attempts to charge more courses will fail, and you will not be registered.

For example, you may add one to many courses for one student into your shopping cart at any one time, and charge them to the ProCard, and you should receive a "registration successful!" page at the end. This is because you registered ONCE for ONE student. If you attempt to register and pay again, for example, for a different student, this will trigger the UT ProCard security system to stop payment, and your registration will not be successful. A page stating this fact will occur after you attempt to process payment. It looks a lot like the "registration was successful" page.

Ways to avoid this are: use the ProCard after 24 hours have passed, or the student may use their credit card and be reimbursed later through the usual UT accounting methods, or process the registration with an IDT, otherwise known as an Interdepartmental Transfer (talk to someone in your department that handles the accounts).

Course Semester
Mon, Nov 03
Start Date
10:00 am - 11:00 am

Free

Best Practices in Mouse Colony Management

Member for

2 years 9 months
Full name
Gary Chiang

The goal of this course is to provide an overview of best practices for maintaining genetically engineered mouse colonies. Topics will include mouse reproductive basics, genetic validation, colony sizing, record keeping, and genetic drift.

Preferred or Prerequisite Skills:
No prerequisites, although an understanding of basic genetics is presumed.

CB26006
Instructor

William Shawlot (Director, Mouse Genetic Engineering Facility, CBRS)

Bill Shawlot received his Ph.D. from the Baylor College of Medicine and did his post-doctoral training with Richard Behringer at the M.D. Anderson Cancer Center. He was an Assistant Professor in the Department of Genetics, Cell Biology, and Development at the University of Minnesota, studying mammalian embryogenesis before joining the Texas A&M Institute for Genomic Medicine (TIGM) to help lead TIGM’s efforts in the International Knockout Mouse Consortium program. He has over 30 years of experience in the transgenic mouse field and serves on the External Advisory Committee for the NIH’s Mutant Mouse Resource and Research Center program.

Status
Open
Modality
In-person
Course Closes
Mon, Oct 20
Procard Disclaimer

If you use the UT ProCard for payment of courses, please be aware that you can only charge ONCE per 24 hour period. Any attempts to charge more courses will fail, and you will not be registered.

For example, you may add one to many courses for one student into your shopping cart at any one time, and charge them to the ProCard, and you should receive a "registration successful!" page at the end. This is because you registered ONCE for ONE student. If you attempt to register and pay again, for example, for a different student, this will trigger the UT ProCard security system to stop payment, and your registration will not be successful. A page stating this fact will occur after you attempt to process payment. It looks a lot like the "registration was successful" page.

Ways to avoid this are: use the ProCard after 24 hours have passed, or the student may use their credit card and be reimbursed later through the usual UT accounting methods, or process the registration with an IDT, otherwise known as an Interdepartmental Transfer (talk to someone in your department that handles the accounts).

Course Semester
Fri, Oct 24
Start Date
9:30 am - 12:30 pm

$10

Data Visualization using R

Member for

2 years 9 months
Full name
Gary Chiang

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 R will be presented. Students should bring their own laptops to the course with R and the associated packages dplyr, ggplot2 and pheatmap installed.

Preferred or Prerequisite Skills:
Some prior knowledge of R is required to get the most out of this class. The “Introduction to R” class would be useful for those not already comfortable with R programming prior to this course.

CB26011
Instructor

Dennis Wylie (Co-Director, Bioinformatics Consulting Group, CBRS)

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 PhD in Biophysics from UC Berkeley applying stochastic simulation methods in immunology, did postdoctoral work modeling the transmission of infectious disease, and spent six years as a bioinformatician in industry.

Status
Open
Modality
Hybrid, but in-person encouraged
Course Closes
Wed, Nov 26
Procard Disclaimer

If you use the UT ProCard for payment of courses, please be aware that you can only charge ONCE per 24 hour period. Any attempts to charge more courses will fail, and you will not be registered.

For example, you may add one to many courses for one student into your shopping cart at any one time, and charge them to the ProCard, and you should receive a "registration successful!" page at the end. This is because you registered ONCE for ONE student. If you attempt to register and pay again, for example, for a different student, this will trigger the UT ProCard security system to stop payment, and your registration will not be successful. A page stating this fact will occur after you attempt to process payment. It looks a lot like the "registration was successful" page.

Ways to avoid this are: use the ProCard after 24 hours have passed, or the student may use their credit card and be reimbursed later through the usual UT accounting methods, or process the registration with an IDT, otherwise known as an Interdepartmental Transfer (talk to someone in your department that handles the accounts).

