2014 12 07 USDA BigData Workshop - RNA-Seq Train-the-Trainers
Organizers | Kapeel Chougule, Jason Williams, Doreen Ware |
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iPlant Trainers | Kapeel Chougule, Jason Williams |
Date | Dec 7-10, 2014 |
Location | CSHL |
Workshop Checklist
1. iPlant Account
- Get your free account at http://user.iplantcollaborative.org.
2. Atmosphere Access
- Once you have your account, go to https://user.iplantcollaborative.org/dashboard/ and under Available Services, request access to Atmosphere. Indicate that you are attending a workshop when you are asked for justification.
3. Laptop
Please bring your own WiFi enabled laptop to the workshop. Make sure your laptop has the following:
- VNC Viewer: Download the DMG (for MAC) or exe (for PC): http://www.realvnc.com/download/viewer/
- Java: Please have JAVA installed and enabled (help)
- Browser: Please have an up-to-date web browser (Recommended Firefox or Safari )
- Widows Users: Please instal PuTTY (http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html)
Agenda
Sunday
Time | Topic | Slides | Links | Presenter(s) |
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06:00 | Dinner (Blackford Hall - Racker Reading Room) |
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07:30 | Big Data at USDA/ARS |
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| Doreen |
08:00 | Setting the vision for Big Data training workshops |
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| DeWayne |
08:15 | ARS Exercise I - "Data Use Analyses/Outcomes" |
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09:00 | Group discussion |
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Monday (Hershey West Conference Room)
Time | Topic | Slides | Links | Presenter(s) |
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09:00 | Logistics and Setup |
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| Jason |
09:15 | Working with Data and Metadata in iPlant (iDrop, iCommands, DE, Sharing, Searching) | Jason | ||
10:30 | Coffee Break |
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10:45 | Working with the Discovery Environment (apps/workflows/analyses) |
| Jason | |
11:15 | Introduction to Atmosphere | Jason | ||
12:30 | Lunch |
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01:30 | Atmosphere work continued |
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| Jason |
02:00 | Discussion - How to create user road maps - from data to publication |
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03:00 | Coffee Break |
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03:15 | Sequence Acquisition/metadata capture, QC, normalization |
| Jason/Kapeel | |
04:00 | Guest Speaker - Evaluating assembly quality |
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| M. Schatz |
05:00 | Evaluating assembly quality lab (N50 sizes, Contig stats, CEGMA) |
| Kapeel | |
06:00 | Dinner |
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07:30 | Generating sequence annotations from transcriptome data lab (trinotate) |
| Kapeel | |
08:15 | ARS Exercise II “Data Management Plans” |
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09:00 | Group projects |
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Tuesday
Time | Topic | Slides | Links | Presenter(s) |
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09:00 | Review of yesterday’s work on annotation and evaluate goals |
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09:30 | Intro to RNA-Seq workflow, start individual RNA-Seq jobs |
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10:30 | Coffee Break |
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10:45 | Group work on RNA-Seq projects |
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12:00 | Lunch |
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01:00 | Extending the CI: integrating new tools, working with XSEDE lab |
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02:30 | Coffee Break |
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02:45 | Getting and working with iPlant support mechanisms to help yourself and others |
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03:30 | Guest speaker - Planning and Executing RNA-Seq experiments |
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| M. Hammell |
04:30 | Visualizing RNA-Seq data |
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05:30 | Extended RNA-Seq analysis with GO enrichment/pathway analysis tools (lab) |
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06:00 | Group Work continued |
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6:30 | Dinner |
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07:30 | Group Work Continued |
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Wednesday
Time | Topic | Slides | Links | Presenter(s) |
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09:00 | Presentations on Group Analyses |
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10:30 | Coffee Break |
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10:45 | Presentations Cont'd |
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11:30 | Lunch |
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12:30 | Feedback and Future Directions |
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02:00 | Departures |
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Etherpad
The etherpad we are testing for this workshop is here:http://etherpad.iplantcollaborative.org/p/ARS1
Attendees
The full list of attendees can be found here:
https://docs.google.com/spreadsheets/d/1S6vSgmRDa_wCBJOn6NxAJhLyQbRUmUuqBcoNOPWCiIE/edit?usp=sharing
Travel to CSHL, Accommodations
1. Attendees are responsible for making flight arrangements through USDA
2. Travel Suggestions
Arriving at JFK:
The AirTrain is the cheapest/most convenient. From any terminal, take the AirTrain to Jamaica Train Station. From Jamaica, you will take the Port Jefferson Line train to Syossett (We don't recommend taking the train to the Cold Spring Harbor Stop as that station is isolated, and their aren't any shops to wait in). The LIRR Schedule is here: http://web.mta.info/lirr/Timetable/Branch/PortJeffersonBranch.pdf . On Sunday, there are trains from Jamaica in the afternoon at 13 and 45 minutes past the hour.
Text us to let us know what train you are on, and we can drive up to get you. You will get an email with our contact info ahead of the workshop.
Arriving at LaGuardia:
A cab can get you to the Jamaica Train Station in 20 minutes (depending on traffic). From Jamaica, you will take the Port Jefferson Line train to Syossett (We don't recommend taking the train to the Cold Spring Harbor Stop as that station is isolated, and their aren't any shops to wait in). The LIRR Schedule is here: http://web.mta.info/lirr/Timetable/Branch/PortJeffersonBranch.pdf . On Sunday, there are trains from Jamaica in the afternoon at 13 and 45 minutes past the hour.
Text us to let us know what train you are on, and we can drive up to get you. You will get an email with our contact info ahead of the workshop.
Using Syosset Limo
You can also take a limo directly from any airport. The form the lab uses is here: http://meetings.cshl.edu/syossetlimo/SyossetLimoForm.htm Syosset limo will try to coordinate ride sharing (Be sure to indicate Rideshare only if you want the cheapest rate and someone looks to be arriving within an hour or so of your arrival), although you can probably also reserve as a group if several of you decide on times.
3. All Attendees have been assigned a room at CSHL. Check in is Sunday. All Attendees must check out by 11AM Wednesday 10/10.
4. Travel back to the Airport
Departing CSHL
Using Public Transport:
The laboratory has regular schedules M-F to Syosset train station:
http://meetings.cshl.edu/shuttle.pdf
You can use the same LIRR schedule to get back to Jamaica train station:
http://web.mta.info/lirr/Timetable/Branch/PortJeffersonBranch.pdf
Using Syosset Limo
You can call to reserve at (516)364-9681. Again, based on departure times, rideshares can also be arranged.https://pods.iplantcollaborative.org/wiki/pages/editpage.action?pageId=12888089