Phylotastic/Schedule

Phylotastic: ToL's Killer App, in Just 5 Days

Day 1

Session 1 (morning): User scenarios

The idea: The reason Phylotastic is so exciting is that it finally will facilitate a useful and highly automated flow of Tree-o-Life knowledge from producers to consumers. The key to creating this flow is to focus on what users need. Thus, after an initial overview on re-use of phylogenetic knowledge, we will begin with talks describing how an imaginary phylotastic will be used in scientific research.

How to participate

• volunteer (alone, or with others) to develop and present a user scenario
• ask questions to understand user needs

Detailed schedule (add a link to your presentation-in-progress here)

• Welcome and orientation (TBD) (welcom ppt)
• intro: making the tree of life accessible for research (Arlin) (intro ppt and extras from Stoltzfus, et a review)
• Gene Tree/Species Tree Reconciliation (slides Naim)
• (phylomatic) Cam Webb (slides)
• (metagenomics) Holly Bik slides on slideshare
• Use cases from community ecology and character analysis (Arlin) usecases ppt
• Luke Harmon, slides on slideshare

Session 2 (late morning): Brainstorm

The idea: In this session, the entire group will participate in a high-level design discussion. Now that we know what Phylotastic will be used for, what components and connections will work together to satisfy user needs? This is not the time for technical discussions. Technical discussions will be allowed to the extent that they inform high-level design choices.

How to participate

• be ready to contribute all of your experience and knowledge to design decisions.
• Notes on Google doc

Session 3 (early afternoon): Boot Camp

The idea: Many participants will benefit from a rapid introduction to key technologies (e.g., NeXML, TNRS, etc).

How to participate

• request a boot camp on a particular technology
  • I'd like to request a boot camp on SADI --JamesEstill@gmail.com 16:33, 24 May 2012 (EDT)
• offer to give a boot camp on a particular technology.

Detailed schedule

• Rutger Vos, "NeXML: the next big thing in Next Big Things" [1] [2]
• Ben Vandervalk, Intro to Web Services, Semantic Web, and SADI
  • Part 1: Intro to Semantic Web, Web Services, and Semantic Web Services (Google Docs)
  • Part 2: Intro to SADI from (SADI Training Course)
• Helena Deus, "Using federated sparql for retrieving data from multiple sources"
• Naim Matasci, "The iPlant TNRS", tree service arch

Session 4 (late afternoon): Self-assembly

The idea: Participants will self-assemble into sub-groups to work on specific tasks. Presumably most task groups will focus on a particular component, however some groups may have a multi-component focus on documentation, testing, integration, etc.

How to participate

• start thinking about what is the best use of your time and talent
• propose an idea (called a "pitch") for a task group with specific deliverables
  • deliverables
  • approach
  • key challenges
  • strategic partners (how are you going to work with other groups)
• ask critical questions (about the value of proposed deliverables, and about the manner of achieving them)

Detailed schedule

• 3:15 pitches (a few minutes each) list of pitches
• 3:40 self-assembly of groups
• 4:30 re-pitches
• 4:50 gap analysis and integration

Session 5 (after dinner): Self-disassembly

The idea: unwind, get to know fellow participants.

How to participate: Meet at Fullsteam Brewery at 7:30 pm. This is a short half mile walk from Duke Tower. Here's a map. On Monday nights, a local chef cooks up an Indian buffet from 5:00-8:00, if you want to grab food there.

Day 2

Morning session 9:30 to 12:00

• coffee breaks as needed

iPlant Tools and Services for Phylogenetic Analyses, Naim Matasci, 12:00 pm

• lunch will be provided?

Afternoon session 1:30 to 5:30

• coffee breaks as needed

Days 3 and 4

work, work, work, work, work, work, work, work, work the whole day through

Morning session 9:30 to 12:30

• coffee breaks as needed

Afternoon session 1:30 to 5:30

• coffee breaks as needed

Day 5

Morning session 9:30 to 12:30

• coffee breaks as needed

Wrap-up session 1:30 to 3:00