2015 01 29 Tools and Services Workshop - Clemson University
Organizers |
Stephen Kresovich, Victoria Artigliere, Jason Williams |
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iPlant Trainers |
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Clemson University |
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Date |
Jan 29-30, 2015 |
Location |
Academic Success Center Room 118, |
Workshop Checklist
1. iPlant Account
- Get your free account at http://user.iplantcollaborative.org.
2. Atmosphere Access
- Once you have your account, go to https://user.iplantcollaborative.org/dashboard/ and under Available Services, request access to Atmosphere. Indicate that you are attending a workshop when you are asked for justification.
3. Laptop
Please bring your own WiFi enabled laptop to the workshop. Make sure your laptop has the following:
- VNC Viewer: Download the DMG (for MAC) or exe (for PC): http://www.realvnc.com/download/viewer/
- Java: Please have JAVA installed and enabled (help)
- Browser: Please have an up-to-date web browser (Recommended Firefox or Safari )
- Widows Users: Please instal PuTTY (http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html)
4. Pre-Workshop Guide and Homework
Download and complete the exercises in this guide to get the most out of the workshop: Jan 2015 Guide
Office Hour
We will be online live for any special assistance you need prior to the workshop (e.g. if you ran into trouble setting up your computer or uploading data). The live help for this workshop will be:
Friday, May 1st 12:00-12:30PM - session is finished if no one requests joins/requests help by 12:15 EDT)
URL: http://cshl.adobeconnect.com/iplant_livehelp
Etherpad
We will use the following etherpad for workshop live chat/help:
http://etherpad.iplantcollaborative.org/p/uga2015
Livestream
You can watch the Livestream of this event. Please register first at: http://www.iplantcollaborative.org/content/livestream-registration-clemson-workshop-jan-29th-30th-2015
Instructions for virtual attendees:
While it is not possible to have the exact in-person experience, you can follow along to a good extent, please observe the following suggestions:
- Use the instructions in the homework packet to request access to Atmosphere. Launch the following Image at least one day before the workshop: TSW Workshop Williams 1.0
- Please use the etherpad chat rather than the Livestream chat; if any question is not followed up on, please post to ask.iplantcollaborative.org
Livestream URLS:
Day 1: https://new.livestream.com/cshl-dnalc/uga-day-I
Day 2: https://new.livestream.com/cshl-dnalc/uga-day-II
Instructional Materials
You can download a copy of the workshop packet to follow along: Jan_2015_ClemsonPacket.pdf
Draft Workshop Program (DAY 1)
Time |
Description |
Slides |
Links |
Presenter |
09:00 AM |
Arrive / Sign-in / Verify iPlant Accounts |
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|
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09:30 AM |
Welcome - Presenter/Participant Self-Introductions |
All |
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09:45 AM |
Overview of the iPlant Collaborative |
Jason |
||
10:00 AM |
Overview of the iPlant Discovery Environment (DE) |
Jason |
||
10:45 AM |
Coffee Break |
|
|
|
11:00 AM |
iPlant Data Store - Managing "Big Data" |
Christos |
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11:30 AM |
Workflows in the DE; Phylogenetics Example |
|
Christos |
|
12:10 PM |
Lunch |
|
|
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01:00 PM |
Using the DE for RNA-Seq |
Jason |
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02:00 PM |
Atmosphere Cloud Computing |
Christos |
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03:00 PM |
Coffee Break |
|
|
|
03:15 PM |
Tools Integration in the DE |
|
|
Jason |
03:45 PM |
Educational Bioinformatics - DNA Subway |
|
|
Jason |
04:15 PM |
Workshop summary and conclusion |
|
Jason |
Draft Workshop Program (Day 2)
Time |
Description |
Slides |
Links |
Presenter |
---|---|---|---|---|
09:30 AM |
Overview and demo of iPlant GWAS / Transcriptome assembly |
|
Jason |
|
10:30 AM |
Coffee Break |
|
|
|
10:45 AM |
Getting started with Annotation: MAKER |
Christos |
||
11:15 AM |
Visualization of RNA-Seq results in Atmosphere |
Jason |
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12:00 PM |
Lunch (On your own) |
|
|
|
01:00 PM |
Integrated Browser Demo |
Nowlan |
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01:45 PM |
iCommands and other Data Store applications: |
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https://pods.iplantcollaborative.org/wiki/display/start/Using+icommandsicommands tutorial |
Christos |
02:30 PM |
Individual Consultations |
|
|
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03:30 PM |
“The opportunities and challenges of using |
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Location: Biosystems Research Complex G100 |
Steve Goff |
Travel and Campus Map and Parking
Information on the Clemson Campus can be found here: http://www.clemson.edu/visit/
Metered parking closest to the Life Sciences Building would be Strom Thurmond Institute, Brooks Center and Hendrix Center. See details, rules, and maps below.
http://www.clemson.edu/campus-life/campus-services/parking/visitors.html