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iPlant Events and Workshops for 2013

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iPlant Contact

Institution Contact




Jan 3-5

Anaheim, CA

Nirav Merchant

Sandy Sharp, CSU LA Taskforce Chair

Workshop:  Atmosphere Cloud Computing for Education and Research
Trainers: Nirav Merchant, Andre Mercer

2013 Tucson Winter Institute in Plant Breeding


Jan 7-11

Bio5 Institute, Tucson, AZ

S. Goff

B. Walsh, BIO5

Module 4 (Slides): iPlant Overview, Discovery Environment, Heterosis, Cloud Computing, Climate Models, Data Store (Quick Start Guide), CoGe, Molecular Breeding, Integrated Breeding Platform
Trainers: Steve Goff and Nirav Merchant

International Biogeography Society Mtg

Annual Meeting

Jan 9-12

Miami, FL

M. Narro


Presentation: Brian Enquist, The commonness and distribution of rarity: Quantifying the botanical diversity of all plant species in the Americas
- Benjamin Blonder*, Assembly of plant communities in climate space
- John C. Donoghue, Quantifying the fundamental unit of biogeography: Assessing different methods to measure geographic range size and why it matters
- Benoit Parmentier, Climate interpolation of daily maximum temperature: improvements for the production of climate datasets
* Lists M Narro as co-author

BeanCAP Adv Cmte Meeting

Annual Meeting

Jan 10

Handlery Hotel and Resort
950 Hotel Circle North
San Diego, CA

S. Goff

Phil McClean
BeanCAP Project Director

Steve Goff invited; not attending as he'll be teaching at Winter Breeding Institute.

National Institute for Food and Agriculture - Animal Project Directors' Meeting


Jan 11

San Diego, CA

D. Ware


Presentation: Doreen Ware, Overview of iPlant

Tools and Services Workshop @ PAG


Jan 11

Sheraton San Diego Hotel & Marina

J. Williams


Half-day workshop (~1:00PM-7:00PM) one day before the start of PAG.  The Sheraton is adjacent to the San Diego airport.

PAG XXI (wikipage)


Jan 12-16

San Diego, CA

S. Goff


PAGXXI (website)
Early Pre-Registration - accepted up through and including October 31
Standard Pre-Registration - November 1 through January 9th
On site Registration - available after January 9th, 2013

Ensembl Browser Workshop @ UA


Jan 22

Tucson, AZ

N. Merchant, F. McCarthy

Bert Overduin
Vertebrate Genomics Team
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

Participants will include iPlant staff, plus UA departments.  Room: Keating 103
Limit: 45 people

Ensembl API Workshop @ UA


Jan 23

Tucson, AZ

N. Merchant, F. McCarthy

Bert Overduin
Vertebrate Genomics Team
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

Participants will include iPlant staff, plus UA departments.  Room: Drachman 119
Limit: 20 people

iPlant HIP Hackathon


Jan 28-Feb 1

Tucson, AZ

N. Matasci, 411

Arlin Stoltzfus
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD, 20850

HIP = Hackathons, Interoperability, and Phylogenies Group at NESCent
Room: Keating 103 (and breakout rooms) 

4th AgMIP Development Sprint


Feb 4-8

Austin, TX

Jayme Brown

Steve Welch

Invited workshop for AgMIP community. The main goal of the workshop is to develop data translation tools to enable multiple crop models to be used by AgMIP researchers.  Info about AgMIP Development Workshops can be found here.

