2015 06 15 Tools and Services Workshop - South Dakota State University/ University of South Dakota

Organizers	C.Lushbough, S. Subramanian, J. Williams
iPlant Trainers	Jason Williams, Kapeel Chougule, Uwe Hilgert
Local TAs	TBA
Date	June 15-16, 2015
Location	South Dakota State University Brookings, SD Northern Plains Biostress Lab, SNP 67

Required Workshop Prep

1. iPlant 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 iPlant cloud service Atmosphere (see next bullet). Please avoid gmail, yahoo, hotmail and the like for your iPlant 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.iplantcollaborative.org/dashboard/ 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 iPlant 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 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)

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

Etherpad/Chatroom

We will use the following etherpad for workshop:

https://etherpad.mozilla.org/eQo40po5lz

Instructional Materials

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

Download Workshop Packet

Draft Workshop Program (DAY 1)

Time	Description	Toolkit	Slides	Links	Presenter
08:30 AM	Arrive / Sign-in / Setup Troubleshooting			Pre-Survey
09:00 AM	Welcome - Presenter/Participant Self-Introductions		slides	PLOS Bioinformatics Competency Paper	Jason
09:30 AM	Overview of the iPlant Collaborative		slides	Getting Started with iPlant	Jason
09:45 AM	Managing "Big Data" using the iPlant Data Store	Download/use iDrop (p.10) Quick iCommands demo (follow) Importing files via URL (p. 29) Creating Public links (p.11) Sharing Folders (p.12-13)	slides	Data Store Overview YouTube Playlist Demo URLs iDrop for your OS Using iDrop iCommands for your OS iCommands iPlant Data Commons metadata	Kapeel
10:15 AM	Navigate the iPlant Discovery Environment (DE)	MUSCLE analysis (p. 16-17)	slides	DE Manual DE Apps list	Kapeel
10:30 AM	Coffee Break
10:45 AM	Navigate the iPlant Discovery Environment (DE) cont'd	Simple upload/download (follow) Moving, renaming, creating (follow) Adding metadata (p. 32) Searching (follow)			Uwe
11:15 AM	Analyses in the DE; Phylogenetics Example	Self-guided (p. 16-18)	slides	DE Manual on Workflows	Jason
12:00 PM	Lunch
01:00 PM	DNA Subway (Workflows for Bioinformatics Education)		slides	DNA Subway Website	Uwe
01:15 PM	Using the DE for RNA-Seq	Launching TopHat (p. 33) Examining outputs (follow along) Visualizing alignments (follow along)		Learning Center Expanded online tutorial RNA-seq protocol paper FASTQC Explanations	Jason
02:15 PM	Atmosphere Cloud Computing	Launching an instance (p. 23-24) Connecting via VNC (p. 24) Desktop sharing via VNC (follow) Connect via SSH (follow)	slides	Atmosphere Manual VNC Viewer download Demo account info	Kapeel
03:00 PM	Coffee Break
03:15 PM	Tool Integration in the DE	Building Phyml App(P. 36-40)	slides		Jason
03:45 PM	BioExtract Server Demo		slides
04:15 PM	Workshop summary and Conclusion			Post Survey

Draft Workshop Program (DAY 2)

Time	Description	Slides	Links
09:30 AM	Overview and demo of iPlant GWAS / Transcriptome assembly	slides (TA) slides (GW)	SOAP Tutorial Tutorials (including GWAS) YouTube GWAS videos
10:30 AM	Coffee Break
10:45 AM	Getting started with Annotation: MAKER Getting started with Assembly: ALLPATHS	slides (MP)	MAKER JBrowse tutorial MAKER publication GMOD MAKER tutorial ALLPATHS FAQ Maker tutorial (Atmosophere) Maker tutorial (DE) Comprehensive YouTube playlist Additional ALLPATHS slides
11:15 AM	Visualization of RNA-Seq results in Atmosphere	slides	Tutorial CummeRbund manual
12:00 PM	Lunch (On your own)
01:00 PM	iCommands and other Data Store applications: Get started with your own data	slides
01:30 PM	“What Graduate Students should Know about Cyberinfrastructure - How to be a Successful Data Driven Biologist”
02:30 PM	Individual Consultations		Please posts your requests for 10-15 min consultations to the Etherpad (from 2:30-3 or so)

Thank you dear hosts - SDSU rocks!!!!

SDSU_FearlessHosts_800.jpg

Travel and Campus Map and Parking

Maps and parking information can be found here: https://www.sdstate.edu/resources/maps/index.cfm

Travel

Brookings is served by the municipal airport at Sioux Falls (FSD). From there you could travel the 60 miles to Brookings by bus, shuttle or rental car. See also these SDSU travel tips.

If flight connections require spending a night in Sioux Falls, the Holiday Inn Sioux Falls City Centre has excellent rates for government/state employees.Lodging

Brookings has several accommodation options. Excellent hotels that are located a few driving minutes from SDSU include:

Holiday Inn Express, 3020 Lefevre Dr., Brookings, SD 57006. Phone: (605) 692-9060
Fairfiled Inn & Suites, 3000 Lefevre Dr., Brookings, SD 57006. Phone: (605) 692-3500