Course Semester
Mon, Dec 01
Start Date
9:30 am - 12:30 pm

$50

Introduction to R

Member for

2 years 9 months
Full name
Gary Chiang

This course will introduce the fundamentals of programming in R. Topics will include coding guidelines, data types, functions, reading/writing files, and data manipulations within dataframes. We will also step into the world of the Tidyverse and learn how to manipulate dataframes within this new paradigm. This course is designed for students with little to no programming experience (prior installation of R is not required). The goal of this course is to become comfortable working in an R environment.

Preferred or Prerequisite Skills:
Students are expected to bring their own laptop and are able to connect to the UT WiFi network. As an introductory course, no prior knowledge of R programming is required.

CB26010
Instructor

Matt Bramble (Bioinformatician, Bioinformatics Consulting Group, CBRS)

Matt Bramble joined the CBRS team after working at MD Anderson Cancer Center analyzing a wide range of NGS data in epigenomics. His areas of expertise include: Hi-C (chromatin conformation) analysis, mouse somatic variant analysis, and single cell RNAseq analysis. He has 10 years of experience with R and Python, and Master’s degrees from UT in Molecular Biology and Statistics.

Status
Open
Modality
Hybrid, but in-person encouraged
Course Closes
Wed, Nov 12
Procard Disclaimer

If you use the UT ProCard for payment of courses, please be aware that you can only charge ONCE per 24 hour period. Any attempts to charge more courses will fail, and you will not be registered.

For example, you may add one to many courses for one student into your shopping cart at any one time, and charge them to the ProCard, and you should receive a "registration successful!" page at the end. This is because you registered ONCE for ONE student. If you attempt to register and pay again, for example, for a different student, this will trigger the UT ProCard security system to stop payment, and your registration will not be successful. A page stating this fact will occur after you attempt to process payment. It looks a lot like the "registration was successful" page.

Ways to avoid this are: use the ProCard after 24 hours have passed, or the student may use their credit card and be reimbursed later through the usual UT accounting methods, or process the registration with an IDT, otherwise known as an Interdepartmental Transfer (talk to someone in your department that handles the accounts).

Course Semester
Mon, Nov 17
Start Date
9:30 am - 12:30 pm

$50

Introduction to RNA-seq

Member for

2 years 9 months
Full name
Gary Chiang

This is a theory course that will introduce some basics (both in experimental design and bioinformatics) that need to be considered when doing an RNA-Seq experiment. We will discuss library prep options, quality assessment, and bioinformatics analysis pipelines. We will also talk about analysis of single-cell and 3′ targeted RNA-Seq data. This course is designed to give you an idea of the options that are available when designing an RNA-Seq study or analyzing an RNA-Seq data set.

CB26007
Instructor

Dhivya Arasappan (Co-Director, Bioinformatics Consulting Group, CBRS)

Dhivya Arasappan has over 15 years experience analyzing NGS data from multiple platforms. Her areas of expertise include RNA-Seq analysis (specifically involving large-scale brain expression datasets and coexpression network analysis), de novo genome assembly (particularly using hybrid sequencing data) and benchmarking of bioinformatics tools. She is the research educator for the Big Data in Biology Freshman Research Initiative stream.

Status
Open
Modality
Hybrid (In-person or Zoom)
Course Closes
Wed, Oct 22
Procard Disclaimer

If you use the UT ProCard for payment of courses, please be aware that you can only charge ONCE per 24 hour period. Any attempts to charge more courses will fail, and you will not be registered.

For example, you may add one to many courses for one student into your shopping cart at any one time, and charge them to the ProCard, and you should receive a "registration successful!" page at the end. This is because you registered ONCE for ONE student. If you attempt to register and pay again, for example, for a different student, this will trigger the UT ProCard security system to stop payment, and your registration will not be successful. A page stating this fact will occur after you attempt to process payment. It looks a lot like the "registration was successful" page.

Ways to avoid this are: use the ProCard after 24 hours have passed, or the student may use their credit card and be reimbursed later through the usual UT accounting methods, or process the registration with an IDT, otherwise known as an Interdepartmental Transfer (talk to someone in your department that handles the accounts).

Course Semester
Mon, Oct 27
Start Date
9:30 am - 12:30 pm

$50

Introduction to Next Generation Sequencing

Member for

2 years 9 months
Full name
Gary Chiang

This course provides a high-level introduction to concepts and best practices for Next Generation Sequencing (NGS) analysis. Participants will gain familiarity with NGS vocabulary and file formats as well as popular tools commonly used in early processing. We will touch on the main skills and resources you need to get started, and aim to help you better understand what it takes to bridge the bench-scientist-to-bioinformatician divide.

