Bioinformatics@HSL: BBT Workshop Descriptions

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 the UNIX Shell: A Six Workshop Sequence

The six, one-hour 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 the file system, setting up bioinformatics projects, and introductory scripting. Each class will build upon the prior class and each part is a prerequisite for the next class in the six-workshop UNIX Shell sequence.

The six workshops in the UNIX block are in turn prerequisites for the five, one-hour Introduction to Bioinformatics Basics workshops which follow in the entire eleven workshop series.

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1. UNIX Shell Basics 1 (Online via Zoom) Completed

Time: Tuesday 9/1/2020, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via Zoom

Account Requirement: You will need an account on the “Longleaf” Linux cluster managed by ITS Research Computing. Follow instructions for requesting a “Longleaf” account on the ITS Research Computing website: https://its.unc.edu/research-computing/request-a-cluster-account/. 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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2. UNIX Shell Basics 2 (Online via Zoom) Completed

Time: Tuesday 9/8/2020, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via Zoom

Account Requirement: See UNIX Shell Basics 1 Account Requirement above.

Prerequisites: UNIX Shell Basics 1 is a prerequisite for this UNIX Shell Basics 2 workshop.

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3. Working with Files (Online via Zoom) Completed

Time: Tuesday 9/15/2020, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via Zoom

Account Requirement: See UNIX Shell Basics 1 Account Requirement above.

Prerequisites: UNIX Shell Basics 1 and UNIX Shell Basics 2 are prerequisites for this Working with Files workshop.

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4. Useful Tools and Pipes (Online via Zoom) Completed

Time: Tuesday 9/22/2020, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via Zoom

Account Requirement: See UNIX Shell Basics 1 Account Requirement above.

Prerequisites: UNIX Shell Basics 1, UNIX Shell Basics 2, and Working with Files are prerequisites for this Useful Tools and Pipes workshop.

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5. Loops and Scripts (Online via Zoom) Completed

Time: Tuesday 9/29/2020, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via Zoom

Account Requirement: See UNIX Shell Basics 1 Account Requirement above.

Prerequisites: UNIX Shell Basics 1, UNIX Shell Basics 2, Working with Files, and Useful Tools and Pipes are prerequisites for this Loops and Scripts workshop.

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6. Introduction to Slurm (Online via Zoom) Completed

Time: Tuesday 10/6/2020, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via Zoom

Account Requirement: See UNIX Shell Basics 1 Account Requirement above.

Prerequisites: UNIX Shell Basics 1, UNIX Shell Basics 2, Working with Files, Useful Tools and Pipes, and Loops and Scripts are prerequisites for this Introduction to Slurm workshop.

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Introduction to Bioinformatics Basics: A Five Workshop Sequence

This five-workshop sequence will cover bioinformatics data types, basic quality control of short read data including assessing quality and filtering data, and basic bioinformatics methods including how to align data to a reference genome and call variants. Time permitting, some scripting will be covered as well.

The six workshops in UNIX Shell sequence above are prerequisites for the five-workshop Introduction to Bioinformatics Basics sequence. Additionally, each class in the Introduction to Bioinformatics Basics sequence will build upon the prior class and each session is a prerequisite for the next class in the sequence.

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7. Intro to Bioinformatics Basics: Quality Control and Trimming (Online via Zoom) Completed

Time: Tuesday 10/13/2020, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via Zoom

Account Requirement: See UNIX Shell Basics 1 Account Requirement above.

Prerequisites: The six workshops in UNIX Shell sequence above (UNIX Shell Basics 1, UNIX Shell Basics 2, Working with Files, Useful Tools and Pipes, Loops and Scripts, and Introduction to Slurm) are prerequisites for this Quality Control and Trimming workshop.

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8. Intro to Bioinformatics Basics: Aligning Reads (Online via Zoom) Completed

Time: Tuesday 10/20/2020, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via Zoom

Account Requirement: See UNIX Shell Basics 1 Account Requirement above.

Prerequisites:

The six workshops in UNIX Shell sequence above
Intro to Bioinformatics Basics: Quality Control and Trimming

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9. Differential Expression Analysis: Intro and Counting (Online via Zoom) Completed

Time: Tuesday 10/27/2020, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via Zoom

Account Requirement: See UNIX Shell Basics 1 Account Requirement above.

