2015 07 02 iPlant Tools & Services Workshop TGAC
Scientific Organizers | V. Schneider, J. Williams |
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Event Organizer | Matt 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:
- Internet Browser: Please have an up-to-date web browser (We strongly recommend Firefox or Safari - Internet Explorer and Chrome have Java and other compatibility 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/iplant-workshop-tgac
Instructional Materials
You can download a copy of the workshop packet (iPlant Toolkit) to follow along:
Draft Workshop Program (DAY 1)
Time | Description | Toolkit | Slides | Links | Presenter |
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08:30 | Arrive / Sign-in / Setup Troubleshooting |
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09:00 | Welcome - Presenter/Participant Self-Introductions | slides |
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09:30 | Overview of the iPlant Collaborative | slides | |||
10:00 | iPlant UK and COPO | Anthony, Rob | |||
10:15 | Managing "Big Data" using the iPlant Data Store |
| slides | Data Store Overview | John |
10:45 | Coffee Break |
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11:00 | Navigate the iPlant Discovery Environment (DE) |
| slides | John | |
12:00 | Lunch | ||||
13:00 | Analyses in the DE; Phylogenetics Example |
| slides | Jason | |
13:30 | Using the DE for RNA-Seq |
| slides | Jason | |
14:15 | Atmosphere Cloud Computing |
| slides | Jason | |
15:30 | Coffee Break |
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15:45 | Tool Integration in the DE |
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16:15 | Workshop summary and Conclusion |
Draft Workshop Program (DAY 2)
Time | Description | Slides | Links | Presenter |
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09:30 | Overview and demo of iPlant GWAS / Transcriptome assembly |
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10:30 | Coffee Break |
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10:45 | Getting started with Annotation: MAKER |
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12:00 | Lunch | |||
13:00 | Visualization of RNA-Seq results in Atmosphere | slides |
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13:45 | iCommands and other Data Store applications: | slides |
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14:00 | Self-Guided Tutorials (GWAS/ChiP-Seq/etc.) |
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15:00 | Individual 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 |
£100.00 | 2.9 miles | £5.00 | NR4 7SB | |
£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 |