2016 03 17 Tools and Services Workshop - The Ohio State University
Organizers: | T. Meulia |
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Local Point of Contact: | Tea Meulia |
Trainers: | Joslynn Lee, Jason Williams |
Date: | March 17-18, 2016 |
Location: | College of Food, Agricultural, and Environmental Sciences Shisler Conference Center 1680 Madison Avenue Wooster, OH 44691 |
Parking Information/Permits |
Required Workshop Prep
1. CyVerse Account
- Get your free account at http://user.iplantcollaborative.org/ . (Make sure to REMEMBER your username and password.) Please register with an institutional email account as only this will give you access to the CyVerse cloud service Atmosphere (see next bullet). Please avoid gmail, yahoo, hotmail and the like for your CyVerse registration as you would not be able to register for Atmosphere with those.
2. Atmosphere Access
- Once you have your account, go to http://user.iplantcollaborative.org/ and log in. Under "Apps and Services," scroll down to "Available Services" and request access to Atmosphere and DNA Subway. Indicate that you are attending a workshop when you are asked for justification. (This will only be granted if you registered for CyVerse using an institutional account; see above.)
3. Laptop
Please bring your own WiFi enabled laptop to the workshop. Make sure your laptop has the following:
- Internet Browser: Please have an up-to-date web browser (We strongly recommend Firefox or Safari; Internet Explorer, Chrome and others have significant issues.)
- Java: Have JAVA installed, enabled and working with Firefox or Safari. (Help)
- Data Store: Download and install iCommands (iCommands for your OS)
- VNC Viewer: Download the DMG (for MAC) or exe (for PC) (http://www.realvnc.com/download/viewer/)
- Windows Users only: Download and install PuTTY (http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html)
- Download Cyberduck: Using Cyberduck for Uploading and Downloading to the Data Store - Installing and Configuring Cyberduck
4. Pre-Workshop Guide and Homework
- Download and complete the exercises in the PRE-WORKSHOP PACKET to get the most out of the workshop.
- Complete this Pre-Workshop Survey
Livestream
You can watch the Livestream of this event:
Day 1: http://livestream.com/cshl-dnalc/ohio-state-day1-2016
Day 2: http://livestream.com/cshl-dnalc/ohio-state-day2-2016
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.
- Use etherpad chat to ask question. if we don't get a chance to address your question please post to ask.iplantcollaborative.org
- Download the Workshop Packet to follow along
- Please complete the post-survey.
Etherpad
Connect to the etherpad at http://lannister.iplantcollaborative.org/p/ohio2016-tsw
You can use the etherpad at the workshop to ask questions and share information, links, etc.
Instructional Materials
You can download a copy of the workshop packet (CyVerse Toolkit) to follow along:
Draft Workshop Program (DAY 1)
Time | Description | Toolkit | Slides | Links | Presenter |
08:30 AM | Arrive / Sign-in / Setup Troubleshooting |
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09:00 AM | Welcome - Presenter/Participant Self-Introductions | slides | Jason | ||
09:30 AM | Overview of the CyVerse | Getting Started with CyVerse | Jason | ||
09:45 AM | Managing "Big Data" using the CyVerse Data Store |
| slides | Data Store Overview | Joslynn |
10:30 AM | Coffee Break |
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10:45 AM | Navigate the CyVerse Discovery Environment (DE)
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| slides | Jason | |
11:15 AM | Analyses in the DE; Phylogenetics Example |
| Jason | ||
12:00 PM | Lunch Provided (UPDATED) |
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01:00 PM | DNA Subway (Workflows for Bioinformatics Education) | DNA Subway Website | Jason | ||
01:15 PM | Using the DE for RNA-Seq |
| slides | Jason | |
02:15 PM | Atmosphere Cloud Computing |
| slides | Joslynn | |
03:00 PM | Coffee Break |
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03:15 PM | Tool Integration in the DE |
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| Jason | |
03:45 PM | Sequence Read Archive Demo |
| slides | Jason | |
04:15 PM | Workshop summary and conclusion |
| Jason |
Draft Workshop Program (DAY 2)
slides
Time | Description | Slides | Links | Presenter |
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09:30 AM | Overview and demo of CyVerse GWAS / Transcriptome assembly (TA) | Jason | ||
10:30 AM | Coffee Break |
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10:45 AM | Getting started with Annotation: MAKER (MP) | Jason | ||
11:15 AM | Visualization of RNA-Seq results in Atmosphere | slides (V2) | ||
12:00 PM | Lunch Provided (UPDATED) |
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01:00 PM | iCommands and other Data Store applications: |
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01:30 PM | “What Graduate Students should Know about Cyberinfrastructure |
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02:30 PM | Individual consultations |
| Please posts your requests for 10-15 min consultations in Etherpad |
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Important Pre-Workshop Travel Info
Neither CyVerse/iPlant Collaborative nor the local host can reimburse lodging or other expenses associated with attending the workshop.
Maps and parking information can be found here: http://oardc.osu.edu/sites/oardc/files/imce/files/about/OARDC_WOOSTER_MAP_11x17.pdf
Travel/Lodging
See the city of Wooster, OH website: http://www.woosteroh.com/where-stay