Bioinformatics@HSL: BBT Workshop Descriptions

Created by Health Science Librarians

UNC Bioinformatics Workshops: 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. The Basic Bioinformatics Tools (BBT) Workshop series provides seminar and hands-on computer classes on bioinformatics tools and resources to faculty, staff and students of UNC-Chapel Hill. This workshop series is sponsored by the UNC Health Sciences Library in partnership with the UNC Bioinformatics and Analytics Research Collaborative (BARC).

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 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 Shell sequence are in turn prerequisites for the six, one-hour Introduction to Bioinformatics Basics workshops listed below which follow in the semester-long workshop series.

NOTE: These classes can fill quickly. Seats that open up when registrants cancel/withdraw will be offered to those on the waitlist in order of registration. REGISTER ONLY if you plan to ATTEND the live workshop and are willing to review any missed prerequisite content.

Alternatively, if you are a UNC affiliate, you can access Zoom recordings and class materials from past workshops with an ONYEN via the Basic Bioinformatics Tools Workshops site on UNC Sakai. You may use these resources to review selected recordings to complete the prerequisites for the live workshops you register to attend OR to work through the content on your own.

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1. UNIX Shell Basics 1

Time: Monday 9/18/2023, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329

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://help.rc.unc.edu/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

Time: Wednesday 9/20/2023, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329

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

Time: Monday 9/25/2023, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329

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 Register

Time: Monday 10/2/2023, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329

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 Register

Time: Wednesday 10/4/2023, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329

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 Register

Time: Monday 10/9/2023, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329

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 Six Workshop Sequence

This six 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 six-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 Register

Time: Monday 10/23/2023, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329

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 Register

Time: Wednesday 10/25/2023, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329

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 Register

Time: Monday 10/30/2023, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329

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 Register

Time: Monday 11/6/2023, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329

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 Register

Time: Wednesday 11/8/2023, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329

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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12. Simple Multiomics Register

Time: Monday 11/13/2023, 2:00pm - 3:00pm

Instructor: Tristan De Buysscher, Bioinformatics Scientist, Bioinformatics and Analytics Research Collaborative (BARC)
Location: HSL 329

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
Differential Expression Analysis: DESeq Basics
Differential Expression Analysis: Intermediate DESeq & RStudio

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UNC-Hosted Bioinformatics Tools Workshops by External Providers: Descriptions

Browsing Genes and Genomes with Ensembl and Ensembl Genomes (full day, in-person) Completed

Time: Thursday 5/11/2023, 9:00 am - 5:00 pm

Instructor: Louisse Paola Mirabueno, PhD, EMBL-EBI

UNC Ensembl Workshop Training Site: All workshop materials

Registration Fee: None; Instructor travel costs supported by the UNC Bioinformatics and Analytics Research Collaborative (BARC)

Location: HSL 307

Sponsorship: This workshop is sponsored by the Health Sciences Library in partnership with the UNC Bioinformatics and Analytics Research Collaborative (BARC).

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 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.

This full day workshop consists of a series of modules selected from the list 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 workshop will consist of the first three of these modules, plus two to three 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: accessing and analyzing variation data (SNPs and other polymorphisms) and how to use Ensembl VEP tool

Comparative genomics: orthologues, protein families, whole genome alignments and syntenic region.
Regulation: Sequences that may be involved in gene regulation, and integration of ENCODE data for human and mouse
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.

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

Time: Not currently scheduled
Instructor: Robert Kuhn, PhD, UCSC Genome Browser

Registration Fee: TBA

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 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.

Ingenuity Pathway Analysis (IPA) Workshop

Time: Not currently scheduled 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.