iPlant Workshop @VT
Sept 12-14, 2011
3060 Torg.
Agenda
Day 1 Morning Session 1: 8:45 -10:15AM. Ruth Facilitates.
1. iPlant’s Goals: Matt/Dan
2. Welcome, Introductions, Goals of the Workshop: Ruth
3. Brief Overview of Use Cases, Background, and Their Significance: “What is the
central question? What is already known? Why do we care? What do we need to
know now? Why do we need iPlant?” (12 minutes each, and three minutes for
questions). Plant Biology only, please.
3A. “Cellular Signaling Pathways Responsive to Abiotic Stress in Arabidopsis
Roots and Shoots.” Ruth and Kuan
3B. “The Acquisition of Winter Hardiness in Conifers“. Jason, Haktan, and
Elijah
3C. “Why do Maize and Rice Embryos Exhibit Heightened Susceptibility to
Drought Stress?” Madan, Akshay, Elijah, and Ruth
Coffee Break: 10:15- 10:30AM
Morning Session 2: 10:30-11:45. Dan Facilitates.
1. " The iPlant Discovery Environment. How It Works. Criteria for Inclusion” Matt.
2. Questions for Matt and/or Dan
Lunch on your own. VT students and faculty will accompany our visitors to local
eateries.
Afternoon Sessions. The afternoon sessions will be devoted to showcasing
individual tools, discussing results obtained from application of selected tools to
data associated with use cases 3A, B, and C, and putting tools into the DE.
Afternoon Session 1: 1:15 - 3:30. Eva Facilitates.
1. “A Plant Systems Biology Approach to the Regulation of Cellular Events during
Seed Filling”. Eva and Fang
2. “The Beacon Project. Plans to Depict Stress Signaling Pathways in a Drawing
Language”. Lenny
3. Visitors and VT “tool gurus” briefly demo analysis tools at separate
workstations: Nick (BAR tools), Bjoern and Elijah (MapMan), Kuan,
(GeneMania), Haktan (Ontologizer), Curtis (Biclustering), Akshay (RNA-Seq
Analysis and PAGE), Christos (Atmosphere).
3:30 PM. Coffee Break.
Afternoon Session 2. 3:45-5:45. John Facilitates.
A. 3:45 – 4:30 Results obtained from applying analysis tools to use case data
from 3A, 3B, and 3C, including use of large screen displays. Results
presented by grad students, Kuan and Curtis (Large screen display and
3060 Torg), Akshay (3060 Torg), Haktan and Elijah (Large screen
display), and faculty member Chris Franck (3060 Torg), (Ruth, Jason, and
Guillaume hover).
B. 4:30 – 5:45. Analysis tools into the DE. iPlant personnel, helped by VT
tool gurus (Kuan, Elijah, Akshay, Haktan, and Curtis).
C. 4:30 -5:45. Individual conversations among users (non tool gurus).
6PM. Reception/Dinner in Graduate Life Center. Wine and beer will be served.
Day 2. September 13th
Morning Session 1. 8:15 -10:00. Guillaume facilitates
Ten minute bird’s eye views of other VT plant biology projects, 5 minutes for
questions.
1. Christos ‘ use case.
2. “Host-Parasite Interactions”. Jim W. and Gunjune
3. “Responses of Arabidopsis to Pathogen Invasion”. John McD. and Kevin
Morning Session 2. 10:30 –noon. Lenny facilitates team organization.
“Lab Work”. With guidance from iPlant personnel, and the VT tool gurus, the
group, subdivided into teams, will learn how to put tools into the DE. Teams are
requested to take notes, to be used later on. Observed by students from the
Center for Human-Computer Interactions, Chris North, PI. “Usability Study”.
Working Lunch at Graduate Life Center : noon
Afternoon Session 1. 1:30-5:00. Coffee Break 3PM. Jason Facilitates.
Lab Work continued. Teams will begin to analyze omics data provided by Eva, Jim,
and John. Guillaume and Yu Shi will join a group, depending on their interests.
Individual teams will focus on the application of particular tools to the data sets.
This activity is expected to take the majority of, if not the entire, afternoon. If
time permits, representatives from each team (Eva, Jim, John, Guillaume, and/or
their students) will briefly report on their progress, their frustrations, and their
conclusions (usability and plant biology) to the entire workshop. Observed by
students from the Center for Human-Computer Interactions, Chris North, PI.
“Homework “ for the teams: What is missing? What would make analysis
easier? Diagrams, lists, workflows, outlines of suggestions in PowerPoint format
encouraged.
7PM. Group dinner at local restaurant. Do your homework!
Day 3. September 14. Morning Only. 8:30-11AM. Coffee Break at 10AM.
Brainstorming Session. Matt facilitates. Teams present their “homework”.
What worked?
What didn’t work?
Insights, with respect to either the science, or the methodology?
Input from usability team.
What additional tools are needed? Input from the plant biology teams.
What more could iPlant do for us?
Responses from iPlant personnel.
Complete usability survey.