2012 05 21 TSW Purdue University
Organizers: | |
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Local Point of Contact: | Peter Baker, Jyothi Thimmapuram |
Trainers: | Jason Williams, Sheldon McKay, Naim Matasci and Andy Lenards |
Date: | May 21-22, 2012 |
Location: | Purdue University, NLSN 1195 |
Online Registration: | |
Important Dates: | Registration Opens: April 6th |
Section Navigation
Pre-Workshop Homework
1. Please try out 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 be sure that your name is listed in the Attendee List (below) for the workshop section(s) you were accepted to. If there is a discrepancy, please email 411@iplantcollaborative.org
3. Please check your email, and this wiki prior to the workshop, as this is the way we will communicate any important changes.
4. The use of Atmosphere will require a VNC viewer which can be downloaded here.
Workshop Notes
Here are a few important links that you may wish to refer to during and after the workshop:
Account/Password Problems http://user.iplantcollaborative.org
iPlant Help and Discussion Forums
General iPlant Support Issues
iPlant Privacy (And other) policies - "Your Data are Your Data"
Goal
The goal of this workshop is to demonstrate some of the ways that iPlant Cyberinfrastructure can advance your scientific objectives. As you navigate the through demonstrations and hands-on activities presented at the workshop, you will gain a sense of how to use and customize iPlant tools and services for your investigations.
Agenda
Please check here for the latest updates to this workshop agenda
Monday May 21st
Time | Presentation | Slides | Links |
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08:30 AM - 09:00 AM | Arrive/Sign-in/ Verify iPlant accounts |
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09:00 AM - 09:30 AM | Welcome - Presenter/Participant Introductions |
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09:30 AM - 09:50 AM | An Overview of the iPlant Collaborative |
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09:50 AM - 10:15 AM | Overview of the iPlant Discovery Environment (DE) |
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10:15 AM - 10:30 AM | Coffee Break |
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10:30 AM - 11:15 AM | iPlant Data Store - Managing "Big Data" |
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11:15 AM - 12:00 PM | Atmosphere - Custom Cloud Computing |
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12:00 PM - 01:00 PM | Lunch (Delivered) |
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01:00 PM - 01:30 PM | Building and Using Workflows Within the DE; Phylogenetics |
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01:30 PM - 02:45 PM | Using the DE to Examine Differential Expression Within an RNA-seq Dataset | | |
02:45 PM - 03:00 PM | Coffee Break |
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03:00 PM - 04:30 PM | Extending the DE for Your Research: Tool Integration and Customization |
| Integrating a New Tool Interface into the Discovery Environment |
04:30 PM - 05:00 PM | Collaborating with iPlant: Future Projects and Workshop Summary |
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Tuesday May 22nd
Time | Presentation | Sides | Links |
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08:45 AM - 09:00 AM | Sign-in/Welcome | |
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09:00 AM - 10:30 AM | Advanced CHiP-seq in the iPlant Cyberinfrastructure |
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10:30 AM - 10:45 AM | Coffee Break |
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10:45 AM - 11:30 AM | Advanced CHiP-seq in the iPlant Cyberinfrastructure (cont'd) |
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11:30 AM - 12:00 PM | Comparative Phylogenetic Methods in the iPlant Cyberinfrastructure | |
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12:00 PM - 01:00 PM | Lunch (On your own) |
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| Data Clinic Appointments |
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01:00 PM - 02:00 PM | Powered by iPlant - Consuming iPlant Services in Your Portals | | |
02:00 PM - 03:00 PM | Using XSEDE for Bioinformatics | |
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03:00 PM - 04:30 PM | Additional RNA-seq analysis applications/ hands-on |
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Attendee List (those waitlisted in blue) ()
Name | Research Area | Dept | Position | Lab PI | User Acct | |
|---|---|---|---|---|---|---|
Gladys Andino | Genetics and Nucleic Acids | Entomology | Graduate Student | Greg Hunt | X, | |
Tatiana Arias-Garzon | Plant Biology | Biological Sciences | Graduate Student | Chris Pires | X, no atmo | |
Nadia Atallah | Molecular Biosciences | Botany Y | Graduate Student | Jody Banks |
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Peter Baker | Software Engineering | Cyber Center, Discovery Park | University/College Staff | Cyber Center | X , no atmo | |
Ketaki Bhide | Other | Bioinformatics Core,Cyber Center | University/College Staff | Dr.Jyothi Thimmapuram | X, no atmo | |
David Bos | Genetics and Nucleic Acids | Biological Sciences | University/College Faculty | David Bos | X, no atmo | |
Naila Cannes | Molecular Biosciences | Comparative pathobiology | Postdoctorate | Joanne Messick | X , no atmo | |
Basudev Chowdhury | Molecular Biosciences | Biology | Graduate Student | Joseph Irudayaraj |
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Hyonho Chun | Statistics and Probability | Statistics | University/College Faculty |
| X, no atmo | |
Emily Dierking | Plant Biology | Agronomy | Other | Emily Dierking | X, no atmo | |
Navin Elango | Biological and Critical Systems | Information Technology and Data Analysis | Industrial User | Jacob Koehler | X, no atmo | |
Alan Galbreth | Plant Biology | Genetics Program | Other | Emily Dierking |
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Ana Guimaraes | Other |