2012 05 17 TSW U of Arkansas
Organizers | Jason Williams (mailto: williams@cshl.edu), 411 |
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Local Point of Contact | |
Trainers | Jason Williams, Sheldon McKay, John Fonner, and Joshua Stein |
Date | May 17-18, 2012 |
Location | University of Arkansas at Little Rock |
Catering: | Contact Kindra @ Sodexo 501.569.3360; catering delivered/consumed in EIT 303 |
Page Contents
Pre-Workshop Homework
Please note. All participants are required to bring a laptop to this workshop. A limited number of laptops may be available. Please email williams@cshl.edu ASAP if you need us to provide you with a laptop.
1.Please ensure you have up-to-date antivirus software installed on your laptop. You can obtain free antivirus software at: http://free.avg.com/us-en/free-antivirus-download
2. Please make sure you have the latest version of your web browser. Firefox is preferred. You may find browsers at the links below:
Firefox (preferred): http://www.mozilla.org/en-US/firefox/new/
Google Chrome:https://www.google.com/chrome
Safari:http://www.apple.com/safari/
3. 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
4. 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
5. Please check your email, and this wiki prior to the workshop, as this is the way we will communicate any important changes.
6. 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 is Your Data"
Wireless and account info and FTP URLs for Demo
Please use the assigned wireless credentials here (https://pods.iplantcollaborative.org/wiki/display/Events/Wireless+access+and+demo+links)
If your name is not listed here and you need a wireless account please see an instructor.
Workshop handouts
The stept-by-step handouts are available here: Arkansas Workshop Handout
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
Thursday May 17th
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 | | |
09:50 AM - 10:15 AM | Overview of the iPlant Discovery Environment (DE) | ||
10:15 AM - 10:30 AM | Coffee Break |
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10:30 AM - 11:15 AM | iPlant Data Store - Managing "Big Data" | ||
11:15 AM - 12:00 PM | Atmosphere - Custom Cloud Computing | ||
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 | ||
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 | ||
04:30 PM - 05:00 PM | Collaborating with iPlant: Future Projects and Workshop Summary |
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Friday May 18th
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 | ||
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 (No Show in blue)
First Name | Last Name | Research Area | Institution | Department | Position | User Acct? | |
|---|---|---|---|---|---|---|---|
Siddique | Aboobucker | Molecular Biosciences | siddique.aboobucker@smail.astate.edu | Arkansas State University | Arkansas Biosciences Institute | Grad Student | X |
Solomon | Adekunle | Genetics and Nucleic Acids | sadekunl@suno.edu | southern university at new orleans | natural sciences | University/College Faculty | X, no atmo |
Tony | Arick | Computer and Computation Research | maa146@igbb.msstate.edu | Mississippi State University | IGBB | University/College Staff | X |
Carlos | Avila | Plant Biology | cavila@uark.edu | University of Arkansas | Entomology | University/College Faculty | X |
Linda | Ballard | Genetics and Nucleic Acids | linda.ballard@ars.usda.gov | USDA-ARS | Genomics and Bioinformatics Research Unit | Government User | X |
Caroline | Borges Bevilacqua | OtherSeed science and technology | carolinebevi@gmail.com | University of Arkansas | Crop Soil and Environment Sciences | Graduate Student | X |
Teresia | Buza | Molecular Biosciences Bioinformatics | ndelly@gmail.com | Mississippi State University | CVM Basic sciences | Postdoctorate | X |
Venu R. | Channarayappa | Plant Biology | venurekha12@gmail.com | USDA- Dale Bumpers National Rice Research Center | Molecular Plant Pathology | Postdoctorate | X |
Jose | Condori | BioStrategies LC | jcondori@biostrategies-lc.com | Lectin | Therapeutic protein | Research Scientist | X, no atmo |
Richard | Connor | Molecular Biosciences | raconnor1@ualr.edu | University of Arkansas at Little Rock | Applied Science | Graduate Student | X, no atmo |
Carole | Cramer | Biochemistry and Molecular Structure and Function | ccramer@astate.edu | Arkansas State University | Arkansas Biosciences Institute | University/College Faculty | X |
Randy | Dinkins | Plant Biology | Randy.dinkins@ars.usda.gov | USDA ARS |
| Government User | X |
Robert |