2015 05 07 Tools and Services Workshop - University of Georgia, Athens
Organizers | C.J. Tsai, W. Lorenz, A. Zaid, J. Williams |
---|---|
iPlant Trainers | |
UGA | |
Date | May 7-8, 2015 |
Location | Forestry Complex Building 1, Rm. 304 |
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 )
- Windows Users: Please install 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: PRE-WORKSHOP PACKET
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 from 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/Chatroom
We will use the following etherpad for workshop live chat/help:
https://etherpad.mozilla.org/cTKp2HLnc6
Livestream
You can watch the Livestream of this event.
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 PRE-WORKSHOP PACKET to request access to Atmosphere. Launch the following Image (at default tiny1 size)tat least one day before the workshop: TSW Workshop Williams 1.0
- Please use the etherpad chat (https://etherpad.mozilla.org/cTKp2HLnc6) to ask questions. Livestream chat will not be monitored. if any question is not followed up on, please post to ask.iplantcollaborative.org
- Download the Workshop Packet to follow along
- Please complete the post-survey
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:
Draft Workshop Program (DAY 1)
Time | Description | Slides | Links | Presenter |
09:00 AM | Arrive / Sign-in / Verify iPlant Accounts |
|
| |
09:30 AM | Welcome - Presenter/Participant Self-Introductions | slides |
| |
09:45 AM | Overview of the iPlant Collaborative | Jason | ||
10:00 AM | Overview of the iPlant Discovery Environment (DE) | Jeremy | ||
10:45 AM | Coffee Break |
|
|
|
11:00 AM | iPlant Data Store - Managing "Big Data" | Jeremy | ||
11:30 AM | Workflows in the DE; Phylogenetics Example | Jeremy | ||
12:10 PM | Lunch |
|
|
|
01:00 PM | Using the DE for RNA-Seq | slides | Jason | |
02:00 PM | Atmosphere Cloud Computing | slides | Jason | |
03:00 PM | Coffee Break |
|
|
|
03:15 PM | Tools Integration in the DE |
| Jeremy | |
03:45 PM | Educational Bioinformatics - DNA Subway |
| Jason | |
04:15 PM | Workshop summary and conclusion |
|
|
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 | Jason | ||
11:15 AM | Visualization of RNA-Seq results in Atmosphere | slides | Jason | |
12:00 PM | Lunch (On your own) |
|
|
|
01:00 PM | iCommands and other Data Store applications: |
| Jeremy | |
01:30 PM | “What Graduate Students should Know about Cyberinfrastructure |
|
|
|
02:30 PM | Individual Consultations |
| Please posts your requests for 10-15 min consultations to the Etherpad (from 2:30-3 or so) |
|
Travel and Campus Map and Parking
Information on the UGA Campus can be found here: http://www.architects.uga.edu/maps/current