Big Data Computing: Building a Vision for ARS Information Management


Feb. 5-6

GWCC, Beltsville, MD

D. Ware, M. Vaughn


The USDA ARS is hosting a meeting on big data.  
Doreen Ware, 
Matthew Vaughn,

Biotechnology - Life Sciences Seminar Series at University of Nebraska, Lincoln


Feb. 6

Lincoln, NE

S. Goff

Thomas C. Hoegemeyer
362 H Plant Science Hall
University of Nebraska-Lincoln
Lincoln, NE  68583-0915 402-472-7049

Presentation: Steve Goff, The heterosis model, why iPlant tools/CI are necessary to solve this, and other basic biology questions

BIOSA/BIO5 Student Industry Networking Event


Feb 13

Tucson, AZ

U. Hilgert


Andre Mercer, Chris LaRose, Monica Lent, and Tina Lee to provide information about Big Data in biomedical research to UA graduate and undergraduate students. 

Technology in Tucson: Industry and Education Showcase 

Trade Show

Feb 16

Tucson, AZ

U. Hilgert

AZ Tech Council

Uwe Hilgert to staff booth providing information about iPlant Collaborative. 

GinE @ National Biotechnology Education Conference


Feb 16

Santa Clara, CA

D. Micklos


Workshop: DNA Barcoding
Trainers: Dave Micklos

Gordon Research Conference in Quantitative Genetics and Genomics


Feb. 17- 22

Galveston, TX

D. Ware, S. Goff, A. Stapleton


Presentation: Steve Goff, The iPlant Collaborative
This will be given in Doreen's stead.
Attendees: Ann Stapleton, Bruce Walsh, and many other associated collaborators.

Phenotype RCN


Feb 23-25

NESCent, Durham, NC

R. Walls


Ramona Walls to represent iPlant at the meeting.

UA Microbiology Dept. Lecture Series


Feb 27

Tucson, AZ

S. Goff

Maggie So, Immunology Dept.

Presentation: Steve Goff, The heterosis model, why iPlant tools/CI are necessary to solve this, and other basic biology questions. 1PM, MRB102

Genomes to Germplasm


Feb 28 - Mar 2

INRA, Versailles, France

N. Merchant, E. Lyons

P. Kersey, EMBL

Nirav Merchant and Eric Lyons to represent iPlant on "...(ii) informatics needs and solutions: what infrastructure and data standards are available, and what componenets are missing or underdeveloped, particularly in the context of globally distributed activities,..."  and "...(iv) tools needed to practically apply these data for the purposes of plant breeding and crop development."

RCN Pollen Meeting


Mar 2

Tucson, AZ

M. Narro,

Ravi Palanivelu

Presentation: Martha Narro and Steve Goff, Overview of iPlant, Data Store, and DE
Presentation: Naim Matasic, Atmosphere 
Presentation: Shannon Oliver and Andrew Predoehl, Bisque
Presentation: Matt Bomhoff, CoGe

Murray State University


Mar 8

Murray, KY

A. Stapleton


Presentation: Ann Stapleton, iPlant Overview 

Tucson Festival of Books

Informal Talk for General Public

Mar 9

Tucson, AZ

E. Lyons


Presentation: Eric Lyons,  "What you can learn from your genome"
Part of Science Cafe Talks at the Book Festival, Main Stage, 3PM.

Ecological and Functional Genomics Group @ SUNY Stony Brook


Mar 11

Stony Brook, NY

C. Noustsos


Presentation: Christos Noutsos, "Big Data in Plant Biology: an example in Ecology and Evolution"

High Tech Anthropology by Menlo Innovations


Mar 11-15

Ann Arbor, MI

S. Oliver


Training for Shannon Oliver on Agile software Development
Designated Lodging: Campus Inn Ann Arbor

TSW @ Maize Genetics Conference


Mar 14

Pheasant Run Resort, St. Charles, IL

U. Hilgert

Margy Moore 

Half-day workshop (~10:00AM-3:00PM) one day before the Maize Genetics Conference 2013.

Pittsburgh Supercomputing Center


Mar 18-19

Pittsburgh, PA

S. Goff

Phil Blood

Presentation: Steve Goff, Using the iPlant cyberinfratstructure to explore the potential connection between protein metabolism, hybrid vigor, and cellular aging. Designated lodging: Wyndham Hotel University Center.

