2016 03 18 University of Arizona Tools and Services Workshop - Plant Reproduction 2016
Organizers | Ravi Palanivelu; Ramin Yadegari
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CyVerse Trainers | Eric Lyons, Jeremy DeBarry, Upendra Devisetty |
Date and Time | March 18, 2016, 2-5pm
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Location | University of Arizona, Tucson (Marriott Hotel, Ventana Room) |
Information on 24th International Congress on Sexual Plant Reproduction
Workshop Checklist and Software Downloads - Please Review and Complete to Prepare
1. CyVerse (formerly iPlant Collaborative) Account
- Get your free account at http://user.cyverse.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 https://user.cyverse.org/dashboard/ and under Available Services, request access to Atmosphere. 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).
- Some users may be asked for additional information, including a Project Title, Project, Scientific, and Technical descriptions, and Resources Required. If you are prompted for this information, indicate in all required fields that you are, 'Requesting an Atmosphere account for the University of Arizona Tools and Services Workshop on 3/18/2016'. For resources, you can enter 'Workshop Minimum'.
3. CoGe Account
- Register for a CoGe account: https://genomevolution.org/wiki/index.php/How_to_get_a_CoGe_account
4. 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)
- Download Cyberduck: Using Cyberduck for Uploading and Downloading to the Data Store#InstallingandconfiguringCyberduck
The following are optional for the workshop, but required if you wish to complete all exercises in the workshop packet:
- Data Store: Download and install iDrop (iDrop for your OS) and iCommands (iCommands for your OS)
- VNC Viewer: Download the DMG (for MAC) or exe (for PC) (http://www.realvnc.com/download/viewer/)
- Windows Users: Download and install PuTTY (http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html)
5. Pre-workshop Homework:
- Download and complete the exercises in the pre-workshop packet to get the most out of the workshop
- Download a copy of the workshop packet to follow along during the workshop
Workshop Program (March 18)
Time | Description | Slides / Workshop Packet Page Numbers | Links | Presenter |
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2:00pm | Arrive / Sign-in / Verify CyVerse Accounts Introductions of instructors | Your choice to follow along:
| Eric, Jeremy, Upendra | |
2:15 | Overview of CyVerse |
| Eric | |
2:45 | CyVerse Data Store - Managing "Big Data" |
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| Jeremy |
3:15 | Break |
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3:30 | Overview of the CyVerse Discovery Environment (DE) Overview of Atmosphere (Brief) Example Science Applications (Very Brief) |
| Jeremy | |
4:00 | Genome management, visualization, and analysis: RNASeq, variant calling, comparative genomics with CoGe | Keynote, PDF, and PPT | Eric Lyons | |
5:00 | Workshop summary and conclusion | Eric, Jeremy, Upendra |