/
2013 10 03 TSW NYBG

2013 10 03 TSW NYBG

Organizers

Jason Williams, Amy Litt

Trainers

Jason Williams, Sheldon McKay, Ramona Walls

Date

Thursday, Oct 3, 2013

Location

Pfizer Plant Research Laboratory - Conference Room

Please Remember to Bring

  • Wi-Fi enabled laptop and power supply:
  1. Please have JAVA installed and enabled (help)
  2. Please have an up-to-date web browser (Recommended Firefox or Safari )

Directions and Parking

For offsite participants:

Enter Mosholu Gate, which is directly opposite the Botanical Garden Metro-North station on Southern Blvd.  This is NOT the main entrance, which is also on Southern Blvd but is opposite the main entrance to Fordham University.  The Mosholu Gate is just a bit farther north along Southern Blvd. (which in some places may still be labelled Kazimiroff Blvd)

Turn left, park, and the lab is directly ahead of them, straight down the road.  It says "Pfizer Plant Research Laboratory". The door to the lab building will be open. The conference room is on the first floor, to the left as you enter the atrium.

For further travel info see the Garden's direction page

http://www.nybg.org/visit/directions.php

Map page:

www.nybg.org/map/

or email Amy Litt.

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"

Workshop Handout

Workshop Program

Time

Description

Slides

Links

Presenter

9:00 AM

Arrive / Sign-in / Verify iPlant Accounts 

 

 

 

9:15 AM

Welcome - Presenter/Participant Self-Introductions

 

 

All

9:30 AM

Overview of the iPlant Collaborative

Slides

Getting Started with iPlant

Jason

09:45 AM

Overview of the iPlant Discovery Environment (DE)

Slides

DE Manual

Jason

10:15 AM

iPlant Data Store - Managing "Big Data"

Slides

Data Store Overview

Jason

10:45 AM

Coffee Break

 

 

 

11:00 AM

RNA-Seq I: Tuxedo workflow in the Discovery Environment


Sheldon

12:00 PM

Lunch

 

 

 

1:00 PM

Building Workflows

Slides

 

Sheldon

1:45 PM

RNA-Seq II: Cloud Computing with Atmosphere

Slides


Sheldon

2:30 PM

Genome assembly and annotation SOAP and MAKER

 

Assemblathon Paper
SOAP tutorial
Maker paper
Maker tutorial

Jason

3:00 PM

Stretch Break




3:15 PM

Biological Image Analysis with PhtyoBisque

Slides

Bisque video tutorials
Bisque application

Ramona

3:45 PM

Workshop summary and conclusion

Slides


Jason

4:00 PM

Individual consultations

 

 

All

Attendee List (max: 20)

Name

Research Area

E-mail

Acct Status

Amy Litt

Plant Biol

alitt@nybg.org

X

Maya Strahl

Mol Biosciences

mstrahl@nybg.org

X

Xian Wang

Systematic & Pop Biol

xwang@nybg.org

X

Fabian Michelangeli

Systematic & Pop Biol

fabian@nybg.org

X

Annie Virnig

Plant Biol

avirnig@nybg.org

X

Barbara Ambrose

Dev Biol

bambrose@nybg.org

X

Alejandra Vasco

Dev Biol

avasco@nybg.org

X

CANCELLED Rachel Meyer

Plant Biol

rm181@nyu.edu

X

Jessica Allen

Eco Studies

jallen@nybg.org

X

Anne Plessis

Plant Biol

ap133@nyu.edu

X

Fernanda Santos-Silva

Plant Biol

fssbiolgia@gmail.com

X

Karen Hicks

Plant Biol

hicksk@kenyon.edu

X

Stephen Gottschalk

IT and Orgs

sgottschalk@nybg.org

X

Elizabeth Tineo

Spec Projects

etineo@nybg.org

X

Jenna Dorey

Plant Biol

adekka11@gmail.com

X

Paola Pedraza

Systematic & Pop Biol

ppdedraza@nybg.org

 

Elizabeth McCarthy

Plant Biol

emccarthy@nybg.org

X

Jingjing Tong

Mol Biosciences

tongjingjingapp@gmail.com

X

Xiaoling Yao

Plant Biol

yao20092010@hotmail.com

 

Julian Aguirre-Santoro

Systematic & Pop Biol

jagguirre@nybg.org

X

Beatriz Perez-Sweeney

Genetics & Nucleic Acides

bperezsweeney@fordham.edu

X

WAITLIST

 

 

 

Yi-Hsuan Chu

Genetics & Nucleic Acids

chushania@gmail.com

 

Eudald Illa

Plant Genetics

illaberenguer.1@osu.edu

X

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?