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FNT 1.104

Introduction to Biocomputing: from files to functions to plots

Member for

2 years 6 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This course will cover the Unix command line and data analysis in R within the context of biocomputing. We will start at the Unix command line and cover command line tools for manipulating data files, before transitioning to RStudio to engage with some more complex data analysis methods in R. The course will finish up with tidyverse tools and methods for visualizing data using ggplot2.

Preferred or Prerequisite Skills:
Some general familiarity with a programming language is assumed. Introductory topics in R will be covered, but at a relatively fast pace.

Computer Requirement:
Students should have their own laptop computer. UT EID is required for wireless access on campus. Please be sure you know your UT EID when you come to class. To obtain a UT EID, go here.

CB25033
Instructor

Matt Bramble (Bioinformatician, Bioinformatics Consulting Group, CBRS)

Matt Bramble has recently joined the CBRS team after six years 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
Closed
Location
Modality
Hybrid
Course Closes
Thu, May 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
Summer 2025
Course Type
Big Data in Biology Summer School
May 27 - May 30
Start Date
1:30 pm - 4:30 pm

See Registration and Payment.

Introduction to Core NGS Concepts and Tools

Member for

2 years 6 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This five-day course provides an introduction to the concepts and vocabulary of Next Generation Sequencing (NGS) with an emphasis on common protocols, tools and file formats used in NGS data analysis. Subjects covered include quality assessment and manipulation of raw NGS sequences (FastQC, cutadapt), read mapping (bwa, bowtie2), the Sequence Alignment Map (SAM) format, and tools for manipulating BAM files (samtools, bedtools). Participants will gain hands-on experience using these and other NGS tools in the Linux command line environment at TACC, as well as exposure to the many bioinformatics resources TACC makes available.

Preferred or Prerequisite Skills:
None. UNIX/Linux command line experience is not required, and becoming familiar with how to use the command line for NGS analysis will be a major focus of this course. However, to get a head start on developing this important skill you can register for our Introductory UNIX short courses.

Computer Requirement:
In order to participate fully in the hands-on exercises students should have their own laptop computer with an SSH client program. Macs have SSH available in the Terminal application. Recent Windows versions have an SSH client built into its PowerShell and Command Prompt programs, or PuTTy can be used if SSH is not available. A TACC Account and UT EID are also required. To obtain a UT EID, go here. To sign up for a TACC account, go here.

CB25034
Instructor

Anna Battenhouse (Bioinformatics Consultant and Biomedical Research Computing Facility Manager)

Anna Battenhouse is a research scientist in the lab of Dr. Edward Marcotte, is a Bioinformatics Consultant, and leads the Biomedical Research Computing 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, develops and maintains analysis scripts for the Bioinformatics Consulting Group, and teaches the Introduction to NGS Tools course in the Big Data in Biology Summer School as well as several CBRS short courses.

Status
Open
Location
Modality
Hybrid, but in-person recommended
Course Closes
Thu, May 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
Summer 2025
Course Type
Big Data in Biology Summer School
June 2 - June 6
Start Date
9:00 am - 12:00 pm

See Registration and Payment.

Introduction to R for Biologists

Member for

2 years 6 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This four-day course will introduce how to use the R programming language to analyze and visualize biological data on small and large scales. We will focus on the practical tools you need to quickly import your data, clean it up, analyze it, and then generate publication-quality plots. Along the way we’ll briefly address best practices for coding in R and how to effectively find help online. The structure of the course is “learn one, see one, do one”–for each topic (e.g., data manipulation or visualization), there will be a brief lecture on the basic principles, then a demonstration of the code in R, and then you will complete a similar problem in a coding worksheet. This course primarily uses the tidyverse ecosystem of R packages, and upon completion you’ll have used dplyr, tidyr, ggplot2, tidygraph, and more.

Preferred or Prerequisite Skills:
No previous programming experience is required.

