2013 09 23 TSW Texas A&M
Organizers |
|
|---|---|
Trainers |
Jason Williams (CSHL), John Fonner (TACC) |
Date |
Monday and Tuesday, Sept 23 - 24, 2013 |
Location |
Department of Plant Pathology and Microbiology |
Please Remember to Bring
- Wi-Fi enabled laptop and power supply:
- Please have JAVA installed and enabled (help)
- Please have an up-to-date web browser (Recommended Firefox or Safari )
Workshop Notes
Here are a few important links that you may wish to refer to during and after the workshop:
Account/Password Problems
iPlant Help and Discussion Forums
General iPlant Support Issues
iPlant Privacy (And other) policies - "Your Data is Your Data"
- www.iplantcollaborative.org/privacy
- www.iplantcollaborative.org/about/data-set-hosting
- www.iplantcollaborative.org/about/general-usage-policy
Workshop Program (Monday, September 23rd)
Time |
Description |
Slides |
Links |
Presenter |
09:00 AM |
Arrive / Sign-in / Verify iPlant Accounts |
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09:30 AM |
Welcome - Presenter/Participant Self-Introductions |
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All |
09:45 AM |
Overview of the iPlant Collaborative |
Jason |
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10:00 AM |
Overview of the iPlant Discovery Environment (DE) |
Jason |
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10:45 AM |
Coffee Break |
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11:00 AM |
iPlant Data Store - Managing "Big Data" |
John |
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11:45 AM |
Workflows in the DE; Phylogenetics Example |
John |
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12:15 PM |
Lunch |
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01:15 PM |
Using the DE for RNA-Seq |
Jason |
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02:15 PM |
User Presentation: Transcriptome analyses of Brachypodium distachyon |
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03:00 PM |
Break |
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03:15 PM |
Atmosphere Cloud Computing |
Jason |
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04:00 PM |
Tools for Image Analysis - Phytobisque |
John |
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04:30 PM |
Workshop summary and conclusion |
Jason |
Workshop Program (Tuesday, September 24th)
Time |
Description |
Slides |
Links |
Presenter |
|---|---|---|---|---|
09:30 AM |
Visualization of RNA-Seq results in Atmosphere |
|
Jason |
|
10:15 AM |
Getting started with Annotation: SOAPdeNovo and MAKER |
Jason |
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10:45 AM |
Break |
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|
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11:00 AM |
Graduate Seminar on CI - Talk and discussion |
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|
John |
12:00 PM |
Lunch (on your own) |
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01:00 PM |
Advanced CI: iPlant Foundation API |
|
John |
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01:45 PM |
iCommands and other Data Store applications: Get started with your own data |
|
|
John |
02:15 PM - End |
Individual consultations |
|
|
Jason/John |
Attendee List (max: 30)
Name |
Research Area |
Acct Status |
|
|---|---|---|---|
Marcos Oliveira |
Plant Biol |
marcos.oliveira@ag.tamu.edu |
X |
Veria Alvarado |
Plant Biol |
veriachavez@yahoo.com |
X |
JunMyoung Yu |
Cell Biol |
junmyu@gmail.com |
X |
Julien Levy |
Plant Biol |
julienlevy@tamu.edu |
X |
Fanhong Meng |
Plant Biol |
fmeng2@gmail.com |
X |
Pei-cheng Huang |
Plant Biol |
masonhuang0208@tamu.edu |
X |
Angelyn Hilton |
Plant Biol |
angelyn1128@tamu.edu |
X |
Huan Zhang |
Plant Biol |
huanzhfly@gmail.com |
X |
Sreenath Palle |
Plant Biol |
sreesree14@yahoo.com |
X |
Mona Damaj |
Plant Biol |
mbdamaj@ag.tamu.edu |
X |
Michelle Dominguez |
Plant Biol |
Mmdominguez@ag.tamu.edu |
X |
Sabarinath Sundaram |
Plant Biol |
pksnath@neo.tamu.edu |
X |
Will Cody |
Plant Biol |
willcody@tamu.edu |
X |
Aravind Ravindran |
Other |
aravind.ravindran@ag.tamu.edu |
X |
Kranthi Mandadi |
Plant Biol |
kmandadi@bio.tamu.edu |
X |
Jesse Pyle |
Molec Biosci |
jessedpyle@tamu.edu |
X |
Bryan Gibbon |
Plant Biol |
bryan_gibbon@baylor.edu |
X but no groups |
Hector Miranda |
Env Biol |
mirandahc@tsu.edu |
|
Vimlarani Chopra |
Cell Biol |
vimlarani.chopra@hccs.edu |
|
Fatemah Mastouri |
Bio & Critical Systems |
fm79@cornell.edu |
|
Arlene Pacheco |
Mol Biosciences |
arlenepacheco@tamu.edu |
|
Ramadhika Damarwinasis |
Plant Biol |
rdamarwinasis@gmail.com |
X |
Shabfam Eslamfam |
Computer Research |
shabnam127@hotmail.com |
X |
Ken-Der Wang |
Plant Biol |
kenwang@tamu.edu |
X |
Mahnaz Kiani-Fahriz |
Genetics & Nucleic Acids |
mhkiani@tamu.edu |
X |
Nihkil Patil |
Genetics & Nucleic Acids |
nikaptil84@gmail.com |
X |
Kim Hixson |
Plant Biol |
kim.hixson@live.com |
X |
David Stelly |
Genetics & Nucleic Acids |
stelly@tamu.edu |
X |
Amanda Hulse |
Genetics & Nucleic Acids |
ahulse@tamu.edu |
X |
Christopher Lyons |
Cell Biol |
christopherwplyons@tamu.edu |
X |
Lauren Dobson |
Genetics & Nucleic Acids |
ldobson@cvm.tamu.edu |
|
Who Should Attend?
Any investigator (PIs, post-docs, grad students, industry users) who is or will be working with large datasets and computation-intensive research questions in the life-sciences (plants and animals!). Space is limited; register at:
What Should I Bring?
This workshop is hands-on so please bring a Wi-fi enabled laptop. Lunch and breaks will be provided.
How Do I Get There?
Campus Directions and Parking:
Attendees don't need a permit if they park in designated visitor parking garages that are all over the campus. The closest one to our Plant Pathology Department (Peterson building) where the workshop is going to be held is Central Campus Garage (CCG). Below is the link to the TAMU parking map. The parking fee in these garages goes hourly at about $2 per hour or $8 per 8 hours. Please see the attached parking app quote for CCG rates.
http://transportmap.tamu.edu/parkingmap/tsmap.htm?map=vis
Department guests usually stay at Vineyard Court Designer Suites Hotel (1500 George Bush Dr E, College Station, Texas, USA, 77840).
There is also a Hilton (801 University Dr E, College Station, TX, 77840) and Hyatt Place (1100 University Drive East, College Station, Texas, USA, 77840) campus.