2013 10 28 TSW Colorado State
Organizers |
Jason Williams, Jan Leach |
---|---|
Trainers |
Jason W., Sriram S., John F. |
Date |
Monday and Tuesday, Oct 28 - 29, 2013 |
Location |
Lory Student Center Rm. 228 |
Designated Lodging |
Hilton Fort Collins |
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 Handout
Workshop Program
Workshop Program (Monday, October 28th)
Time |
Description |
Slides |
Links |
Presenter |
09:00 AM |
Arrive / Sign-in / Verify iPlant Accounts |
|
|
|
09:30 AM |
Welcome - Presenter/Participant Self-Introductions |
|
|
|
09:45 AM |
Overview of the iPlant Collaborative |
Jason |
||
10:00 AM |
Overview of the iPlant Discovery Environment (DE) |
Sriram |
||
10:45 AM |
Coffee Break |
|
|
|
11:00 AM |
iPlant Data Store - Managing "Big Data" |
John |
||
11:45 AM |
Workflows in the DE; Phylogenetics Example |
|
Sriram |
|
12:15 PM |
Lunch |
|
|
|
12:45 PM |
Using the DE for RNA-Seq |
Jason |
||
01:15 PM |
Atmosphere Cloud Computing |
Jason |
||
02:00 PM |
Tools Integration in the DE |
|
|
Sriram |
02:45 PM |
Workshop summary and conclusion |
Jason |
Workshop Program (Tuesday, October 29th)
Time |
Description |
Slides |
Links |
Presenter |
---|---|---|---|---|
09:30 AM |
Visualization of RNA-Seq results in Atmosphere |
Jason |
||
10:30 AM |
Getting started with Annotation: |
|
Jason |
|
10:45 AM |
Break |
|
|
|
11:00 AM |
ChIP Seq - Motif detection |
John |
||
12:00 PM |
Lunch (On your own) |
|
|
|
01:00 PM |
Advanced CI: iPlant Foundation API |
|
John |
|
01:45 PM |
iCommands and other Data Store applications: |
|
|
|
02:00 PM |
Graduate Student Seminar: |
|
John |
Attendee List (max: 35)
Name |
Research Area |
Acct Status |
|
---|---|---|---|
Lindsay Triplett |
Plant Biol |
lindsay.triplett@colostate.edu |
X |
Paul Langlois |
Molec Biosciences |
palang@rams.colostate.edu |
X |
Tony Compillo |
Plant Biol |
t.campillo@hotmai.fr |
|
Youchun Li |
Plant Biol |
youchun.li@anheuser-busch.com |
|
Anne Sylvester |
Plant Biol |
annesyl@uwyo.edu |
X |
Stephen Herbert |
Plant Biol |
sherbert@uwyo.edu |
x |
Ava Hoffman |
Ecol Studies |
amh4ec@virginia.edu |
x |
June Medford |
Synthetic Biology |
june.medford@colostate.edu |
x |
Robert Baker |
Plant Biol |
robert.baker@uwyo.edu |
x |
Judy Harrington |
Genetics & Nucleic Acides |
judy.harrington@colostate.edu |
x |
Patrick Byrne |
Plant Biol |
patrick.byrne@colostate.edu |
x |
James Craven |
Biochem/Mol Structure & Function |
dinmenel@gmail.com |
x |
Christopher Van Horn |
Mol Biosciences |
christopher.van_horn@colostate.edu |
x |
Cory Culligan |
Mol Biosciences |
cory.culligan@yahoo.com |
x |
Wahid Awad |
Genetics and Nucleic Acids |
waheedagain@gmail.com |
|
Sarah Grogan |
Plant Biol |
sarahgrogan@gmail.com |
|
Jiameng Wang |
Plant Biol |
wang94@rams.colostate.edu |
x |
Addison Reed |
Plant Biol |
addison.reed@ars.usda.gov |
x |
Andrew Thran |
Plant Biol |
aethran@rams.colostate.edu |
x |
Patrick Reeves |
Plant Biol |
pat.reeves@ars.usda.gov |
x |
Jiayi Sun |
Biochem and Mol Structure and Function |
jiayisun@eng.colostate.edu |
|
Darci Giacomini |
Plant Biol |
dagiac@rams.colostate.edu |