GinE @ Hinxton, UK


Mar 21-22 

Hinxton, UK

D. Micklos


Workshop: DNA Barcoding / DNA Subway
Trainers: Dave Micklos
Presentation: DNA Barcoding 101: A Practical and Planning Workshop for Science Centers



Mar 25-29

Seattle, WA

R. Walls


Ramona Walls to attend.  Hosted by the I3BR EAGER project.

Software Carpentry Workshop: Programming for Biologists


Apr 4-5

Tucson, AZ

N. Merchant, J. Messier

Titus Brown

Online Registration
Business purpose: "Our goal is to help scientists and engineers become more productive by teaching them basic computing skills, like program design, version control, testing, and task automation. In our teaching we emphasise how these skills can contribute to quality, usable, reproducible research. In this two-day boot camp, short tutorials will alternate with hands-on practical exercises. Attendees will be encouraged both to help one another, and to apply what they have learned to their own research problems during and between sessions."  iPlant is sponsoring the travel expenses of Dr. Titus Brown.

North Carolina Academy of Science Annual Meeting


Apr 6

Pembroke, NC

D. Micklos


Presentation: Dave Micklos, Engineering Society: The American Eugenics Movement 
Presentation: Dave Mcklos, iPlant Collaborative Project

PSI Advisory Board Mtg


Apr 5

Ames, IA

S. Goff

Deanne Brill

Steve Goff to participate in Plant Science Institute Council/Board Meeting.

Institute of Bioinformatics State-of-the-Art Next Generation Sequence Symposium


Apr 8-9

Athens, GA

E. Lyons

Travis Glenn

Presentation: Eric Lyons, iPlant Data Store: Managing Your Data's Lifescycle
Presentation: Eric Lyons, CoGe: Web Based Services for Comparative Genomics

Genome/Transcriptome Assembly & RNA Seq Training


Apr 11

Blacksburg, VA

R. Barthelson

Dorothea Tholl, Shelley Moore, Gunjune Kim

Workshop:  Genome/Transcriptome Assembly & RNA Seq Training
Trainer:  Roger Barthelson
Audience: Molecular Plant Sciences Program students at Virginia Tech
Agenda: AM Sessions include Plantagora & Genome Assembly; PM Sessions include iPlant DE; RNA Seq; transcriptome assembly.

Bioinformatics Seminar Series


Apr 12

Kannapolis, NC

S. Goff

Debby Roseman/Ann Loraine

Presentation: Steve Goff,  What iPlant Can Do For You 

Genomics Standards Consortium


Apr 21-26

Bethesda, MD

R. Walls


Ramona Walls to attend.  Hosted by RCN4GSC.

G-8 International Conference on Open Data for Agriculture


Apr 29-30

Washington, DC

D. Stanzione

Jack Okamuro

Presentation (invited): Dan Stanzione,

Plant Phenotype Pilot Project Meeting


Apr 30 - May 3

Ames, IA

R. Walls


Ramona Walls to attend.  Hosted by Phenotype Ontology RCN.

Nanoinformatics Workshop


May 7

Los Angeles, CA

N. Merchant

Yoram Cohen

A workshop that will use iPlant CI as part of the CEIN collaboration.
Trainer: Nirav Merchant

Syngenta Corporation


May 8


S. Goff


Steve meeting to discuss Syngenta database in Data Store.

Iowa State Software Integration Tutorial


May 13-14

Ames, IA

M. Vaughn

James Koltes

A training workshop to teach software integration into iPlant DE, use of the FAPI, Atmosphere, and XSEDE resources.
Trainer: Matt Vaughn

Mars Corporation


May 14-15

Davis, CA

S. Goff


Steve Goff to meet with members of the Mars Corporation to discuss potential synergies and present on iPlant resources available for genomics research/molecular breeding.

Plant Ontology, Gene Ontology, and Protein Ontology Group


May 15-17

Buffalo, NY

R. Walls


Ramona Walls to attend.