Prerequisites:

The six workshops in UNIX Shell sequence above
Intro to Bioinformatics Basics: Quality Control and Trimming
Intro to Bioinformatics Basics: Aligning Reads

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10. Differential Expression Analysis: DESeq Basics (Online via Zoom) Register

Time: Tuesday 11/3/2020, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via Zoom

Account Requirement: See UNIX Shell Basics 1 Account Requirement above.

Prerequisites:

The six workshops in UNIX Shell sequence above
Intro to Bioinformatics Basics: Quality Control and Trimming
Intro to Bioinformatics Basics: Aligning Reads
Differential Expression Analysis: Intro and Counting

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11. Differential Expression Analysis: Intermediate DESeq & RStudio (Online via Zoom) Register

Time: Tuesday 11/10/2020, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, UNC Center for Bioinformatics
Location: Online via Zoom

Account Requirement: See UNIX Shell Basics 1 Account Requirement above.

Prerequisites:

The six workshops in UNIX Shell sequence above
Intro to Bioinformatics Basics: Quality Control and Trimming
Intro to Bioinformatics Basics: Aligning Reads
Differential Expression Analysis: Intro and Counting
Differential Expression Analysis: DESeq Basics

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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 Completed Fall 2019

Time: Wednesday 11/6/2019, 9:00am - 11:00am

Instructor: Yucheng Yang, Postdoctoral Research Associate, Department of Genetics
Location: HSL 307

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.

You can download R from CRAN (Comprehensive R Archive Network): https://cran.r-project.org
You can download RStudio from https://www.rstudio.com

UCSC Genome Browser - Gateway to Whole-Genome Data Completed Spring 2020

Time: Tuesday, 1/28/2020. 9:00am - 5:00pm
Instructor: Robert Kuhn, PhD, UCSC Genome Browser

Registration Fee: $40.00

Registration Priority: Through Friday, January 17th, workshop seats will be held for UNC-Chapel Hill-affiliated registrants. Beginning Saturday, January 18th, all registrants will be allocated a workshop seat in the order they register until capacity is reached. Note that registration will CLOSE on Monday, January 27th.

Location: HSL 307 computer classroom (This is a 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 fully charged 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.

Sponsorship: This workshop is sponsored by the Health Sciences Library Research Hub with support from the Integrative Program for Biological and Genome Sciences (iBGS).

About the Workshop:
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 Completed Fall 2019

Time: Friday, 9/6/2019, 9:00am - 5:30pm
Note: There will be a 45-minute break for lunch (on your own) and 20 minute breaks in the morning and afternoon. The workshop is scheduled to conclude at 5:30pm.

Instructor: Benjamin Moore, PhD, EMBL-EBI

Registration Fee: $20.00

Location: HSL 307

Sponsorship: This workshop is sponsored by the Health Sciences Library Research Hub with support from the School of Medicine Office of Research and the Integrative Program for Biological and Genome Sciences (iBGS).

About Ensembl and the Workshop:
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.

This introductory 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 the participants' choice. Participants' interests and preferences for the modules will be determined through a pre-course survey of registrants.

Introduction to Ensembl: origin, goals and organisation of the Ensembl project
Genebuild: how are Ensembl gene and transcripts predictions made?
Variation: SNPs and other polymorphisms, haplotypes, linkage disequilibrium, structural variants like CNVs
Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic region.
Regulation: Sequences that may be involved in gene regulation, and integration of ENCODE data
Data export with BioMart: retrieving genomic information using a web interface (no programming required).

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

Ingenuity Pathway Analysis (IPA) Workshop

Time: Wednesday, 6/26/2019, 8:30am - 12:00pm Completed Fall 2019

Instructor: IPA support scientist
Location: HSL 307

Ingenuity Pathway Analysis (IPA) instructor will visit campus on Wednesday, June 26th to provide a hands-on training workshop to UNC users. UNC subscribes to this software which is maintained by the Center for Bioinformatics.

There will be 30 minute slots available for one-to-one consultations with IPA support scientist during the afternoon session for those who have questions about their own data/results. These limited slots will be available on a first-come basis and will require prior (and separate) reservation. Additional information to follow soon.