2015 12 02 Half-day workshop on Genome Assembly, Annotation, and RNA-Seq

Organizers	J. Williams
iPlant Trainers	Jason Williams, Kapeel Chougule, Fritz Sedlazeck
Date	Dec. 2, 2015
Location	Hershey East Conference Room, CSHL

Workshop Checklist

1. iPlant Account

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)
R Studio: Please have it installed(https://www.rstudio.com/products/rstudio/download/)

4. Pre-Workshop Guide and Homework

Download and complete this optional set of exercises in this guide to get the most out of the workshop: PRE-WORKSHOP PACKET

Virtual attendees can use the chat room at the Livestream link below.

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) at least one day before the workshop: TSW Workshop Williams 1.2 or 1.1
Use Livestream 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

You can download a copy of the workshop packet to follow along:

Time	Description	Slides	Links	Presenter
12:00 PM	Boxed-Lunch / Sign-in / Verify iPlant Accounts/ Welcome		Pre-Survey	Jason
12:15 PM	Welcome - Presenter/Participant Self-Introductions/ Overview of iPlant	slides		Jason
12:30 PM	Whole Genome Assembly with iPlant	slides		Fritz
1:30 PM	Data Sharing and Annotation Projects - MAKER-P	slides	Cyberduck Download [software] [profile] Maker in Atmosphere w/cc Tools Maker-P in Discovery Environment Example Maker-P test data Maker-P with CC tools tutorial Maker and JBrowse	Jason
02:15 PM	Coffee Break
02:30 PM	New RNA-Seq Workflows: Kallisto Demo in DE	slides	demo	Kapeel
03:00 PM	Atmosphere Cloud Computing Environment	slides	Atmosphere manual (packet p.24-25)	Jason
03:15 PM	Exploring RNA-Seq data with Sleuth		demo	Kapeel
04:00 PM	Conclusion			Jason

The workshop will be held in the Hershey Building - East Conference Room (2nd Floor)

Meeting attendees will have already received parking info. Any other visitors may park in Hillside Parking: See space 30 on the map linked above.