2016 03 31 Tools and Services Workshop - Southern Illinois University Carbondale

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

Instructional Materials

You can download a copy of the workshop packet (CyVerse Toolkit) to follow along:

  Download Workshop Packet

Draft Workshop Program (DAY 1)

Draft Workshop Program (DAY 2)

slides

Links to paper/tools/resources

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim et al.
Nature Protocols Mar 1, 2012

Sleuth http://pachterlab.github.io/sleuth/about.html

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://parking.siu.edu/on-campus/index.html

Visitor Information: http://admissions.siu.edu/visit/visitor-information.php 

Travel/Lodging

See the city of Carbondale, IL website: http://www.carbondaletourism.org/categories/stay