2015 07 02 iPlant Tools & Services Workshop TGAC

2015 07 02 iPlant Tools & Services Workshop TGAC

Scientific Organizers

V. Schneider, J. Williams

Event OrganizerMatt Drew

iPlant Trainers

John Fonner (TACC) and Jason Williams (CSHL)

Date

July 02-03, 2015

Location

The Genome Analysis Centre

Norwich Research Park, Norwich NR4 7UH, UK

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 (e.g. '.edu' or '.org') only these types of email addresses will be granted access to the iPlant cloud service Atmosphere (see next bullet).

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.)

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

Etherpad/Chatroom

We will use the following Etherpad for workshop:

https://etherpad.mozilla.org/iplant-workshop-tgac

Instructional Materials

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

 Workshop Packet

Draft Workshop Program (DAY 1)

Time

Description

Toolkit

Slides

Links

Presenter

08:30

Arrive / Sign-in / Setup Troubleshooting

 

 

Pre-Survey

 

09:00

Welcome - Presenter/Participant Self-Introductions

 slides

PLOS Bioinformatics Competency Paper

 

09:30

Overview of the iPlant Collaborative

 slides

Getting Started with iPlant

 
10:00iPlant UK and COPO  Anthony, Rob

10:15

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)
slidesData Store OverviewJohn

10:45

Coffee Break

 

 

 

 
11:00Navigate the iPlant Discovery Environment (DE)
  • MUSCLE analysis (p. 16-17)
  • Simple upload/download (follow)
  • Moving, renaming, creating (follow)
  • Adding metadata (p. 32)
  • Searching (follow)
slidesJohn
12:00Lunch    

13:00

Analyses in the DE; Phylogenetics Example

  • Self-guided (p. 16-18)
slides

DE Manual on Workflows

Jason

13:30

Using the DE for RNA-Seq

  • Launching TopHat (p. 33)
  • Examining outputs (follow along)
  • Visualizing alignments (follow along)
slidesJason

14:15

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

Jason

15:30

Coffee Break

 

 

 

 

15:45

Tool Integration in the DE

  • Building Phyml App(P. 36-40)
 

 

 
16:15Workshop summary and Conclusion                    

Draft Workshop Program (DAY 2)

Time

Description

Slides

Links

Presenter

09:30

Overview and demo of iPlant GWAS /

Transcriptome assembly

slides (TA)

slides (GW)

 

10:30

Coffee Break

 

 

 

10:45

Getting started with Annotation: MAKER
Getting started with Assembly: ALLPATHS

slides (MP)

 

12:00Lunch   

13:00

Visualization of RNA-Seq results in Atmosphere

slides

 

13:45

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

slides

 

14:00

Self-Guided Tutorials (GWAS/ChiP-Seq/etc.)

 

 

15:00Individual Consultations   

Logistics, Accommodations, and other details

Arrival Time

Please ensure you arrive on day one at 08:30am for registration this is to ensure there are no delays to the workshop.

Getting to TGAC

For location details and directions to TGAC please follow here. Parking is available on-site – please following the signs to ‘Visitors Parking’ and ensure you leave your car registration number with the TGAC Training Team at registration.

Catering

Lunch and coffee is provided by TGAC over the course of the two-day workshop. We have informed catering about any dietary requirement which were inputted during online registration.

Suggested Hotel Accommodation

Hotel

Average Cost per night

Distance from TGAC

Approx taxi cost

Postcode

Travelodge – Thickthorn Services  

£40.00

2.3 miles

£5.00

NR9 3AU

Cringleford Guest House                        

£100.00

2.9 miles

£5.00

NR4 7SB

Central Hotel                                               

£60.00

6.1 miles

£10.00

NR1 1SQ

Travelodge Norwich Central                    

£47.00

4.3 miles

£10.00

NR1 3PR

Holiday Inn Ipswich Road                         

£89.00

4.4 miles

£10.00

NR4 6EP