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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 Elluminate.

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


Introduction to UNIX for Biologists, Part 1 Completed for Spring 2014

Time: Tuesday 2/4/2014, 1:00pm - 3:00pm

Instructor: Hemant Kelkar, Ph.D., UNC Center for Bioinformatics
Location: HSL 307

The ability to operate in a command line environment is becoming increasingly valuable in the genomics era. This workshop and the subsequent "Introduction to UNIX for Biologists, Part 2" 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.

No prior knowledge of UNIX is required. Participants are expected to have a valid UNC “ONYEN”. You should request an account on “KillDevil” and on “Kure” Linux clusters 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. Instructions for requesting a “Kure” account are available at this link:http://help.unc.edu/help/getting-started-on-kure/#P24_1521. Please submit your 2 account requests at least 3-4 days before class. It generally takes 24-48 hours for account creation.

Note: For those unfamiliar with UNIX and Kure/UNC computer cluster usage, this class and UNIX for Biologists, Part 2 are highly recommended preparation/prerequisites for the next generation sequencing classes offered in the basic bioinformatics workshop series.

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Introduction to UNIX for Biologists, Part 2 Completed for Spring 2014

Time: Tuesday 2/11/2014, 1:00pm - 3:00pm

Instructor: Hemant Kelkar, Ph.D., UNC Center for Bioinformatics
Location: HSL 307

The ability to operate in a command line environment is becoming increasingly valuable in the genomics era. This workshop and the earlier "Introduction to UNIX for Biologists, Part 1" workshop are designed for experimental biologists who want to familiarize themselves with UNIX. This workshop will introduce UNC 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” and “Kure” compute clusters and the software used for managing jobs on these clusters. Finally, participants will learn to use two basic bioinformatics tools (NCBI BLAST and UCSC BLAT) on the command line on the KillDevil and Kure clusters. It would be very helpful to attend the Part 1 of this class, if you are not familiar with UNIX. If you are somewhat familiar with UNIX then you could potentially skip attending Part 1.

You will need accounts on “KillDevil” and on “Kure” Linux clusters 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. Instructions for requesting a “Kure” account are available at this link: http://help.unc.edu/help/getting-started-on-kure/#P24_1521. Please submit your 2 account requests at least 3-4 days before class. It generally takes 24-48 hours for account creation.

Note: For those unfamiliar with UNIX and Kure/UNC computer cluster usage, this class and UNIX for Biologists, Part 1 are highly recommended preparation/prerequisites for the next generation sequencing classes offered in the basic bioinformatics workshop series.

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Introduction to Sequencing Technology    Completed for Spring 2014

Time: Thursday 2/27/2014, 12:30pm - 1:30pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: HSL 307 and online via Elluminate

This class will introduce the basics of high throughput sequencing technologies. This session will include an overview of the technologies themselves (e.g. Illumina, Ion Torrent/Proton, Pacific Biosciences) and a tutorial on examining sequence quality scores using examples from all three technologies.

Prerequisites: For those unfamiliar with UNIX and Kure/UNC computer cluster usage, UNIX for Biologists, Part 1 and UNIX for Biologists, Part 2 are highly recommended preparation/prerequisites for this class.

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Introduction to Analysis of Next Generation Sequencing Data    Completed for Spring 2014

Time: Friday 2/28/2014, 1:30pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: HSL 307 and online via Elluminate

This class provides an introduction to use and analysis of high throughput sequencing data. This session will include both an overview of the concepts behind the analyses and practical application with an example data set.

An account on the “Kure” Linux cluster (managed by ITS-Research Computing) is required for this class. Instructions for requesting a “Kure” account are available at this link: http://help.unc.edu/help/getting-started-on-kure/#P24_1521. Please submit your account request at least 3-4 days before class. It generally takes 24-48 hours for account creation.

 

Prerequisites: For those unfamiliar with UNIX and Kure/UNC computer cluster usage, UNIX for Biologists, Part 1 and UNIX for Biologists, Part 2 are highly recommended preparation/prerequisites for this class.

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Introduction to the Protein Data Bank and Pymol  Not Offered in Spring 2014

Time: Not currently scheduled

Instructor: Brenda Temple, Ph.D., UNC Structural Bioinformatics Core Facility
Location: HSL 307 and online via Elluminate

 

This workshop will introduce participants to the Protein Data Bank (PDB), a macromolecular structure database for crystallographic and NMR experimental structures, and to PyMOL, a molecular visualization system for rendering 3D structures.

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Browsing Genes and Genomes with Ensembl and Ensembl Genomes (A full day workshop)    Completed for Spring 2014

Time: Friday, 3/7/14, 9:00am - 5:00pm

Instructor: Denise Carvalho-Silva, PhD, EMBL-EBI
Location: HSL 307

 

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 three "core" modules below, plus two other modules from the list below the Core Modules. The additional two modules 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, gene and transcript annotation, data organization and different access points (e.g. browser, BioMart, FTP site, APIs)
  • Website live demo: guided tour of the most important pages of the Ensembl website focusing on the Location tab, Gene tab, Transcript tab, and Variation tab
  • BioMart: retrieving datasets using the web tool BioMart (no programming skills required)

Two modules to be selected from list below based on a pre-course survey of registrants:

 

  • Variation: short scale variation (SNPs, indels), large scale variation, (CNVs, deletions, etc), phenotype and population genetics data, VEP (Variant Effect Predictor)
  • Comparative genomics: gene trees (protein-coding and non-coding genes), orthologues, protein families, whole genome alignments and synteny
  • Regulation: ENCODE data hub, and annotation of regulatory elements based on ChIP-Seq, DNase1-Seq, FAIRE-Seq, and TFBS

 

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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