Computer Requirement:
Students must have their own laptops that are able to connect to the utexas network. Prior installation of R and RStudio is not necessary but will be covered in this course.

CB25032
Instructor

Alexandra Lukasiewicz

Dr. Alexandra Lukasiewicz is a current post-doctoral researcher in the lab of Dr. Lydia Contreras, with extensive research experience in computational biology and bioinformatics. Their research focuses on biophysical systems modeling of protein-RNA interactions in bacteria. They have 6 years of experience programming in R, Python, and Unix/ Bash, as well as assisting in instruction of introductory programming courses.

Status
Closed
Location
Modality
In-person
Course Closes
Thu, May 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
Summer 2025
Course Type
Big Data in Biology Summer School
May 20 - May 23
Start Date
1:30 pm - 4:30 pm

See Registration and Payment.

Advanced Bash Scripting

Member for

2 years 6 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This is a two-part course, with substantial hands-on experience in a shared computing environment. The 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 utilities such as awk and grep, as well as subtleties of UNIX streams and text manipulation.

CB25031
Instructor

Anna Battenhouse (Bioinformatics Consultant and Biomedical Research Computing Facility Manager)

Anna Battenhouse is a research scientist in the lab of Dr. Edward Marcotte, is a Bioinformatics Consultant, and leads the Biomedical Research Computing 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, develops and maintains analysis scripts for the Bioinformatics Consulting Group, and teaches the Introduction to NGS Tools course in the Big Data in Biology Summer School as well as several CBRS short courses.

Status
Closed
Location
Modality
In-person. Zoom access available upon request.
Course Closes
Mon, May 05
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 Type
Short Courses in Bioinformatics and Biocomputing
Wed, May 7 and Fri, May 9
Start Date
9:00 am - 12:00 pm

$50 (includes both days)

Introduction to Light Microscopy

Member for

2 years 6 months
Full name
Gary Chiang
Submitted by Gary Chiang on

Light microscopy allows scientists to visualize and analyze the structure and function of biological and material samples. In this class, Quinn will cover the fundamentals of fluorescence and image resolution; the theory behind a variety of microscopy techniques, including confocal, spinning disk confocal, TIRF, multiphoton, and super-resolution microscopes; applications of these techniques; and best practices for imaging experiments.

CB25030
Instructor

Quinn Lee (Light Microscopy Specialist)

Quinn Lee has over 8 years of experience with advanced microscopy techniques. She joined the Microscopy and Flow Cytometry Facility as Light Microscopy Specialist after earning her PhD at the University of Illinois at Chicago.

Status
Closed
Location
Modality
Hybrid
Course Closes
Wed, Apr 30
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 Type
Short Courses in Bioinformatics and Biocomputing
Mon, May 05
Start Date
10:00 am - 12:00 pm

$20

Intermediate Unix

Member for

2 years 6 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This is a two-part course, with substantial hands-on practice in a shared computing environment. Participants will learn more about using UNIX/Linux from the command line. Topics will build on those in the introductory course, including more on the filesystem, the Bash shell, and text processing. The course will emphasize manipulating text using standard Linux utilities and stringing commands together using pipes. We’ll also introduce some of the powerful Linux utilities such as cut, sort, grep and awk, with the goal of continuing the climb up the steep Linux learning curve.

CB25028
Instructor

Anna Battenhouse (Bioinformatics Consultant and Biomedical Research Computing Facility Manager)

Anna Battenhouse is a research scientist in the lab of Dr. Edward Marcotte, is a Bioinformatics Consultant, and leads the Biomedical Research Computing 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, develops and maintains analysis scripts for the Bioinformatics Consulting Group, and teaches the Introduction to NGS Tools course in the Big Data in Biology Summer School as well as several CBRS short courses.