x |
Saiprasad Palusa |
Plant Biol |
saigoud@lamar.colostate.edu |
|
David Xing |
Mol Biosciences |
denghui.xing@colostate.edu |
x |
Kevin Morey |
Plant Biol |
Kevin.morey@colostate.edu |
x |
Lee Panella |
Genetics & Nucleic Acids |
lee.panella@ars.usda.gov |
x |
Faith Robison |
Plant Biol |
frobison@rams.colostate.edu |
x |
Anireddy Reddy |
Plant Biol |
reddy@colostate.edu |
x |
Christie Peebles |
Plant Biol |
christie.peebles@colostate.edu |
x |
Graham Peers |
Algae Biology |
graham.peers@colostate.edu |
x |
Cris Argueso |
Plant Bio |
cris.argueso@colostate.edu |
x |
Jacqueline Chaparro |
Plant Biol |
jacquelinechaparro@gmail.com |
x |
Nora Lapitan |
Plant Biol |
nora.lapitan@colostate.edu |
x |
Bettina Broeckling |
Plant Biol |
bbroeckl (lamar)colostate.edi |
x |
Ana Bossa |
Plant Biol |
ambossa@colostate.edu |
x |
Thomas Minrichsen |
Mol Biosciences |
thomas.hinrichsen@colostate.edu |
|
Michael Friedman |
Mol Biosciences |
mmfried@rams.colostate.edu |
x |
Jan Leach |
Plant Biol |
jan.leach@colostate.edu |
X |
Audrey McDonald |
Plant Biol |
audrey.mcdonald@anheuser-busch.com |
|
Loic Deblais |
Plant Biol |
ldeblais@hotmail.fr |
X |
Molly Zeller |
Mol Biosciences |
mjzeller@colostate.edu |
|
Federico Martin |
Plant Biol |
fedem@rams.colostate.edu |
|
Mike Caballero |
Mol Biosciences |
mike.caballero@colostate.edu |
X |
Matthew Youngblood |
Mol Biosciences |
youngblood.matt@gmail.com |
X |
Scott Reid |
Plant Breeding |
scott.reid@colostate.edu |
X |
Xingfeng Huang |
Plant Biol |
xingfeng.huang@colostate.edu |
|
Eric Storlie |
Plant Biol |
estorlie@colostate.edu |
X |
Mohammed Albaqami |
Plant Biol |
almajed403@gmail.com |
X |
Jillian Lang |
Plant Biol |
jillian.lang@colostate.edu |
X |
Ed Peyronnin |
IT & Orgs |
ed.peyronnin@colostate.edu |
X |
Starin McKeen |
Plant Biol |
starin.mckeen@gmail.com |
X |
Heike Sederoff |
Plant Biol |
hwsedero@ncsu.edu |
X |
Jesse Gray |
Ecol Studies |
jesse.gray@colostate.edu |
|
Paola Fory |
Mol Biosciences |
paolafory@gmail.com |
|
Anding Luo |
Plant Biol |
aluo@uwyo.edu |
X |
Carolyn Rasmussen |
Cell Biol |
crasmus8@uwyo.edu |
X |
Chris Richards |
Pop Genetics |
chris.richards@colostate.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 on day one and breaks will be provided.
How Do I Get There?
Designated Lodging:
Hilton Fort Collins
425 West Prospect Road, Fort Collins, Colorado, 80526, USA
TEL: 1-970-482-2626 FAX: 1-970-493-6265
http://www3.hilton.com/en/hotels/colorado/hilton-fort-collins-FNLCOHF/index.html
Ground Transportation - S. Srinivasan
SuperShuttle shared van service to DIA
Pickup: Oct 29 @ 5:20 PM @ CSU Transit Center
Confirmation No. 4764933https://reservations.supershuttle.com/Default.aspx?content=WhereIsMyVan
Campus Maps and Parking:
http://www.colostate.edu/visiting-campus.aspx
The Engineering Parking lot is on the north side of Lory Student Center, which is accessed from Laurel and Meldrum Streets. Zoom in one level on this map, and the Lory Student Center and adjacent parking lot to the north of it are visible: http://www.map.colostate.edu/ The daily rate for on campus parking is $8/day.