Bioinformatics@HSL: BBT Workshop Descriptions

Descriptions of Basic Bioinformatics Tools Workshops

The Basic Bioinformatics Tools Forum series provides seminar and hands-on computer workshops on bioinformatics tools and resources to faculty, staff and students of UNC-Chapel Hill.  Class sessions are held at the Health Sciences Library in the Biogen-Idec Classroom (307; 3rd floor). For some classes, registrants have the option to attend online via Blackboard Collaborate.

Below are descriptions of workshops that have been regularly offered in past semesters.


UNIX for Biologists, Part 1: Introduction   

Time:  Friday, 2/10/2017, 9:00am - 10:30am

Instructor: Hemant Kelkar, Ph.D., UNC Center for Bioinformatics
Location: HSL 307 and online via Blackboard Collaborate

The ability to operate in a command line environment is becoming increasingly valuable in the genomics era. This workshop and the subsequent "UNIX for Biologists, Part 2: Killdevil" workshop are designed for experimental biologists who want to familiarize themselves with UNIX. This workshop will provide a very basic introduction to the UNIX operating system. Participants will learn how to login (software required/procedure) and interact with a UNIX server. We will cover basic UNIX system commands for interacting with the server and navigating the file system. We will learn about UNIX directory structure organization and file permissions.

Account Requirement: You will need an account on the “Killdevil” Linux cluster managed by ITS-Research Computing. Instructions for requesting a “Killdevil” account are available at this link: http://help.unc.edu/help/getting-started-on-killdevil/#P41_2630. Please submit your account request at least 3 days before class. It generally takes 24-48 hours for account creation.

Prerequisites: No prior knowledge of UNIX is required. NOTE: For those unfamiliar with UNIX and Killdevil/UNC computer cluster usage, this class and UNIX for Biologists, Part 2: Killdevil (from this series or prior offerings) are prerequisites for the next generation sequencing classes that follows them in the BBT workshop series: "Introduction to Next Generation Sequencing Data and Quality Control" AND "Alignment of Next Generation Sequencing Data: Background and Practical Considerations."


UNIX for Biologists, Part 2: Killdevil  

Time:  Wednesday, 2/15/2017, 9:00am - 10:30am

Instructor: Hemant Kelkar, Ph.D., UNC Center for Bioinformatics
Location: HSL 307 and online via Blackboard Collaborate

The ability to operate in a command line environment is becoming increasingly valuable in the genomics era. This workshop and the earlier "UNIX for Biologists, Part 1: Introduction" workshop are designed for experimental biologists who want to familiarize themselves with UNIX. This workshop will introduce UNC-Chapel Hill resources available to bioscience researchers and will focus primarily on resources on the "Killdevil" compute cluster operated by UNC ITS-Research Computing. After a quick recap of basic file/folder operations used in a UNIX environment, we will cover how to move files between the server and a local computer. We will introduce the “Killdevil” compute cluster and the module-based software used for managing jobs on the cluster. Finally, participants will learn to use two basic bioinformatics tools (NCBI BLAST and UCSC BLAT) on the command line on the Killdevil cluster and how to access UNIX/Linux systems via a graphical user interface (X-Win32, XQuartz).

Account Requirement: You will need an account on the “Killdevil” Linux cluster managed by ITS-Research Computing. Instructions for requesting a “Killdevil” account are available at this link: http://help.unc.edu/help/getting-started-on-killdevil/#P41_2630. Please submit your account request at least 3 days before class. It generally takes 24-48 hours for account creation.

Prerequisites: It would be very helpful to attend UNIX for Biologists, Part 1: Introduction, if you are not familiar with UNIX. If you are somewhat familiar with UNIX then you could potentially skip attending Part 1.  NOTE: For those unfamiliar with UNIX and Killdevil/UNC computer cluster usage, this class and UNIX for Biologists, Part 1: Introduction (from this series or prior offerings) are prerequisites for the next generation sequencing classes that follows them in the BBT workshop series: "Introduction to Next Generation Sequencing Data and Quality Control" AND "Alignment of Next Generation Sequencing Data: Background and Practical Considerations."


Introduction to Next Generation Sequencing Data and Quality Control   

Time: Tuesday, 2/21/2017, 2:30pm - 4:00pm

Instructor:  Tristan De Buysscher, Bioinformatics Scientist
Location: HSL 307

Genome wide analysis of gene expression has been a popular technique since the advent of microarrays. Next Generation Sequencing (NGS) technology was applied for this purpose early in the life cycle and has since become one of the most popular uses of NGS. We will start with a general overview of NGS technologies and consider commonly used data formats. Because of time/space constraints, we will be using a small subset of sequences (derived from a real dataset). I will introduce FastQC which is a popular application used for quality control (QC) of NGS data. We will then take a look at examples of results from FastQC (aside from the one we will run on our test data). This will be followed by an overview of data scanning/trimming programs. These programs look for contaminating sequences (e.g. adapters) and can also trim data based on various other criteria.

Account Requirement: You will need an account on the “Killdevil” Linux cluster managed by ITS-Research Computing. Instructions for requesting a “Killdevil” account are available at this link: http://help.unc.edu/help/getting-started-on-killdevil/#P41_2630. Please submit your account request at least 3 days before class. It generally takes 24-48 hours for account creation.