Next-Generation Sequencing Workshop @ UNC Charlotte


May 16-17

Charlotte, NC

J. Williams, M. Vaughn 

Ann Loraine

Presentation: Matt Vaughn, How the iPlant Cyberinfrastructure Can Help Accelerate Your Science
Workshop: Scalable Metagenomic Analysis Using the iPlant Discovery Environment and Atmosphere
Trainer: Matt Vaughn

Forest Modeling


May 22

Tucson, AZ

M. Narro

Brian Enquist

Kickoff meeting for Forest Modeling project



May 28


S. Goff


Continuing discussions re: database.

National Association of Plant Breeders


Jun 2- 5

Tampa, FL

S. Goff, D. Ware

David Francis

Presentation:  Steve Goff,  Overview of iPlant CI and its Applications, Wed. June 5, 8:05 am, Ballroom
Data Workshop:  D. Francis and D. Ware presiding, Wed. June 5, 1 pm
Attendees:  Doreen Ware, Steve Goff, Liya Wang, Jason Williams, Nicole Hopkins 

KBase-iPlant Collaborations


Jun 4-6

Lemont, Illinois

D. Stanzione, N. Merchant, S. McKay, E. Skidmore, et al.

India Gordon

Goal: to discuss KBase-iPlant Collaborations

Navigating New Risk
Landscapes & Opportunities in Global Food Systems


Jun 11-13

Tallberg, Sweden

S. Goff

M. Jahn, D. LeZaks

Steve Goff is invited to this meeting for 40 senior distinguished colleagues from private and public sectors entitled "Navigating New Risk Landscapes & Opportunities in Global Food Systems." This meeting will start in the afternoon of Tuesday, June 11th and run through early afternoon June 13th 2013 in Tällberg, Sweden.

IBP Annual Meeting


June 18-21

Montpellier, France

S. Goff

Xavier Delannay

Steve Goff invited to represent iPlant.

iRODS Tutorial for UITS

Workshop (UA internal)

June 24-25

Tucson, AZ

N. Merchant

L. Breeger, iRODS

Trainer: Lisa Breeger, iRODS

Galaxy Meeting

Internal iPlant Meeting

June 24 - 28

Austin, TX

N. Merchant, E. Skidmore, N. Matasci, D. Stanzione, M. Vaughn


Meeting with Galaxy/TACC/UA to discuss synergies /shared resources between the two projects.
Designated lodging:  Westin Austin at the Domain

Science for Team Science 4th Annual Conference


Jun 26

Evanston, IL

Catherine Freeman


Presentation: Catherine Freeman, Examining the iPlant Collaborative from a Team Science Perspective

Training Material for CI for Use by Biologists


July 8-9

Baltimore, MD

N. Merchant, S. McKay


Part of the BEACON-led NSF "training material for CI use by Biologists " Workshop

UArizona IT Summit

Closed Workshop

July 10

Tucson, AZ

E. Skidmore

Michele Norin
Chief Information Officer
University of Arizona

Presentation: Sangeeta Kuchimanchi, Log Monitoring and Visualization  
Presentation: JMatt Peterson, Monica Lent, and Steve Gregory, The Cloud Is For Everyone 
Presentation:  Edwin Skidmore, OpenStack: The Sky is the Limit

2013 CUAHSI Conference on Hydroinformatics and Modeling


July 17-19

Logan, UT

D. Gessler


Presentation: Damian Gessler,

ASPB/Plant Biology 2013



Jul 20 - 24

Providence, RI

J. Williams


Presentation: Doreen Ware, Cyberinfrastructures for Plant Science: iPlant and KBase 
Poster: Christos Noutsos, iPlant collaborative: A case study on Soybean RNA-expression analysis
Attendees: Jason Williams,

RCN-UBE Incubator Workshop: Enhancing Data Discovery and Usability for Inquiry in Biology


