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FNT 1.104

Introduction to Python

Member for

3 years 1 month
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.

Course ID
CB26001
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
9:30 am - 12:30 pm

$50

Introduction to Statistical Modeling

Member for

3 years 1 month
Full name
Gary Chiang

This course is a hands-on introduction to building and interpreting statistical models in R, with a focus on real-world applications. We will cover key concepts in hypothesis testing, multiple linear regression, and logistic regression. You will learn how to choose appropriate modeling approaches, fit models using R, check assumptions, interpret results, and clearly communicate your findings. Each topic will include a brief introduction to foundational concepts, a demonstration of analysis in R, and guided practice through interactive coding exercises. Emphasis will be placed on using statistical modeling to answer research questions within reproducible workflows. By the end of the course, the goal is for you to be able to apply statistical modeling to your own data.

Preferred or Prerequisite Skills:
This course is recommended for students with some prior knowledge of R (in particular, we recommend taking the “Introduction to R for Biologists” summer school course offered above).

Computer Requirement:
Participants are expected to provide their own laptops.

Course ID
CB25035
Status
Closed
Instructor
Modality
Hybrid, but in-person encouraged
Course Closes
Wed, May 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 Semester
June 2 - June 6
1:30 pm - 4:30 pm

Principles of Machine Learning for Bioinformatics

Member for

3 years 1 month
Full name
Gary Chiang

This four-day course will introduce a selection of machine learning methods used in bioinformatic analyses with a focus on RNA-seq gene expression data. We will cover unsupervised learning, dimensionality reduction and clustering; feature selection and extraction; and supervised learning methods for classification (e.g., random forests, SVM, LDA, kNN, etc.) and regression (with an emphasis on regularization methods appropriate for high-dimensional problems). Participants will have the opportunity to apply these methods as implemented in R and python to publicly available data.

Preferred or Prerequisite Skills:
This course is recommended for students with some prior knowledge of either R or python. Participants are expected to provide their own laptops with recent versions of R and/or python installed. Students will be instructed to download several free software packages (including R packages and python libraries including pandas and sklearn).

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

Course ID
CB25038
Status
Closed
Modality
Hybrid
Course Closes
Thu, Jun 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
June 16 - June 20 (no class on June 19)
9:00 am - 12:00 pm

Introduction to RNA-Seq

Member for

3 years 1 month
Full name
Gary Chiang

This five-day course provides an introduction to methods for analysis of RNA-seq data. It assumes familiarity and comfort with Linux command line. A typical RNA-seq workflow will be featured, starting from quality assessment of raw data, mapping (bwa, kallisto), differential expression analysis (DESeq2), and downstream analyses and visualization. The course also describes analysis methods for dealing with single-cell RNA-Seq data. Participants will gain hands-on experience using these tools in a Linux command line environment.

Preferred or Prerequisite Skills:
Familiarity working in a UNIX environment. Consider taking the “Introduction to Biocomputing” or “Introduction to Core NGS Concepts and Tools” summer school course to refresh your UNIX skills.

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.

Course ID
CB25037
Status
Open
Modality
Hybrid, but in-person encouraged
Course Closes
Wed, Jun 04
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
June 9 - June 13
1:00 pm - 4:00 pm

Introduction to Python

Member for

3 years 1 month
Full name
Gary Chiang

This five-day course will introduce students to basic concepts in programming using the Python language, establishing a foundation for scientific computing. Trainees will learn introductory topics such as data structures, control flow, functions, file input/output, and data parsing. The class will work with SciPy libraries like Pandas. Trainees will have full access to the teacher’s course book and course content (datasets, scripts, and jupyter notebooks).

Preferred or Prerequisite Skills:
None

Computer Requirement:
This class is offered in-person. Students must provide laptops able to connect to the internet, and a Firefox or Chrome browser. UT EID is required for wireless access. Please be sure you know your UT EID when you come to class. To obtain a UT EID, go here.

Course ID
CB25036
Status
Closed
Modality
In-person
Course Closes
Wed, Jun 04
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
June 9 - June 13
9:00 am - 12:00 pm

Introduction to Biocomputing: from files to functions to plots

Member for

3 years 1 month
Full name
Gary Chiang

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.

Course ID
CB25033
Status
Closed
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
May 27 - May 30
1:30 pm - 4:30 pm

Introduction to Core NGS Concepts and Tools

Member for

3 years 1 month
Full name
Gary Chiang

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.

Course ID
CB25034
Status
Open
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
June 2 - June 6
9:00 am - 12:00 pm

Introduction to R for Biologists

Member for

3 years 1 month
Full name
Gary Chiang

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.

Course ID
CB25032
Status
Closed
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
May 20 - May 23
1:30 pm - 4:30 pm

Advanced Bash Scripting

Member for

3 years 1 month
Full name
Gary Chiang

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.

Course ID
CB25031
Status
Closed
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).

Wed, May 7 and Fri, May 9
9:00 am - 12:00 pm

$50 (includes both days)

Introduction to Light Microscopy

Member for

3 years 1 month
Full name
Gary Chiang

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.

Course ID
CB25030
Status
Closed
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).

Mon, May 05
10:00 am - 12:00 pm

$20

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