Status
Closed
Location
Modality
In-person. Zoom access available upon request.
Course Closes
Mon, Apr 28
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 Type
Short Courses in Bioinformatics and Biocomputing
Wed, Apr 30 and Fri, May 2
Start Date
9:00 am - 12:00 pm

$50 (includes both days)

Introduction to Flow Cytometry Analysis & Cell Sorting

Member for

2 years 6 months
Full name
Gary Chiang
Submitted by Gary Chiang on

Flow cytometry allows for rapid, simultaneous analysis of multiple parameters of single cells, which can then be sorted into individual populations according to these parameters. In this class, Richard will cover flow cytometry and cell sorting technology, applications of these techniques, best practices for experiments, the use of spectral flow cytometry for complex antibody panels, the fundamentals of performing compensation, and methods for presenting flow cytometry data.

CB25029
Instructor

Richard Salinas (Senior Flow Cytometry Specialist)

Richard Salinas has over 20 years of experience in flow cytometry with multiple cell analyzer and sorting platforms: BD Biosciences, Sony Biotechnology, Cytek Biosciences and Beckman-Coulter. He also has extensive data analysis experience in using FlowJo and FCS Express software.

Status
Closed
Location
Modality
Hybrid
Course Closes
Wed, Apr 23
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 Type
Short Courses in Bioinformatics and Biocomputing
Mon, Apr 28
Start Date
10:00 am - 12:00 pm

$20

Introduction to Unix

Member for

2 years 6 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This is a two-part course, with substantial hands-on practice in a shared computing environment. Participants will learn the basics of using UNIX from the command line. Introductory topics include 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.

CB25027
Instructor

Anna Battenhouse (Bioinformatics Consultant and Biomedical Research Computing Facility Manager)

Anna Battenhouse is a research scientist in the lab of Dr. Edward Marcotte, is a Bioinformatics Consultant, and leads the Biomedical Research Computing 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, develops and maintains analysis scripts for the Bioinformatics Consulting Group, and teaches the Introduction to NGS Tools course in the Big Data in Biology Summer School as well as several CBRS short courses.

Status
Closed
Location
Modality
In-person. Zoom access available upon request.
Course Closes
Mon, Apr 21
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 Type
Short Courses in Bioinformatics and Biocomputing
Wed, Apr 23 and Fri, Apr 25
Start Date
9:00 am - 12:00 pm

$50 (includes both days)

Statistical Modeling for Biologists

Member for

2 years 6 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This course will survey some of the basic principles of statistics crucial to the modeling of biological data. Specific topics will include hypothesis testing, false discovery rate adjustment, and applications and generalizations of linear models.

CB25026
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 to problems in immunology, did postdoctoral work modeling the transmission of infectious disease, and spent six years as a bioinformatician in industry.

Status
Closed
Location
Modality
Hybrid
Course Closes
Fri, Apr 11
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 Type
Short Courses in Bioinformatics and Biocomputing
Wed, Apr 16
Start Date
9:30 am - 12:30 pm

$50

Introduction to Microscopy and Flow Cytometry Resources

Member for

2 years 6 months
Full name
Gary Chiang
Submitted by Gary Chiang on

This course offers an overview of how the Microscopy and Flow Cytometry Facility can help researchers answer their scientific questions. Participants will learn about the state-of-the-art instruments and services available at the MFC, including advanced fluorescence microscopes, flow cytometers, and cell sorters. The course will also cover the types of experiments that can be conducted using these instruments, introduce the facility’s expert staff scientists, and provide detailed information on how to access and use the MFC’s resources.

CB25025
Instructor

Anna Webb (Director, Microscopy and Flow Cytometry Facility)

Before becoming director of the Microscopy and Flow Cytometry Facility in 2021, Anna Webb was the light microscopy specialist at the MFC for 5 years and has worked in light microscopy support in core facilities for 15 years.

Status
Closed
Location
Modality
Hybrid
Course Closes
Wed, Apr 09
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 Type
Short Courses in Bioinformatics and Biocomputing
Mon, Apr 14
Start Date
10:00 am - 12:00 pm

Free

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