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UNIX for Biologists, Part 1: Introduction
4/6/2015 from 10:00am to 12:00pm, HSL - 307

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: Kure 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 Kure Linux cluster managed by ITS-Research Computing. 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 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 Kure/UNC computer cluster usage, this class and UNIX for Biologists, Part 2: Kure (from this series or prior offerings) are prerequisites for the next generation sequencing classes that follow them in the BBT workshop series: Next Generation Sequence Data: Introduction and Quality Control and RNAseq: The TopHat Suite.

(Basic Bioinformatics Tools Series)

Instructor: Hemant Kelkar, Ph.D., UNC Center for Bioinformatics
Class Full, you will be placed on the waitlist.


UNIX for Biologists, Part 2: Kure
4/8/2015 from 10:00am to 12:00pm, HSL - 307

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 resources available to bioscience researchers and will focus primarily on resources on the Kure 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 Kure compute cluster and the 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 Kure cluster.

Account Requirement: You will need an account on the Kure Linux cluster managed by ITS-Research Computing. 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 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 Kure/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 follow them in the BBT workshop series: Next Generation Sequence Data: Introduction and Quality Control and RNAseq: The TopHat Suite.

(Basic Bioinformatics Tools Series)

Instructor: Hemant Kelkar, Ph.D., UNC Center for Bioinformatics
1 seats available.


Basic EndNote
4/10/2015 from 10:00am to 11:00am, HSL - 329
This Basic EndNote class will touch on the fundamental functions of the EndNote software. Building your library, managing your sources, and inserting your citations into your documents will be the focus of what we will cover. This class is structured for new to beginning users.
Class Full, you will be placed on the waitlist.


Introduction to Next Generation Sequence Data and Quality Control
4/13/2015 from 10:00am to 12:00pm, 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 by doing 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 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 looks 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 Kure Linux cluster managed by ITS-Research Computing. 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 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 (from this series or prior offerings) are prerequisites for this class.

(Basic Bioinformatics Tools Series)

Instructor: Hemant Kelkar, Ph.D., UNC Center for Bioinformatics
10 seats available.


Basic RefWorks
4/14/2015 from 2:00pm to 3:00pm, HSL - 329
The Basic RefWorks class will cover the basic features of RefWorks. We will focus on accessing RefWorks, importing citations from PubMed, inserting your citations into your documents, and creating bibliography lists. This class is structured for new to beginning users.
9 seats available.


Using the Tuxedo Suite for Analysis of RNAseq Data
4/15/2015 from 10:00am to 12:00pm, HSL - 307

The Tuxedo Suite consists of several programs (TopHat, Cufflinks, Cuffdiff). We will loosely base our exploration of the Tuxedo suite of programs on this Nature Protocols paper (http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html). We will also look at a read counting program (featureCounts) that can generate summarized count data from alignment files which is required for other packages such as DESeq2.

The agenda for this session will be fairly open. Depending on the progress we make we may need to schedule one additional session.

Account Requirement: You will need an account on the Kure Linux cluster managed by ITS-Research Computing. 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 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 (from this series or prior offerings) are prerequisites for this class.

(Basic Bioinformatics Tools Series)

Instructor: Hemant Kelkar, Ph.D., UNC Center for Bioinformatics
15 seats available.


So you wanna do a systematic review? Session #5
4/16/2015 from 12:00pm to 1:00pm, Online
See the description for in-class version of So you wanna do a systematic review? Session #5. This is the same class, but participants attend online via Elluminate/Blackboard Collaborate. (Accelerate Your Research Series)
10 seats available.


So you wanna do a systematic review? Session #5
4/16/2015 from 12:00pm to 1:00pm, HSL - 227
Is This a Good Study? Study Selection & Assessment.

For more information, visit our course guide

(Accelerate Your Research Series)
10 seats available.


NIH Biosketch & Federal Public Access Policies
4/20/2015 from 2:30pm to 3:30pm, HSL - 307
This session will cover the NIH and AHRQ Public Access Policies and their compliance requirements, including a hands-on tour of the bibliography management and compliance monitoring functions in My NCBI. This session will also introduce the new NIH Biographical Sketch format requirements effective for NIH and AHRQ grant applications submitted on or after May 25, 2015. This class will include a walk through of the logistical steps in My NCBI for 1) NIH/AHRQ Policy compliance and 2) preparing a bibliography with a public link for addition to the new Biosketch. Participants will have the opportunity to login and follow along with their own My NCBI accounts. Attendees wishing to participate in the hands-on walk through will need to complete the steps below that apply to them: 1. Create a My NCBI account (if you do not have one already) a. If you already have an eRA Commons account, sign in using your eRA Commons information b. If you do not have an eRA Commons account, you can either register for a new NCBI account, or you can sign in with your ONYEN and password using the 3rd party sign in option. 2. Link existing accounts (if you have both a MyNCBI account and an eRA Commons account) 3. Assign/accept delegate status (if you are acting as a delegate or plan to have someone act as a delegate for you) For instructions on the steps, consult the My NCBI set up information in the HSL NIH compliance guide: http://guides.lib.unc.edu/compliance/myncbisetup The target audiences for this session include NIH- or AHRQ-funded investigators, including trainees, and research staff serving as delegates for investigators. (Accelerate Your Research Series)
Class Full, you will be placed on the waitlist.


So you wanna do a systematic review? Session #6
4/23/2015 from 12:00pm to 1:00pm, Online
See the description for in-class version of So you wanna do a systematic review? Session #6. This is the same class, but participants attend online via Elluminate/Blackboard Collaborate. (Accelerate Your Research Series)
10 seats available.


So you wanna do a systematic review? Session #6
4/23/2015 from 12:00pm to 1:00pm, HSL - 227
Putting It Together: Presenting Your Results

For more information, visit our course guide

(Accelerate Your Research Series)
11 seats available.


Basic RefWorks
5/5/2015 from 2:00pm to 3:00pm, HSL - 329
The Basic RefWorks class will cover the basic features of RefWorks. We will focus on accessing RefWorks, importing citations from PubMed, inserting your citations into your documents, and creating bibliography lists. This class is structured for new to beginning users.
13 seats available.


Basic EndNote
5/11/2015 from 1:00pm to 2:00pm, HSL - 329
This Basic EndNote class will touch on the fundamental functions of the EndNote software. Building your library, managing your sources, and inserting your citations into your documents will be the focus of what we will cover. This class is structured for new to beginning users.
9 seats available.


Basic EndNote
6/18/2015 from 10:00am to 11:00am, HSL - 329
This Basic EndNote class will touch on the fundamental functions of the EndNote software. Building your library, managing your sources, and inserting your citations into your documents will be the focus of what we will cover. This class is structured for new to beginning users.
15 seats available.


Basic EndNote
7/14/2015 from 3:00pm to 4:00pm, HSL - 329
This Basic EndNote class will touch on the fundamental functions of the EndNote software. Building your library, managing your sources, and inserting your citations into your documents will be the focus of what we will cover. This class is structured for new to beginning users.
15 seats available.


Basic EndNote
8/12/2015 from 10:00am to 11:00am, HSL - 329
This Basic EndNote class will touch on the fundamental functions of the EndNote software. Building your library, managing your sources, and inserting your citations into your documents will be the focus of what we will cover. This class is structured for new to beginning users.
15 seats available.



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