2016 05 30 Tools and Services Workshop - Langebio - Cinvestav
Organizers: | R.R. Álvarez, J. Williams |
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Local Point of Contact: | |
Trainers: | John Fonner (TACC), Jason Williams (CSHL) |
Date: | May 30-31 |
Location: | Langebio - Cinvestav: Auditorium |
Parking Information/Permits | |
Associated Workshop | Data Carpentry: http://jasonjwilliamsny.github.io/2016-06-01-langebio/ |
Required Workshop Prep
See detailed instructions in sections 1-5 of the
Download:
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 (pg. 5-10) to get the most out of the workshop.
Complete this Pre-Workshop Survey
Etherpad
Connect to the etherpad at : TBA
You can use the etherpad at the workshop to ask questions and share information, links, etc.
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 |
| Jason | ||
09:30 AM | Overview of the CyVerse |
| Getting Started with CyVerse | Jason | |
09:45 AM | Managing "Big Data" using the CyVerse Data Store |
| John | ||
10:30 AM | Coffee Break |
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10:45 AM | Navigate the CyVerse Discovery Environment (DE)
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| Jason | ||
11:15 AM | Analyses in the DE; Phylogenetics Example |
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| John | |
12:00 PM | Lunch | Food available for purchase on-site |
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01:00 PM | DNA Subway (Workflows for Bioinformatics Education) |
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| Jason | |
01:15 PM | Using the DE for RNA-Seq |
| Jason | ||
02:15 PM | Atmosphere Cloud Computing |
| John | ||
03:00 PM | Coffee Break |
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03:15 PM | Sequence Read Archive Demo |
| Jason | ||
04:00 PM | Workshop summary and conclusion |
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Draft Workshop Program (DAY 2)
slides
Time | Description | Slides | Links | Presenter |
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09:30 AM | Demo: CyVerse Transcriptome assembly; microbiome tools |
| Jason | |
10:00 AM | Getting started with Annotation: MAKER (MP) | (MP) | Jason | |
10:30 AM | Coffee Break |
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11:15 AM | Visualization of RNA-Seq results in Atmosphere | Jason | ||
12:30 PM | Lunch |
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01:30 PM | Brining your tools to CyVerse with Docker |
| John | |
02:15 PM | Adding new Apps/Systems using the Agave API |
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02:30 PM | Individual consultations |
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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.
Travel/Lodging