2014 01 31 TSW Linfield College

Jason Williams, Sam Fox

Jason W., Ann S., John F.

Friday and Saturday, Jan 31-Feb 1, 2014

Nicholson Library - BLDG 58a
P Instruction Room (188)
Linfield College
900 SE Baker St,
McMinnville, OR 97128

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

Jason

10:45 AM

Coffee Break

11:00 AM

iPlant Data Store - Managing "Big Data"

Slides

Data Store Overview

• YouTube Playlist
• Demo URLs
• iDrop Download
• iCommands
• preview iPlant Data Commons metadata slides

John

11:30 AM

Workflows in the DE; Phylogenetics Example

Slides

DE Manual on Workflows

Ann

12:10 PM

Lunch

01:00 PM

Using the DE for RNA-Seq

Slides

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

Jason

02:00 PM

Atmosphere Cloud Computing

Slides

Atmosphere Manual

• VNC Viewer download
• Demo account info

Ann

03:00 PM

Coffee Break

03:15 PM

Tools Integration in the DE

John

03:45 PM

Educational Genome Annotation in DNA Subway

Slides

Jason

04:15 PM

Workshop summary and conclusion

Slides

Post Survey

Jason

09:30 AM

Overview and demo of iPlant GWAS

Slides

/wiki/spaces/eot/pages/241585195

Ann

10:30 AM

Coffee Break

10:45 AM

Getting started with Annotation: MAKER
Getting started with Assembly: ALLPATHS

Maker Slides
ALLPATHS Slides

• MAKER publication
• GMOD MAKER tutorial
• ALLPATHS FAQ
• Maker tutorial
• Comprehensive YouTube playlist
• Additional ALLPATHS slides

Jason

11:15 AM

Visualization of RNA-Seq results in Atmosphere

Slides

• Tutorial
• http://atmobeta.iplantc.org

Jason

12:00 PM

Lunch (On your own)

01:00 PM

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

Slides

John

01:45 PM

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

Jason

02:00 PM 

Educational DNA Barcoding

Slides

• DNA Barcoding 101
• Urban Barcode Project

Jason

02:30 PM

Individual Consultations

Get Started Cheat Sheet

All

Katie

Clark

katie.clark@pacificu.edu

Pacific University

Estefania

Elorriaga

estefania.elorriaga@oregonstate.edu

Oregon State University

Justin

Elser

elserj@science.oregonstate.edu

Oregon State University

Elahe

Esfandiari

elahe.esfandiari@gmail.com

Oregon State University

Sydney

Everhart

everhars@onid.orst.edu

Oregon State University

Sam

Fox

sfox@linfield.edu

Linfield College

Christopher

Gaiser

cgaiser@linfield.edu

Linfield College

Matthew

Geniza

genizam@onid.orst.edu

Oregon State University

Zhian

Kamvar

kamvarz@onid.orst.edu

Oregon State University

Amy

Klocko

Amy.Klocko@oregonstate.edu

Oregon State University

Anne

Kruchten

akrucht@linfield.edu

Linfield College

Haiwei

Lu

hlu602031@gmail.com

Oregon State University

Kyle

MacLea

kmaclea@linfield.edu

Linfield College

GIRIJESH KUMAR

PATEL

patelgirijesh@gmail.com

Hermiston Agricultural Research & Extension Center

Justin

Preece

preecej@science.oregonstate.edu

Oregon State University

Catherine

Reinke

creinke@linfield.edu

Linfield College

Steven

Roberts

sr320@uw.edu

University of Washington

Stephanie

Rosales

srosales712@gmail.com

OSU

Jon

Schnorr

schnorr@pacificu.edu

Pacific Univesrity

Ron

Strohmeyer

rwstrohmeyer@nnu.edu

Northwest Nazarene University

John

Syring

jsyring@linfield.edu

Linfield College

Javier

Tabima

caifaz01@gmail.com

Oregon State University

Kathryn

Theiss

ktheiss@willamette.edu

Willamette University

Kelly

Vining

kelly.vining@oregonstate.edu

Oregon State University

Wei

Wei

wei.wei@science.oregonstate.edu

Oregon State University

Jeremy

Weisz

jweisz@linfield.edu

Linfield College

Kevin

Weitemier

weitemik@science.oregonstate.edu

Oregon State University