2012 03 21 TSW at UC Riverside

2012 03 21 TSW at UC Riverside

Organizers:

Uwe Hilgert

Local Point of Contact:

Jim Burnette

Trainers:

Naim Matasci, Matt Vaughn, Martha Narro, Fusheng Wei

Date:

9:30 AM - 5 PM on March 21 and 22, 2012

Location:

UC Riverside; Room 104 in Neil A Campbell Science Learning Laboratory located in the University Laboratory Building (seats 24)
Ethernet and wifi available; lunch served in ULB Room 101

Description:

This is a tools and services workshop for UC Riverside.

Important Dates:

Registration closed on 3/11/12 at 25 people

Catering Contact:

McGrath's Catering 951-683-7063 Vanessa Griffith

Goal

To provide an interactive, hands-on training of iPlant Tools and Services so that participants can begin to use iPlant cyberinfrastructure in their plant science research.

Pre-Workshop Homework

1. Please test your iPlant credentials to ensure you have access. You can log-in from user.iplantcollaborative.org, click the button "iPlant Login"

  • Once authenticated, click the "My Services" link
  • Under "My Services" please ensure you have access to: Atmosphere, Discovery Environment, iPlant Data Store. You can also request access to other services here
  • If you have account problems, please email support@iplantcollaborative.org

2. Please check your email and this wiki prior to the workshop, as this is the way we will communicate any important changes.

3. The use of Atmosphere will require a VNC viewer which can be downloaded here.

Agenda

Wednesday March 21: Neil A. Campbell Science Learning Laboratory, University Laboratory Building 104 (next door to the Genomics Building)

Time

Presentation

Slides/Links

Presenter

9:00 AM - 9:30 AM

Arrive/Sign-in

 

 

9:30 AM - 10:00 AM

Welcome - Presenter/Participant Introductions

 

Naim Matasci

10:00 AM - 10:20 AM

An Overview of the iPlant Collaborative

Getting Started w/iPlant Guide, iPlant Overview Video, Slides

Matt Vaughn

10:20 AM - 10:45 AM

Overview of the iPlant Discovery Environment (DE)

SlidesDE Manual, DE Overview Video,

Martha Narro

10:45 AM - 11:00 AM

Break

 

 

11:00 AM - 11:30 AM

iPlant Data Store - Managing "Big Data"

Data Store Guide, Data Store Overview Video

Naim

11:30 AM - 12:30 PM

Using the DE to Examine Differential Expression Within an RNA-seq Dataset

Slides, Detailed /wiki/spaces/eot/pages/241585220

Matt

12:30 PM - 1:30 PM

Lunch (delivered to Rm 101 ULB, vegetarian option available)

 

 

1:30 PM - 2:00 PM

Atmosphere - Custom Cloud Computing

Atmosphere Slides Atmosphere Manual, Atmosphere Overview Video

Naim

2:00 PM - 3:00 PM

Extending the DE for Your Research: Tool Integration and Customization

Slides, Handout (pdf, on wiki)

Martha

3:00 PM - 3:15 PM

Break (Rm 101 ULB)

 

 

3:15 PM - 4:15 PM

Building and Using Workflows Within the DE; Phylogenetics

Slides

Naim

4:15 PM - 5:00 PM

Collaborating with iPlant: Future Projects and Workshop Summary

 

Matt

Thursday March 22: Neil A. Campbell Science Learning Laboratory, University Laboratory Building 104 (next door to the Genomics Building)

Time

Presentation

Slides/Links

Presenter

9:30 AM - 11:30 PM

Advanced CHiP-seq in the iPlant Cyberinfrastructure

Slides, /wiki/spaces/eot/pages/241585258

Matt

11:30 AM - 11:45 AM

Break

 

 

11:45 AM - 12:15 PM

Using the iPlant Data Store as a Reliable Repository for Your Lab

 

Naim

12:15 PM - 1:15 PM

Lunch (delivered, ULB Rm 101, vegetarian option available)

 

 

1:15 PM - 2:15 PM

Powered by iPlant - Using APIs to Consume iPlant Services in Your Portals

Tutorial

Naim

2:15 PM - 3:15 PM

Using XSEDE for Bioinformatics

Slides

Matt

3:30 PM

Adjourn

 

 

Free form

icommands, genome assembly,

 

 

Attendee List

Name

Affiliation

Jim Burnette

Natural & Ag Sci, UCR

Brad Cavinder

Plant Pathology & Microbiology, UCR

Benjamin Cole

Biology, UCSD

Kelli Henry

MCDB, UCLA

Piyada Juntawong

Botany & Plant Sciences, UCR

Siddhartha Kanrar

Biology, Victor Valley College

Brandon Le

MCDB, UCLA

Jer-Young Lin

MCDB, UCLA

Renyi Liu

Botany & Plant Sci, UCR

Lu Lu

Botany, UCR

Hamid Mirebrahim

Computer Sci, UCR

Jinghua Shi

Botany & Plant Sci, UCR

James Wong

Plant Pathology, UCR

Yi Zhu

Plant Biology

Shingo Nagawa

Botany & Plant Sci, UCR

Damien Wood

Dev & Cell Bio, UC Irvine

Rebecca Sun

Institute for Integrative Genome Biology, UCR