July 25- 26

University of Michigan, Ann Arbor

N. Matasci, J. Williams

Tanya Dewey

Participants: Martha Narro, Uwe Hilgert
The goals of the workshop are to discuss the issues around challenges of making data available for use in undergraduate biology classrooms
Meeting Report

Botany 2013



Jul 24 - Aug 1

New Orleans, LA

J. Williams


Sunday July 28th; Full day iPlant Tool and Services workshop; Full day DNA Subway workshop
Trainers: Jason Williams, Sheldon McKay, Uwe Hilgert 

MidAtlantic Plant Molecular Biology Meeting


Aug 15-16

Laurel, MD



Presentation: Sheldon McKay, The iPlant Collaborative: Bringing together high performance computing and biology

SESYNC Vis Tools Short Course

Short Course

Aug 15-16

Annapolis, MD

N. Merchant

D. Carpenter, SESYNC


National Key Laboratory of Crop Genetic Improvement,
Huazhong Agricultural University


Aug 18

Wuhan, China

S. Goff

Jinghua Xiao, Qifa Zhang


Plant Genomics in China XIV


Aug 19-22

Nanjing, China

S. Goff

Na Li

Presentation: Steve Goff, iPlant Resources
International Conference Hotel of Nanjing, No.2 Sifang Cheng, Zhongshanling, PRC 

NSF-iPlant Leadership Meeting


Sep 3-4

Austin, TX

S. Goff, D. Stanzione, D. Ware

Karen Cone

Designated Lodging: Hyatt House Austin Arboretum

NSF Plant Genome Research Program Annual Awardee Meeting


September 5-6

Arlington, VA

D. Ware
J. Williams

Diane Okamuro

Presentation: The iPlant Collaborative, Community Cyberinfrastcuture for Life Science, Jason Williams 
Poster: iPlant Collaborative, Cyberinfrastructure that Brings Data to Life

Data Mining with iPlant


Sept 17-20, 2013

Warwick, UK

D. Stanzione, M. Vaughn, N. Matasci, J. Williams

Charis Cook

Workshop Wiki Page
Venue: The University of Warwick, Gibbet Hill Campus
Date: 17-20 September 2013
Cost: Registration for the whole four-day workshop is £100, including accomodation from 17-20 September.
Registration for the first day only is free. All delegates must cover their own travel expenses.
Registration will close on 16 August.

TSW @ College Station



College Station, TX

J. Williams, J. Fonner

Kranthi Mandadi


Digital Environment for Sample Curation


Sept 23-25

Palisades, NY

R. Walls


Presentation: Ramona Walls, Overview of the iPlant Cyber Infrastructure

GinE @ Prairie View A&M University


Sept 26-27

Prairie View, TX

J. Williams

G. Regisford


Science Gateways


Sept 27

Indianapolis, IN

L. Wang 


Presentation: "Building an open Genome Wide Association Study (GWAS) platform"



Oct 3


J. Williams

Amy Litt, Jerry Eng

Tools and Services Workshop

RNA Seq & BioExtract Server


Oct 11


J. Williams

C. Lushbough

Webinar Co-taught with Carol Lushbough from Univ. South Dakota

Beard Fdn Fall Conf on Appetite


Oct 21-22


S. Goff

J. Halperi,
Ashley Kosiak
Program Assistant Phone: 212-627-1111 ext.572

Presentation: Steve Goff, The Biology of Appetite

GWAS Advisory Group


Oct 26-27

Tucson, AZ

N. Merchant, S. Goff, N. Hopkins

B. Walsh

Convening 3 GWAS scientists for input into GWAS pipeline development.
Attendees: William Muir, Purdue University; Shizhong Xu, Univeristy of California, Riverside; Ignacy Misztal, University of Georgia; Bruce Walsh; University of Arizona
Designated Lodging: Peppertrees B&B 

TSW@ Colorado State University


Oct 28-29

Ft. Collins, CO

J. Williams

Jan Leach

TSW Workshop

TDWG 2013 (Annual Conference for Biodiversity Information Standards)


Oct 28 - Nov 1

Florence, IT

R. Walls


Presentation:  Ramona Walls, "Linking Biodiversity Data with the Biological Collections Ontology"
Ramona Walls is also co-chair of the Ontologies and Formal Models break-out, Semantics for Biodiversity Special Session

GinE @ Community College of Denver


Oct 30-31

Denver, CO

J. Williams

Heidi Loshbaugh

GinE Workshop held adjacent to American Indian Science and Engineering Society National Conference.


