iPlant Collaborative multiworkshop, Sep 21-23


  • Nirav Merchant (University of Arizona),
  • Matthew Vaughn and John Fonner (Texas Advanced Computing Center)
  • Kapeel Chougule and Jason Williams (Cold Spring Harbor Laboratory).

Guest Instructor: Harold Pimentel (UC Berkeley)

Data Carpentry Instructor: Tracy Teal (Data Carpentry PI)

Visiting instructor: Adelaide Rhodes (Oregon State CGRB)

Host: C. Titus Brown and Jessica Mizzi; contact Jessica Mizzi with any questions.

When: September 21-23, 2015.

Times: 9am-5pm, all three days.

Where: Valley Hall (see workshop descriptions, below, for specific rooms)

Cost: there is no fee.

These workshops are open to everyone, including graduate students, postdocs, staff, faculty, and community members. We have extra space for UC Davis VetMed affiliates; contact the host if you are an SVM affiliate. (These spaces will be released to the wait list on Monday, September 14th.)

See workshop descriptions below for registration links.


The iPlant Collaborative enables scientists in all domains of life sciences to connect to public datasets, manage and store their own data and experiments, access high-performance computing, and share results with colleagues.

We will be running four workshops on iPlant:

(Each workshop is all day, every day, so please don’t sign up for overlapping workshops!)

Topics overview - Introduction to iPlant

Monday, Sep 21 - click here to register

Location: 1010 Valley

This one-day workshop is an overview of platforms, tools, and services for large-scale data analysis developed by the iPlant Collaborative (funded by the National Science Foundation). Resources are available for researchers working across all domains of life (microbe, animal, and plant). Hands-on demos and guided exercises give an overview of how to move, manage, and analyze data through local, web, and cloud interfaces. All topics will involve hand-on demos with example data.


  • Data upload and sharing
  • Analyzing data in the Discovery Environment
  • Introductory RNA-Seq Analysis with the Tuxedo workflow
  • Intro to Atmosphere Cloud computing

Who Should Attend? Any investigator (PIs, post-docs, grad students, industry users) who is or will be working with large datasets and computation-intensive research questions in the life-sciences (plants and animals!)

Topics overview - Data Carpentry

Tuesday and Wednesday, Sep 22-23 - click here to register

Location: 1043 Valley (both days)

Data Carpentry workshops are for any researcher who has data they want to analyze; no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. We will be teaching all the basics, including command line skills that will enable you to get started with almost any high-throughput (NGS) sequence data.


  • Organizing computational biology projects
  • Introducing and exploring common genomics/NGS file formats
  • Introduction to the Linux command line
  • Introduction to cloud computing
  • Data wrangling and processing at the command line
  • Data analysis and visualization in R

Who Should Attend? This workshop assumes you have little to no command line experience. We anticipate the workshop will be of interest to PIs, post-docs, grad students, etc. who are or will be working with high-throughput/NGS sequence data. This workshop will NOT be focusing on specific tools/software, but on concepts and best practices. Please register ONLY if you plan to attend both days of the workshop.

Topics overview - Intermediate iPlant

Tuesday, Sep 22 - click here to register

Location: 1041 Valley

This workshop builds on the introductory materials covered in the previous day’s Introductory workshop. We will be covering more detailed aspects of RNA-Seq analysis including benchmarking and use of some of the most recently published RNA-Seq applications. We will also cover more in-depth uses of iPlant resources for data management


  • Working effectively with iRODS and iCommands
  • Using HPC apps (MAKER-P from upload to visualization with JBrowse) on DE/Atmosphere
  • RNA-Seq w/Kallisto (tentative)
  • RNA-Seq visualization with cummeRbund

Who Should Attend? We anticipate this workshop will be of interest to people who currently are working with RNA-Seq data (or will be shortly). General knowledge of RNA-Seq and familiarity with iPlant Tools (especially Atmosphere Cloud Computing) is recommended.

Topics overview - Advanced iPlant

Wednesday, Sep 23 - click here to register

Location: 2020 Valley


  • Intro to Agave and its CLI
  • Auth/Application management
  • Data management
  • Job and workflow management
  • Combining Docker with Agave
  • Integrating HPC and Cloud resources

Who Should Attend? This workshop is targeted at users (and those who manage data and compute for others) who wish to deploy scripts and software within one or more iPlant platforms. The agenda is guide for hackathon-style approach to using iPlant, and will happily be adapted to the interests and use cases of the attendees.

Computer and software requirements

These are hands on workshops, so please bring a network-enabled laptop and a power cord.

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