Prerequisites: For those unfamiliar with UNIX and Killdevil/UNC computer cluster usage, UNIX for Biologists, Part 1 and UNIX for Biologists, Part 2 (from this series or prior offerings) are prerequisites for this class.


BBTools: A Toolbox for High Throughput Sequencing Data Analysis

Time:  Wednesday, 3/1/2017, 9:30am - 11:00am

Instructor: Hemant Kelkar, Ph.D., UNC Center for Bioinformatics
Location: HSL 307 and online via Blackboard Collaborate

The BBTools suite contains tools that assist with multiple types of high throughput (HT) -sequencing data analysis. After an overview of tools included in BBTools toolbox, we will learn how to use “bbduk” (decontamination using k-mers) for scanning/trimming data to remove adapter contamination. This will be followed by “bbmap” (sequence data aligner) which we are going to use to align the test sequence data.

Account Requirement: You will need an account on the “Killdevil” Linux cluster managed by ITS-Research Computing. Instructions for requesting a “Killdevil” account are available at this link: http://help.unc.edu/help/getting-started-on-killdevil/#P41_2630. Please submit your account request at least 3 days before class. It generally takes 24-48 hours for account creation.

Prerequisites: For those unfamiliar with UNIX and Killdevil/UNC computer cluster usage, UNIX for Biologists, Part 1 and UNIX for Biologists, Part 2 (from this series or prior offerings) are prerequisites for this class.


Differential Expression Analysis of RNAseq Data

Time:  Tuesday, 3/7/2017, 2:30pm - 4:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist
Location: HSL 307

RNAseq provides a snapshot of the transcription state of the cells from which RNA was harvested. One of the most common applications of this sequencing data is to look at changes in the transcriptome state between two or more conditions the cells were exposed to. We will discuss the various considerations in analyzing RNAseq data and run through a practical example using DESeq2.

Account Requirement: You will need an account on the “Killdevil” Linux cluster managed by ITS-Research Computing. Instructions for requesting a “Killdevil” account are available at this link: http://help.unc.edu/help/getting-started-on-killdevil/#P41_2630. Please submit your account request at least 3 days before class. It generally takes 24-48 hours for account creation.

Prerequisites: For those unfamiliar with UNIX and Killdevil/UNC computer cluster usage, UNIX for Biologists, Part 1 and UNIX for Biologists, Part 2 (from this series or prior offerings) are prerequisites for this class.


Introduction to NCBI Biomolecular Database Searching     Register

Time:  Wednesday, 3/22/2017, 9:30am -11:00am

Instructor: Barrie Hayes, Bioinformatics & Translational Science Librarian
Location: HSL 307

Bioinformatics and biomolecular databases can be powerful tools to support biomedical and life sciences research. While the National Center for Biotechnology Information (NCBI) provides free access to millions of biomolecular records, learning how to leverage these tools can be daunting. This 90 minute workshop will provide an overview on how to use NCBI databases, and introduce strategies for using Entrez to conduct text searches.

Prerequisites: No prior knowledge of NCBI database searching is required.


Browsing Genes and Genomes with Ensembl and Ensembl Genomes    Register (Closes 4/17/17)

Time:  Tuesday, 4/18/2017, 9:00am - 5:00pm
Note: There will be a 1-hour break for lunch and 15 minute breaks in the morning and afternoon. The workshop is scheduled to conclude at 5:00pm.

Instructor: Helen Sparrow, PhD, EMBL-EBI
Location: HSL 307
Registration Fee: $20.00
Sponsorship: This workshop is sponsored by the Health Sciences Library Research Hub with support from the School of Medicine Office of Research.

The Ensembl and Ensembl Genomes projects provide a comprehensive and integrated source of annotation of vertebrate and non-vertebrate genome sequences, respectively. The browser workshop will include presentation and demonstration, and provide participants an opportunity to gain hands-on experience in the use of Ensembl genome browsers. Depending on the preferences of the participants, more or less emphasis can be allocated to the Ensembl browser (vertebrates) and to the Ensembl Genomes browser (non-vertebrates). Preferences will be determined through a pre-course survey of registrants.

The Ensembl browser workshops typically consist of the first four core modules below, plus one other module (Comparative Genomics or Regulation). The additional module will be determined by a pre-course survey that will be sent to workshop registrants to identify their interests:

Core Modules:

  • Introduction to Ensembl: origin, goals and organisation of the Ensembl project
  • Genebuild: how are Ensembl gene and transcripts predictions made?
  • Data mining with BioMart: retrieving genomic information using a web interface (no programming required).
  • Variation: SNPs and other polymorphisms, haplotypes, structural variants like CNVs and the Ensembl VEP (variant effect predictor)

The final module will be selected from the options below, based on pre-course survey:

  • Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic regions

OR

  • Regulation: Finding sequences that may be involved in gene regulation, and integration of ENCODE, Roadmap Epigenomics and Blueprint data

Prerequisites: The only prerequisite for this workshop is general knowledge of molecular biology and genomics and a familiarity with web browsers.

 


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