2016 02 03 Tools and Services Workshop - University of Delaware

Organizers:	A. Hlousek-Radojcic, J. Williams
Local Point of Contact:	Alenka Hlousek-Radojcic
Trainers:	Joslynn Lee, Jason WIlliams
Date:	Feb. 3-4, 2015
Location:	University of Delaware Newark, DE Room: Interdisciplinary Science and Engineering Laboratory (ISE) - 410 221 Academy St. University of Delaware
Parking Information/Permits	https://udel.t2hosted.com/cmn/index.aspx.

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 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)
Download Cyberduck: Using Cyberduck for Uploading and Downloading to the Data Store#InstallingandconfiguringCyberduck

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)

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
09:30 AM	Overview of the CyVerse		slides	Getting Started with CyVerse
09:45 AM	Managing "Big Data" using the CyVerse 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 CyVerse Data Commons metadata Bulk Metadata tutorial
10:30 AM	Coffee Break
10:45 AM	Navigate the CyVerse Discovery Environment (DE) cont'd	MUSCLE analysis (p. 16-17) Simple upload/download (follow) Moving, renaming, creating (follow) Adding metadata (p. 32) Searching (follow)	slides	DE Manual DE Apps list
11:15 AM	Analyses in the DE; Phylogenetics Example	Self-guided (p. 16-18)		DE Manual on Workflows
12:00 PM	Lunch
01:00 PM	DNA Subway (Workflows for Bioinformatics Education)			DNA Subway Website
01:15 PM	Using the DE for RNA-Seq	Launching TopHat (p. 33) Examining outputs (follow along) Visualizing alignments (follow along)	slides	Learning Center Expanded online tutorial RNA-seq protocol paper FASTQC Explanations
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
03:00 PM	Coffee Break
03:15 PM	Tool Integration in the DE	Building Phyml App(P. 36-40)
03:45 PM	SRA Demo	Sequence submission to SRA	slides	NCBI Sequence Read Archive (SRA) Submission (Workflow Tutorial)
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 CyVerse 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 RNA-Seq Best Practices Overview
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)

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: www.udel.edu/transportation/parking/categories_vendor.html/

Travel/Lodging

See the university website: http://www.udel.edu/visitus/