2013 10 28 TSW Colorado State

Jason Williams, Jan Leach

Jason W., Sriram S., John F.

Monday and Tuesday, Oct 28 - 29, 2013

Lory Student Center Rm. 228
Colorado State University

Hilton Fort Collins
425 West Prospect Road, Fort Collins, CO, 80526 United States ?
800-997-9148

Time

Description

Slides

Links

Presenter

09:00 AM

Arrive / Sign-in / Verify iPlant Accounts 

Pre-Survey

09:30 AM

Welcome - Presenter/Participant Self-Introductions

09:45 AM

Overview of the iPlant Collaborative

Slides

Getting Started with iPlant

Jason

10:00 AM

Overview of the iPlant Discovery Environment (DE)

Slides

DE Manual

Sriram

10:45 AM

Coffee Break

11:00 AM

iPlant Data Store - Managing "Big Data"

Slides

Data Store Overview

• Demo URLs
• iDrop Download
• iCommands

John

11:45 AM

Workflows in the DE; Phylogenetics Example

DE Manual on Workflows

Sriram

12:15 PM

Lunch

12:45 PM

Using the DE for RNA-Seq

Slides

• Learning Center
• /wiki/spaces/eot/pages/241585220
• RNA-seq protocol paper
• FASTQC Explanations

Jason

01:15 PM

Atmosphere Cloud Computing

Slides

Atmosphere Manual

• VNC Viewer download
• Demo account info

Jason

02:00 PM

Tools Integration in the DE

Sriram

02:45 PM

Workshop summary and conclusion

Slides

Post Survey

Jason

09:30 AM

Visualization of RNA-Seq results in Atmosphere

Slides

• /wiki/spaces/eot/pages/241585140
• CummeRbund documentation

Jason

10:30 AM

Getting started with Annotation:
SOAPdeNovo and MAKER

• SOAP website
• SOAP tutorial
• MAKER publication
• GMOD MAKER tutorial

Jason

10:45 AM

Break

11:00 AM

ChIP Seq - Motif detection

Slides

•  /wiki/spaces/eot/pages/241585209

John

12:00 PM

Lunch (On your own)

01:00 PM

Advanced CI: iPlant Foundation API

• Foundation API Tutorial (Metaphlan)
• Foundation API v1 Tutorial (BlastX)

John

01:45 PM

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

02:00 PM 

Graduate Student Seminar:
What a Graduate Student needs to know about Cyberinfrastructure

Slides

John

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