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Organizers:

T. Meulia

Local Point of Contact:

Tea Meulia
Hosted By: MCIC Computational Biology Lab (MCBL);
College of Food, Agricultural, and Environmental Sciences

Trainers:

Joslynn Lee, Jason Williams

Date:

March 17-18, 2016

Location:

College of Food, Agricultural, and Environmental Sciences
Shisler Conference Center
1680 Madison Avenue
Wooster, OH 44691
Parking Information/Permits

A parking permit is NOT needed

 

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:

4. Pre-Workshop Guide and Homework

Livestream

You can watch the Livestream of this event:

Day 1: http://livestream.com/cshl-dnalc/ohio-state-day1-2016

Day 2: http://livestream.com/cshl-dnalc/ohio-state-day2-2016

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:

  1. Use the instructions in the  PRE-WORKSHOP PACKET to request access to Atmosphere.
  2. Use etherpad chat to ask question. if we don't get a chance to address your question please post to ask.iplantcollaborative.org
  3. Download the Workshop Packet to follow along
  4. Please complete the post-survey.

Etherpad

Connect to the etherpad at http://lannister.iplantcollaborative.org/p/ohio2016-tsw

You can use the etherpad at the workshop to ask questions and share information, links, etc.

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

Jason

09:30 AM

Overview of the CyVerse

 

slides

Getting Started with CyVerse

Jason

09:45 AM

Managing "Big Data" using the CyVerse Data Store

  • Use Cyberduck (p.10)
  • Quick iCommands demo (follow)
  • Importing files via URL (p.29)
  • Creating Public links (p.11)
  • Sharing Folders (p.12)
slidesData Store OverviewJoslynn

10:30 AM

Coffee Break

 

 

 

 
10:45 AM

Navigate the CyVerse Discovery Environment (DE)

 

  • MUSCLE analysis (p.17-18)
  • Simple upload/download (follow)
  • Moving, renaming, creating (follow)
  • Adding metadata (p.31)
  • Searching (follow)
slidesJason

11:15 AM

Analyses in the DE; Phylogenetics Example

  • Self-guided (p.18-19)
 

DE Manual on Workflows

Jason

12:00 PM

Lunch Provided (UPDATED)

 

 

 

 

01:00 PM

DNA Subway

(Workflows for Bioinformatics Education)

  DNA Subway WebsiteJason

01:15 PM

Using the DE for RNA-Seq

  • Launching TopHat (p.32)
  • Examining outputs (follow)
  • Visualizing alignments (follow)
slidesJason

02:15 PM

Atmosphere Cloud Computing

  • Launching an instance (p.23)
  • Connecting via VNC (p.24)
  • Desktop sharing via VNC (follow)
  • Connect via SSH (follow)

slides

Atmosphere Manual

Joslynn

03:00 PM

Coffee Break

 

 

 

 

03:15 PM

Tool Integration in the DE

  • Building Phyml App (follow)
 

 

Jason
03:45 PMSequence Read Archive Demo
  • Sequence submission to SRA
slidesJason

04:15 PM

Workshop summary and conclusion

 

 

Jason

Draft Workshop Program (DAY 2)

slides

Time

Description

Slides

Links

Presenter

09:30 AM

Overview and demo of CyVerse GWAS /

Transcriptome assembly (TA)

slides (TA)

slides (GWAS)

Jason

10:30 AM

Coffee Break

 

 

 

10:45 AM

Getting started with Annotation: MAKER (MP)
Getting started with Assembly: ALLPATHS

slides (MP)

Jason

11:15 AM

Visualization of RNA-Seq results in Atmosphere

slides (V2)

12:00 PM

Lunch Provided (UPDATED)

 

 

 

01:00 PM

iCommands and other Data Store applications: 
Get started with your own data

 

 

 

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 in Etherpad

 

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://oardc.osu.edu/sites/oardc/files/imce/files/about/OARDC_WOOSTER_MAP_11x17.pdf

Travel/Lodging

See the city of Wooster, OH website: http://www.woosteroh.com/where-stay

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