Preferred or Prerequisite Skills:
Basic familiarity with DNA and RNA.

CB26005
Instructor

Anna Battenhouse (Associate Research Scientist and Bioinformatics Consultant, CBRS)

Anna Battenhouse is a research scientist in the lab of Dr. Edward Marcotte, is a member of UT Austin’s Bioinformatics Consulting Group, and leads the Biomedical Research Computing Facility’s mission to support IT and computational needs of the biological sciences community. She has extensive experience working with NGS data over the last 15+ years, and develops and maintains NGS analysis scripts for UT’s BioITeam. Anna received a B.A. in English Literature from Carleton College in 1978. After a long career in commercial software development Anna began her “retirement career” at UT Austin in 2007, and obtained a B.S. in Biochemistry in 2013.

Status
Open
Modality
Hybrid (In-person or Zoom)
Course Closes
Wed, Oct 15
Procard Disclaimer

If you use the UT ProCard for payment of courses, please be aware that you can only charge ONCE per 24 hour period. Any attempts to charge more courses will fail, and you will not be registered.

For example, you may add one to many courses for one student into your shopping cart at any one time, and charge them to the ProCard, and you should receive a "registration successful!" page at the end. This is because you registered ONCE for ONE student. If you attempt to register and pay again, for example, for a different student, this will trigger the UT ProCard security system to stop payment, and your registration will not be successful. A page stating this fact will occur after you attempt to process payment. It looks a lot like the "registration was successful" page.

Ways to avoid this are: use the ProCard after 24 hours have passed, or the student may use their credit card and be reimbursed later through the usual UT accounting methods, or process the registration with an IDT, otherwise known as an Interdepartmental Transfer (talk to someone in your department that handles the accounts).

Course Semester
Mon, Oct 20
Start Date
9:00 am - 1:00 pm

$50

Python for Machine Learning/AI

Member for

2 years 9 months
Full name
Gary Chiang

Building further on the concepts covered in the Introduction, Intermediate, and Data Science Python courses, we will introduce Python as a tool for training and testing machine learning (ML) models with a particular focus on deep learning approaches. Specific topics will include an introduction to the PyTorch software library and a brief survey of some of the basic model architectures which it implements. Some prior familiarity with the basic ideas of ML (underfitting vs. overfitting, use of training and test data sets, etc.) and/or linear algebra will be helpful for getting the most out of this course.

CB26004
Instructor

Dennis Wylie (Co-Director, Bioinformatics Consulting Group, CBRS)

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 PhD in Biophysics from UC Berkeley applying stochastic simulation methods in immunology, did postdoctoral work modeling the transmission of infectious disease, and spent six years as a bioinformatician in industry.

Status
Open
Modality
Hybrid (In-person or Zoom)
Course Closes
Mon, Oct 13
Procard Disclaimer

If you use the UT ProCard for payment of courses, please be aware that you can only charge ONCE per 24 hour period. Any attempts to charge more courses will fail, and you will not be registered.

For example, you may add one to many courses for one student into your shopping cart at any one time, and charge them to the ProCard, and you should receive a "registration successful!" page at the end. This is because you registered ONCE for ONE student. If you attempt to register and pay again, for example, for a different student, this will trigger the UT ProCard security system to stop payment, and your registration will not be successful. A page stating this fact will occur after you attempt to process payment. It looks a lot like the "registration was successful" page.

Ways to avoid this are: use the ProCard after 24 hours have passed, or the student may use their credit card and be reimbursed later through the usual UT accounting methods, or process the registration with an IDT, otherwise known as an Interdepartmental Transfer (talk to someone in your department that handles the accounts).

Course Semester
Fri, Oct 17
Start Date
9:30 am - 12:30 pm

$50

Python for Data Science

Member for

2 years 9 months
Full name
Gary Chiang

This course will build up on the concepts covered in the Introduction to Python and Intermediate Python courses. We will introduce the use of Pandas Data frames to read in, subset, analyze and visualize RNA-Seq gene expression data.

CB26003
Instructor

Dhivya Arasappan (Co-Director, Bioinformatics Consulting Group, CBRS)

Dhivya Arasappan has over 15 years experience analyzing NGS data from multiple platforms. Her areas of expertise include RNA-Seq analysis (specifically involving large-scale brain expression datasets and coexpression network analysis), de novo genome assembly (particularly using hybrid sequencing data) and benchmarking of bioinformatics tools. She is the research educator for the Big Data in Biology Freshman Research Initiative stream.

