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CyVerse Data Carpentry, Tools, and Services Workshop, New Mexico State University

 

Aug 28, 2017 (CyVerse Genomics Data Carpentry)     09:30am - 05:00pm (HJLC Rm 206)
Aug 29, 2017 (CyVerse Genomics Data Carpentry)     09:30am - 05:00pm (HJLC Rm 206)
Aug 30, 2017 (CyVerse Tools and Services)     09:30am - 05:00pm (EC3 Rm 301)

 

 

 

 

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.

 

Registration Full - Waitlist only

contact williams (at) cshl.edu for assitance.

 

Aug 28-29: CyVerse Genomics Data Carpentry

These lessons are based on the Data Carpentry workshop (http://www.datacarpentry.org/ ) CyVerse helped to develop, and will be a complete introduction to the tools and practices a biologist needs to work effectively with data. Along the way, we will introduce how to analyze and visualize data in R and work with bioinformatics tools at the command line. While the focus of these lessons is genomics, biologists working with any tabular data (i.e. spreadsheets) will benefit. No prior knowledge of R or the UNIX/LINUX command line is assumed or required.

 

Who Should Attend?

  • Faculty, Postdocs, graduate students who use and analyze biological data of all types.

 

What will we cover at the workshop?

  • Tidy data: We will introduce what it means to have a ‘tidy’ dataset, as well as the tools and practices needed to clean and organize data for effective analysis.

  • Introduction to R and RStudio:  We will introduce R as a popular, open-source language for statistical and data analysis. Using RStudio we will cover from the beginning what a user needs to know to get started with genomics data. Popular tools covered include ‘dplyr’ and ‘ggplot’.

  • Data wrangling: We will cover how to find, import, and manage data from disparate online sources

  • Intro to the Linux shell: We will cover a ‘gentle’ introduction to working at the Linux command line, including how to install and run tools and automate analyses.

  • Genomics data documentation and organization: We will introduce tools and practices for organizing and documenting your work with genomics datasets.

  • Creating workflows: We will illustrate how to tie together bioinformatics tools to build your own automated workflow.

 

What Should I Bring?

This workshop is hands-on. We will be situated in a computer lab, but you may elect to bring a Wi-Fi enabled laptop. Breaks will be provided.

 

Aug 30: 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.)

 

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
    • Transcriptome assembly tools

    • 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. We will be situated in a computer lab, but you may elect to bring a Wi-Fi enabled laptop. Breaks will be provided.

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: 
Las Cruces, NM
Primary Contact: 

Jason Williams - CyVerse

 

End date: 
Wednesday, August 30, 2017 - 17:00