Home

CyVerse Workshops at CGEMS Summer Training Workshop, James Madison University

 

Jul 10, 2017 (Genomics in Education)     09:30am - 05:00pm (Rm: Biosciences 2009)
Jul 11, 2017 (Genomics in Education)     09:30am - 03:30pm (Rm: Biosciences 2009)
Jul 12, 2017 (CyVerse Tools and Services)     09:30am - 05:00pm (Rm: Biosciences 2009)

 

 

 

 

This workshop series provides a comprehensive look at platforms, tools, and services for large-scale data analysis provided by CyVerse, a cyberinfrastructure project funded by the
National Science Foundation.

Register Here

Hosted By:  CGEMS Summer Training Workshop in Genomics & Bioinformatics for Beginners & Beyond

 

July 10-12: CyVerse Genomics in Education

Genomics in Education merges bioinformatics and molecular biology to explore topics in genomics. The workshop introduces a series of laboratory and bioinformatics exercises that be incorporated into existing biology courses DNA Subway (http://www.dnasubway.org) is the primary tool used in this workshop. 

 

Who Should Attend?

  • Faculty teaching undergraduate biology; undergraduate and graduate students; high school faculty

 

What will we do at the workshop?

  • Genome Annotation: Educators will use DNA Subway Red Line to explore how raw DNA sequence is turned into annotated genomes. In the process students learn how to explore the evolving concept of a “gene” by ‘building’ their own genes through the process of annotation.

  • DNA Barcoding: Educators will use DNA Subway Blue Line to analyze DNA sequence to identify organisms. A laboratory exercise will walk you through our simple method for DNA extraction, and we will provide several examples of how this experiment can be used to introduce a number of biological topics, and used in course-based research (CUREs) and independent research projects.

  • RNA-Seq: Educators will use DNA Subway Green Line to analyze the results of transcriptome sequencing for differential gene expression (abundance). We will use publicly available data to walk through the analysis. We will also share teaching resources and examples of how these experiments can be included in the undergraduate curriculum.

  • Microbiome Demo:

 

What Should I Bring?

This workshop is hands-on so please bring a Wi-Fi enabled laptop. Food will be provided: Coffee and light breakfast from Dunkin Donuts and pizza lunch (including non-meat and gluten free pizza) from Domino’s Pizza will be provided for all registered workshop attendees.

 

July 13: CyVerse Tools and Services

Tools and services workshops cover the major platforms of the CyVerse cyberinfrastructure (http://www.cyverse.org/) including the Data Store, Discovery Environment (web-based bioinformatics workbench), Atmosphere (cloud computing), and BisQue (image analysis).  Workshop topics build progressively along a ‘path’ most researchers will need to take from data upload, through to analysis and publication.

 

 

Who Should Attend?

  • Faculty, Postdocs, graduate students who use and analyze biological data of all types (genomics, image data, from animals, plants, etc.); undergraduate and graduate students; high school faculty

 

What will we do at the workshop?

  • Data upload, sharing, and management: We will cover graphical and command line interfaces for uploading and importing your data into CyVerse.

  • Advanced analyses in Discovery Environment: After a brief introduction to these analyses, participants will have guided walkthroughs of their choice of example experiments in the Discovery Environment - a web-based, graphical user interface to hundreds of bioinformatics tools. These examples bring together several tools and will prepare you to analyze your own data using some of the following example workflows:
    • RNA-Seq: Use the Tuxedo or Kallisto pipelines to examine differential transcripts
    • ChIP-Seq: Identify changes in methylation using ZED-align and BisuKit

    • Transcriptome assembly: Use Soapdenovo-Trans to assemble and evaluate a sample transcriptome

    • MAKER: Use the MAKER pipeline to annotate a sample genome

  • Cloud-based Data analysis and Exploration: We will introduce Atmosphere cloud computing a simple and flexible way to access on-demand computing. We will cover a basic introduction, and explore and visualize outputs from previous workshop exercises in the cloud.

 

What Should I Bring?

This workshop is hands-on so please bring a Wi-Fi enabled laptop. Food will be provided: Coffee and light breakfast from Dunkin Donuts and pizza lunch (including non-meat and gluten free pizza) from Domino’s Pizza will be provided for all registered workshop attendees.

Parking

JMU Lot D2 directly across from the Biosciences bldg at 951 Carrier Drive has been designated as the workshop parking lot. Despite the signage, no permit will be required to park in this lot on the workshop dates.

 

Workshop location

The Biosciences Bldg is located at 951 Carrier Drive Harrisonburg VA, 22807. The workshop will be held in room #2009. From the bldg entrance directly across from parking lot D2, proceed up to the 2nd floor and to the end of the hallway furthest from the parking lot. Room #2009 is on the left at the end of the hallway across from the stairwell.

 

All workshops are subject to enrollment - participants should not make travel plans until they receive a confirmation notice. Participants are responsible for all travel costs.

 

Location: 
Harrisonburg, VA
Primary Contact: 

Jason Williams - CyVerse

 

End date: 
Wednesday, July 12, 2017 - 17:00