-
Notifications
You must be signed in to change notification settings - Fork 7
Schedule EDAMAME 2018
Taylor Dunivin edited this page Jun 30, 2018
·
83 revisions
- Ashley Shade (Michigan State) and Adina Howe (Iowa State) - The Buck Stops Here, Folks!
- Jin Choi, ISU
- Shane Dooley, ISU
- Taylor Dunivin, MSU
- Jared Flater, ISU
- Jaejin Lee, ISU
- Lanying Ma, ISU
- Schuyler Smith, ISU
- Jackson Sorensen, MSU
- Paul Villanueva, ISU
- Tomas Vetrovsky, Czech Academy of Sciences
Course notes: EDAMAME etherpad
| Time | Activity | Location |
|---|---|---|
| 15:00 | Check in after 3 pm | Front Desk at McCrary Dining Hall |
| 19:00 | Meet & Greet | Carriage House Classroom |
| Time | Activity | Instructor | Location |
|---|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall | |
| 09:00 | Welcome | Carriage House Classroom | |
| 09:15 | Assessment: Front-end | Ashley | Carriage House Classroom |
| 10:00 |
Lecture: Slides Paper: Computing workflows |
Ashley | Carriage House Classroom |
| 10:45 | Break | GO OUTSIDE! | |
| 11:00 | Tutorial: Logging into EC2 | Adina | Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall | |
| 13:00 | Tutorial: Shell | Jared Co: Shane |
Carriage House Classroom |
| 15:30 | Tutorial: Moving Data To and Fro EC2 | Paul | Carriage House Classroom |
| 16:00 | Afternoon Break | Frolic in nature | |
| 17:00 | Office hours (optional): Metagenomics gene targeted | Jackson and Taylor | Carriage House Classroom |
| 18:00 | Dinner | McCrary Dining Hall | |
| 19:30 | Lightning get-to-know-you presentations | Students! | Carriage House Classroom |
| 20:30 | Evening firepit | outside Carriage House |
| Time | Activity | Instructor(s) | Location |
|---|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall | |
| 09:00 | Tutorial: Local BLAST databases | Shane Co: Adina |
Carriage House Classroom |
| 10:30 | Break | Tea and coffee | |
| 10:45 | Tutorial: Fetching data from NCBI | Adina Co: Shane |
Carriage House Classroom |
| 11:30 | Lunch | McCrary Dining Hall | |
| 12:45 | Tutorial: Moving Data To and Fro EC2 | Paul | Carriage House Classroom |
| 13:15 | Lecture: Slides Tutorial: Intro R and RStudio | Taylor | Carriage House Classroom |
| 14:00 | Break | Stretch! | |
| 14:15 | Tutorial: Data visualization | Taylor | Carriage House Classroom |
| 16:00 | Afternoon Break | Swim! | |
| 17:00 | Office hours (optional): Amplicon sequencing | Tomas | Carriage House Classroom |
| 18:00 | Dinner | McCrary Dining Hall | |
| 19:00 | Evening Lecture: Dr. Ashley Shade, Michigan State University | Carriage House Classroom | |
| 20:00 | Evening firepit | outside Carriage House |
| Time | Activity | Instructor(s) | Location |
|---|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall | |
| 09:00 |
Lecture: Slides Tutorial: mothur |
Pat Schloss | Carriage House Classroom |
| 10:30 | Break | Tea and coffee, please | |
| 10:45 | Tutorial: mothur | Pat Schloss | Carriage House Classroom |
| 11:30 | Lunch | McCrary Dining Hall | |
| 12:45 | Tutorial: mothur | Pat Schloss | Carriage House Classroom |
| 16:30 | Break | Smile! | |
| 17:00 | Guest Lecture: Dr. Pat Schloss, University of Michigan | Carriage house classroom | |
| 18:00 | Dinner | Carriage house classroom | |
| 19:00 | Office hours (optional): Metatranscriptomics | TBD | Carriage House Classroom |
| 21:00 | Evening firepit | outside Carriage House |
| Time | Activity | Instructor(s) | Location |
|---|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall | |
| 08:30 | Group photo | Meet outside Carriage House | |
| 08:45 |
Lecture: Comparative and within-sample diversity Paper: Diversity is not the answer Paper: Bray-Curtis 1957 Cool Activity! Make your own ordination The Answer! Ordination The code! R code |
Ashley | Carriage House Classroom |
| 09:30 | Tutorial: Intro ecological analysis in R | Stuart Jones | Carriage House Classroom |
| 10:30 | Break | ||
| 10:45 | Tutorial: More R | Stuart Jones | Carriage House Classroom |
| 11:30 | Lunch | McCrary Dining Hall | |
| 12:40 | Tutorial: Even more R! | Stuart Jones | Carriage House Classroom |
| 14:00 | Break | ||
| 14:15 | Tutorial: Even more R! | Stuart Jones | Carriage House Classroom |
| 16:00 | Break | ||
| 17:00 | Guest Lecture: Dr. Stuart Jones, University of Notre Dame | Carriage House Classroom | |
| 18:00 | Dinner | McCrary Dining Hall or Kalamazoo | |
| 19:00 | Office hours (optional): Advanced ecological stats | Ashley | Carriage House Classroom |
| 21:00 | Evening firepit | outside Carriage House |
| Time | Activity | Instructor(s) | Location |
|---|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall | |
| 08:30 |
Power hour (optional): Sequence variants analysis References for SV |
Carriage House Classroom | |
| 09:00 | Discussion: Sequencing workflows | Adina | Carriage House Classroom |
| 10:00 | Tutorial: tmux | Jackson Co: Jared |
Carriage House Classroom |
| 10:30 | Break | Tea and coffee, please | |
| 10:45 |
Lecture: Slides Tutorial: metaG sequencing pre-processing, quality control, and trimming |
Jin Co: Jackson |
Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall | |
| 13:00 | Tutorial: metaG assembly | Jin Co: Jackson |
Carriage House Classroom |
| 14:00 | Tutorial: Evaluating Assemblies | Jin Co: Jackson |
Carriage House Classroom |
| 15:00 | Tutorial: Counting abundances with mapped reads | Jin Co: Jackson |
Carriage House Classroom |
| 16:00 | Break | Snacks please | |
| 17:00 | Keynote Speaker: Dr. Thea Whitman, University of Wisconsin-Madison | Carriage House Classroom | |
| 18:00 | Evening out: TBD | Kalamazoo |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast with Thea Whitman | McCrary Dining Hall |
| 09:00 | Guest Lecture: Informal Q&A with Jim Tiedje, Michigan State University | Carriage House Classroom |
| 10:30 | Break | STRETCH |
| 10:45 | Course Close Up: Post-Assessment | Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |