Bioinformatics@HSL: BBT Workshop Descriptions

Descriptions of Basic Bioinformatics Tools Workshops

The Basic Bioinformatics Tools Workshop 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 or are scheduled for the current semester.


Introduction to Next Generation Sequencing  

Time:  Rescheduled due to weather for Friday, 9/21/2018, 1:00pm - 2:30pm Monday, 9/17/2018, 1:00pm - 2:30pm

Instructor: Hemant Kelkar, Ph.D., Director of Scientific Computing, UNC Center for Bioinformatics
Location:  HSL 227 HSL 307

It has been a decade since high-throughput sequencing (also called next generation sequencing or NGS), was first deployed at UNC. Much has changed since that time but some things remain the same. We will review current commercial sequencing technologies and highlight those accessible to UNC researchers. We will go over practical tips to get the most out of your NGS experiment. Finally, we will review informatics considerations and data characteristics.

This is a lecture class with no-hands on exercises planned. This class is NOT a prerequisite for other workshops in the Basic Bioinformatics Tools series.

Prerequisites: No prior knowledge of NGS is required.

 


Introduction to the UNIX Shell, Parts 1, 2 and 3

The 3 Introduction to the UNIX Shell workshops immediately below are a chained sequence of workshops to introduce participants to the UNIX command line, basic commands, navigating file system, setting up bioinformatics projects, and introductory scripting. Each class will build upon the last and each part is a prerequisite for the next class in the 3-workshop UNIX sequence. The 3 workshops in the UNIX block are in turn prerequisites for the 2 Introduction to Bioinformatics Basics workshops which follow in the workshop series.

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Introduction to the UNIX Shell, Part 1  

Time:  Tuesday, 9/25/2018, 2:00pm - 4:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: HSL 307

Account Requirement: You will need an account on the “Longleaf” Linux cluster managed by ITS-Research Computing. Instructions for requesting a “Longleaf” account via the ONYEN Subscribe to Services utility is available at this link: http://help.unc.edu/help/how-do-i-get-an-account-on-killdevil-research-computing-cluster/. 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.

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Introduction to the UNIX Shell, Part 2  

Time:  Tuesday, 10/2/2018, 2:00pm - 4:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: HSL 307

Account Requirement: See Introduction to UNIX Shell, Part 1 Account Requirement above.

Prerequisites: Introduction to UNIX Shell, Part 1 is a prerequisite for this Introduction to UNIX Shell, Part 2 workshop.

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Introduction to the UNIX Shell, Part 3  

Time:  Thursday, 10/11/2018, 2:00pm - 4:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: HSL 307

Account Requirement: See Introduction to UNIX Shell, Part 1 Account Requirement above.

Prerequisites: Introduction to UNIX Shell, Parts 1 and 2 are prerequisites for this Introduction to UNIX Shell, Part 3 workshop.


Introduction to Bioinformatics Basics, Part 1  

Time:  Tuesday, 10/16/2018, 2:00pm - 4:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: HSL 307

This workshop will provide an introduction to bioinformatics data types and basic quality control of short read data, including assessing quality and filtering data.

Account Requirement: See Introduction to UNIX Shell, Part 1 Account Requirement above.

Prerequisites: The UNIX workshop block (Parts 1, 2 and 3) are prerequisites for this Introduction to Bioinformatics Basics, Part 1 workshop.


Introduction to Bioinformatics Basics, Part 2   

Time:  Tuesday, 10/23/2018, 2:00pm - 4:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: HSL 307

This workshop will cover basic methods in bioinformatics including how to align data to a reference genome and call variants. Time permitting, some scripting will be covered as well.

Account Requirement: See Introduction to UNIX Shell, Part 1 Account Requirement above.

Prerequisites: The UNIX workshop block (Parts 1, 2 and 3) and Introduction to Bioinformatics Basics, Part 1 are prerequisites for this Introduction to Bioinformatics Basics, Part 2 workshop.


Introduction to NCBI Biomolecular Database Searching  

Time:  Not currently scheduled

Instructor: Barrie Hayes, Bioinformatics & Research Data Librarian
Location: HSL 307

This workshop will introduce participants to 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.


Introduction to BLAST Searching   

Time:  Not currently scheduled

Instructor: Barrie Hayes, Bioinformatics & Research Data Librarian
Location: HSL 307

This workshop will introduce the basics of sequence similarity searching using the NCBI Basic Local Alignment Search Tool (BLAST). Participants will conduct BLAST searches and examine the type of information retrieved.

Prerequisites: No prior experience with BLAST searching is required.


 Introduction to R: Practical Examples in Linear Regression and ANOVA    Register

Time:    Wednesday, 11/14/2018, 9:00am - 11:00am

Instructor: Yucheng Yang, Postdoctoral Fellow, Department of Genetics
Location: HSL 227

This workshop will introduce participants to the basics of R and illustrate the use of R in linear regression and ANOVA analyses.

Prerequisites and Computer Requirements:

  • No prior knowledge of R software is required. Additionally, this Introduction to R workshop does not require completion of any of the other workshops in the Basic Bioinformatics Tools workshop series.
  • Participants will need to bring a fully charged laptop with latest versions of R and R Studio installed.

UCSC Genome Browser - Gateway to Whole-Genome Data     

Time:  Tuesday, 9/18/2018. 8:30am - 4:30pm; NOTE: IF weather conditions delay instructor travel, the workshop makeup date will be Thursday 9/20/2018, 8:30am - 4:30pm.
Note: There will be a 1-hour break for lunch (on your own) and 15-20 minute breaks in the morning and afternoon. The workshop is scheduled to conclude at 4:30pm.

Instructor: Robert Kuhn, PhD, UCSC Genome Browser

Location: HSL 307 computer classroom (Tentative location - see Location Details and Laptop Requirement below)
Location Details and Laptop Requirement: Prepare to bring your laptop for use in this workshop. The location for the workshop may change to accommodate a larger number of registrants. In this case, each registrant will need to bring their laptop in order to participate. Registrants will be notified a few days before the workshop to confirm the final room/location and the laptop requirement.
Registration Fee: $45.00

Registration Priority: Through Friday, September 7th, only a limited number of seats in this workshop will be available for non-UNC affiliate registrants. The majority of workshop seats will be held for UNC-Chapel Hill-affiliated registrants through that date. Beginning Saturday, September 8th, all registrants will be allocated a workshop seat in the order they register until capacity is reached. Note that registration will CLOSE on Monday, September 17th.
Sponsorship: This workshop is sponsored by the Health Sciences Library Research Hub with support from the Integrative Program for Biological and Genome Sciences (iBGS).

The UCSC Genome Browser (genome.ucsc.edu) is developed and maintained by the Genome Bioinformatics Group, a cross-departmental team within the UCSC Genomics Institute.

The one-day UCSC genome browser workshop will cover the following content. The order of topic coverage may be rearranged to address participant questions as they come up.

Content / Approximate Schedule

8:30 AM to 10:00 AM - Introduction to the UCSC Genome Browser

10:00 AM to 10:20 AM - Break

10:20 AM to 12:30 PM - Advanced Browser Topics

12:30 PM to 1:30 PM - Lunch

1:30 PM to 2:30 PM - Follow-up and Questions

2:30 PM to 2:45 PM - Break

2:45 PM to 4:30 PM - Working through Problem Sets (Hands-On)

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


Browsing Genes and Genomes with Ensembl and Ensembl Genomes     

Time:  Not currently scheduled
Note: There will be a 1-hour break for lunch (on your own) and 15 minute breaks in the morning and afternoon. The workshop is scheduled to conclude at 5:00pm.

Instructor: Astrid Gall, 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 (www.ensembl.org) and Ensembl Genomes (www.ensemblgenomes.org) projects offer integrated genome, variation, gene regulation and comparative genomics data of vertebrate and non-vertebrate genome sequences, respectively, on open access web browser platforms.

The one-day browser workshop offers participants the possibility of gaining lots of hands-on experience in the use of the Ensembl genome browser, but also provides them with the necessary background information. The workshop is primarily targeted at wetlab researchers.

Content

The workshop consists of a series of modules, listed below. Most modules consist of a presentation and a demonstration of the tools, followed by the opportunity to do exercises. Participants are encouraged to bring problems/questions about their research and we will try to tackle these during the workshop using Ensembl. The exact mix of modules can be varied, depending on the preferences of the participants.

A typical one-day workshop will consist of the first three of these modules, plus two other modules of your choice. Participants' interests and preferences for the modules will be determined through a pre-course survey of registrants. 

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


  • No prior knowledge of R software is required. Additionally, this Introduction to R workshop does not require completion of any of the other workshops in the Basic Bioinformatics Tools workshop series.
  • Participants will need to a fully charged laptop with latest versions of R and R Studio installed.
    • You can download R from CRAN (Comprehensive R Archive Network): https://cran.r-project.org
    • You can download RStudio from https://www.rstudio.com
    • General overview of the Browser, what it is, history
    • A guided tour of the basic parts of the UCSC Genome Browser
    • Navigation, including between organisms by homology, zooming and panning; configuring track visibility
    • Data – genesets, annotation, Comparative Genomics, GTEx expression data, CRISPR guides, pathways, Gene Interactions
    • Searches: for regions/positions, gene names, motifs, HGVS, other keywords, BLAT, short match track for sequences
    • Saving/Retrieving/Sharing sessions
    • Custom tracks – loading your own data
    • Variants: benign/pathogenic; small/large
    • Export to .pdf
    • Finding data
    • Variants – benign/pathogenic and CNVs/SNPs
    • Table Browser – extracting data from tables
    • Track Hubs – remotely hosted data
    • Multi-region: exon-only display, defined regions
    • Get DNA and use for PCR primers (in-silico PCR)
    • RNA-seq and Track Collections – co-configuration of datasets
    • Introduction to Ensembl: origin, goals and organization of the Ensembl project
    • Genebuild: how are Ensembl gene and transcripts predictions made?
    • Data export with BioMart: retrieving genomic information using a web interface (no programming required).
    • Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic regions
    • Variation: SNPs and other polymorphisms, haplotypes, linkage disequilibrium, structural variants like CNVs
    • Regulation: Sequences that may be involved in gene regulation, and integration of ENCODE data
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