Status
Open
Modality
Hybrid, but in-person encouraged
Course Closes
Wed, Oct 08
Procard Disclaimer

If you use the UT ProCard for payment of courses, please be aware that you can only charge ONCE per 24 hour period. Any attempts to charge more courses will fail, and you will not be registered.

For example, you may add one to many courses for one student into your shopping cart at any one time, and charge them to the ProCard, and you should receive a "registration successful!" page at the end. This is because you registered ONCE for ONE student. If you attempt to register and pay again, for example, for a different student, this will trigger the UT ProCard security system to stop payment, and your registration will not be successful. A page stating this fact will occur after you attempt to process payment. It looks a lot like the "registration was successful" page.

Ways to avoid this are: use the ProCard after 24 hours have passed, or the student may use their credit card and be reimbursed later through the usual UT accounting methods, or process the registration with an IDT, otherwise known as an Interdepartmental Transfer (talk to someone in your department that handles the accounts).

Course Semester
Mon, Oct 13
Start Date
9:30 am - 12:30 pm

$50

Intermediate Python

Member for

2 years 9 months
Full name
Gary Chiang

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.

CB26002
Instructor

Matt Bramble (Bioinformatician, Bioinformatics Consulting Group, CBRS)

Matt Bramble joined the CBRS team after working at MD Anderson Cancer Center analyzing a wide range of NGS data in epigenomics. His areas of expertise include: Hi-C (chromatin conformation) analysis, mouse somatic variant analysis, and single cell RNAseq analysis. He has 10 years of experience with R and Python, and Master’s degrees from UT in Molecular Biology and Statistics.

Status
Open
Modality
Hybrid, but in-person encouraged
Course Closes
Mon, Oct 06
Procard Disclaimer

If you use the UT ProCard for payment of courses, please be aware that you can only charge ONCE per 24 hour period. Any attempts to charge more courses will fail, and you will not be registered.

For example, you may add one to many courses for one student into your shopping cart at any one time, and charge them to the ProCard, and you should receive a "registration successful!" page at the end. This is because you registered ONCE for ONE student. If you attempt to register and pay again, for example, for a different student, this will trigger the UT ProCard security system to stop payment, and your registration will not be successful. A page stating this fact will occur after you attempt to process payment. It looks a lot like the "registration was successful" page.

Ways to avoid this are: use the ProCard after 24 hours have passed, or the student may use their credit card and be reimbursed later through the usual UT accounting methods, or process the registration with an IDT, otherwise known as an Interdepartmental Transfer (talk to someone in your department that handles the accounts).

Course Semester
Fri, Oct 10
Start Date
9:30 am - 12:30 pm

$50

Introduction to Python

Member for

2 years 9 months
Full name
Gary Chiang

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.

CB26001
Instructor

Matt Bramble (Bioinformatician, Bioinformatics Consulting Group, CBRS)

Matt Bramble joined the CBRS team after working at MD Anderson Cancer Center analyzing a wide range of NGS data in epigenomics. His areas of expertise include: Hi-C (chromatin conformation) analysis, mouse somatic variant analysis, and single cell RNAseq analysis. He has 10 years of experience with R and Python, and Master’s degrees from UT in Molecular Biology and Statistics.

Status
Open
Modality
Hybrid, but in-person encouraged
Course Closes
Wed, Oct 01
Procard Disclaimer

If you use the UT ProCard for payment of courses, please be aware that you can only charge ONCE per 24 hour period. Any attempts to charge more courses will fail, and you will not be registered.

For example, you may add one to many courses for one student into your shopping cart at any one time, and charge them to the ProCard, and you should receive a "registration successful!" page at the end. This is because you registered ONCE for ONE student. If you attempt to register and pay again, for example, for a different student, this will trigger the UT ProCard security system to stop payment, and your registration will not be successful. A page stating this fact will occur after you attempt to process payment. It looks a lot like the "registration was successful" page.

Ways to avoid this are: use the ProCard after 24 hours have passed, or the student may use their credit card and be reimbursed later through the usual UT accounting methods, or process the registration with an IDT, otherwise known as an Interdepartmental Transfer (talk to someone in your department that handles the accounts).

Course Semester
Mon, Oct 06
Start Date
9:30 am - 12:30 pm

$50

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