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. Each course costs $25, and meets for one day, lasting between two to three hours per course.
Below is a listing of courses offered in the Fall 2015 Semester.
● Introduction to Unix Command Line
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Students in this course will learn the basics of using UNIX from the command line. We will cover introductory topics include the file system, the shell, permissions, and text files. Students will manipulate text files and directories, use pipes and filters, write for loops, create shell scripts, and learn commands for finding things. The learning objectives of the course are 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
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.
● Core Next Generation Sequencing Analysis Tools
This course provides a high-level introduction to concepts and best practices for next generation sequencing analysis (NGS). We will touch on the main skills and resources you need to get started. Participants in this course will gain familiarity of NGS vocabulary, and knowledge of basic tools and file formats. We hope this course will help you better understand what it take to bridge the bioinformatician to bench-scientist divide.
● Basics of RNA-seq
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. 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.
● RNA-seq 2
This theory course will introduce a selection of methods for further bioinformatic analysis of RNA-Seq data. The focus will be on unsupervised learning and clustering methods (including principal components analysis (PCA) and hierarchical clustering), weighted gene co-expression network analysis (WGCNA), and data visualization using ggplot2. Participants will have the opportunity to apply these methods as implemented in R to publicly available data.
● Hands-on RNA-seq
This is a hands-on course to which you are encouraged to bring your own RNA-Seq data. You will be provided with the tools to run a standard RNA-Seq workflow which includes quality assessment, mapping, differential expression analysis, and splice variant analysis. This will be followed by one-on-one time during which we will help you run some of these tools on your data.
● Introduction to ChIP-seq
This is an introductory theory course on considerations for performing and analyzing ChIP-seq experiments, focusing on best practices based on the Iyer lab's extensive experience in this field. We will discuss experimental design, library prep options, quality assessment and analysis pipelines. This course is designed to give you an idea of what options are available when designing, sequencing and analyzing a ChIP-seq experiment.
● Introduction to RAD-seq
Restriction-associated DNA (RAD) sequencing techniques are widely used for studying population genomics, genetic connectivity, genome mapping, QTL mapping, and identifying loci under selection. Students in this course will use the UNIX environment and TACC clusters to pre-process raw sequence data, call genotypes using de novo (without a reference genome) and reference-based (GATK) pipelines; filter genotype calls based on replicates; assess the quality of genotyping; and perform some basic statistics and population genetic analysis.
● Git for Version Control and Collaboration (THIS COURSE HAS BEEN CANCELLED)
Students in this course will learn the benefits of and how to use version control system Git. Students will setup a Git repository, track changes, explore version history. Using GitHub, students will work in partners to gain familiarity with online repositories, forks, pull requests, cloned repositories, and setting conflicts.
● Working with MySQL Databases
This is an introductory course on the basics of database technology using MySQL. The course will cover the basics of the structured query language (SQL) along with modes of database interaction specific for bioinformatics workflows. We will begin with an introduction to databases and the MySQLWorkbench user interface. This will include creating and populating a schema, followed by simple and more complex queries to select and manipulate different subsets of data. Finally, we will cover using Python for programmatic access of databases.
