2012 03 21 TSW at UC Riverside
Organizers: |
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Local Point of Contact: |
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Trainers: |
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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) |
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 |
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9:00 AM - 9:30 AM |
Arrive/Sign-in |
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9:30 AM - 10:00 AM |
Welcome - Presenter/Participant Introductions |
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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) |
Martha Narro |
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10:45 AM - 11:00 AM |
Break |
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11:00 AM - 11:30 AM |
iPlant Data Store - Managing "Big Data" |
Naim |
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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) |
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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 |
Martha |
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3:00 PM - 3:15 PM |
Break (Rm 101 ULB) |
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3:15 PM - 4:15 PM |
Building and Using Workflows Within the DE; Phylogenetics |
Naim |
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4:15 PM - 5:00 PM |
Collaborating with iPlant: Future Projects and Workshop Summary |
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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 |
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9:30 AM - 11:30 PM |
Advanced CHiP-seq in the iPlant Cyberinfrastructure |
Matt |
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11:30 AM - 11:45 AM |
Break |
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11:45 AM - 12:15 PM |
Using the iPlant Data Store as a Reliable Repository for Your Lab |
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Naim |
12:15 PM - 1:15 PM |
Lunch (delivered, ULB Rm 101, vegetarian option available) |
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1:15 PM - 2:15 PM |
Powered by iPlant - Using APIs to Consume iPlant Services in Your Portals |
Naim |
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2:15 PM - 3:15 PM |
Using XSEDE for Bioinformatics |
Matt |
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3:30 PM |
Adjourn |
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Free form |
icommands, genome assembly, |
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Attendee List
Name |
Affiliation |
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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 |