Annual Meeting

Nov 3-6

Tampa, FL

S. Goff

Hugh Earl

Crop Science Society of America (CSSA)
Presentation: Steve Goff, "Using the Iplant Cyberinfrastructure to Explore the Connections Between Cellular Respiration, Heterosis and the Molecular Biology of Aging" 
Session date & time: Monday, November 4, 2013, 8:45 AM to 12:00 PM
Session title: Symposium--Crop Respiration - The Other Half of the Carbon Balance
Goff presentation time: 10:20 AM to 10:45 AM

UC Davis Genome Center Meeting


Nov 7

Davis, CA

S. Goff, N. Matasci

Allen Van Deynze, Ph.D., Director of Research at Seed Biotechnology Center at UC Davis

Richard Michelmore, Director of the Genome Center at the Genome and Biomedical Sciences Facility at UC Davis
Tel 530-752-1729

Business Purpose: An all-day meeting at the Genome Center with an introduction of iPlant and IBP followed by faculty talks and discussions on the African project, relations between iPlant and the Genome Center, and how best to work together.

Designated Lodging: Best Western University Lodge
123 B Street, Davis, CA 95616

KBase-iPlant Collaboration Meeting(POSTPONED)


Nov 6-8

Austin, TX

D. Stanzione, N. Merchant,  E. Skidmore, et al.


Follow-up to May 2013 meeting

BioExtract/SSWAP Meeting


Nov 19-20

Vermillion, SD

D. Gessler

Carol Lushbough

Gessler and Lushbough will discuss integration SSWAP into BioExtract.
Designated Lodging: Prairie Inn, 916 N. Dakota St., Vermillion, SD

SQG Conference


Nov 24-26

Seattle, WA

A. Stapleton


Anne presenting poster on iPlant.

African Plant Breeding Academy / Orphan Crops Consortium Steering Cmte


Dec 2-3 

Nairobi, KENYA

S. Goff

Allen Van Deynze
World Agroforestry Center
Nairobi, Kenya

Steve signed the MOU/NDA with IRRI and participated in the Steering Cmte for the Orphan Crops Consortium, including Mars Inc, UC Davis, ICRAF, NEPAD, etc.

iPlant TSW @CSHL Plant Genomes & Biotechnology: From Genes to Networks


Dec 4-7

Cold Spring Harbor, NY

J. Williams


1/2-Day TSW on Dec 4th,
Jason W. Will give the talk "The iPlant Collaborative - A Unified Cyberinfrastructure for Plant Science."

KBase Collaboration Meeting


Dec. 18

Oak Ridge, TN

S. Goff

Martin Keller

Designated Lodging: Homewood Suites, 10935 Turkey Drive, Knoxville, TN
Steve's seminar: "Using the iPlant cyberinfratstructure platform to explore the potential connection between protein metabolism, hybrid vigor, and cellular aging.  Abstract: Transcriptomic profiling was used to determine the relative differences in gene expression between young inbreds, young hybrids, and old hybrids.  The iPlant Discovery Environment facilitated the analysis of the large datasets and storage of the data and analysis results.  Lessons learned in this proof-of-concept exploration of gene expression data are helping to shape the future direction of the tools and services available from iPlant. The analysis results suggest that further studies in this area will help bring clarity to the molecular mechanisms of cellular aging as well as to the application of this knowledge in crop productivity.