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Schedule EDAMAME 2017
JacksonSorensen edited this page Aug 11, 2017
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71 revisions
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06 August 2017
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07 August 2017
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08 August 2017
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09 August 2017
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10 August 2017
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11 August 2017
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12 August 2017
- Jin Choi
- Phil Colgan
- Taylor Dunivin
- Jared Flater
- Nicole Ricker
- Schuyler Smith
- Jackson Sorensen
| 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 | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 09:00 | Welcome | Carriage House Classroom |
| 09:15 | Assessment: Front-end | Carriage House Classroom |
| 10:00 | Discussion/Lecture: Computing workflows for biologists (Tracy) Lecture | |
| 10:30 | Break | GO OUTSIDE! |
| 11:00 | Tutorial: Logging into EC2 (Adina Howe) TA: Phil Colgan | Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:00 |
Shell Tutorial (Jared Flater) TA: Phil Colgan |
Carriage House Classroom |
| 15:30 | Moving Data To and Fro EC2 (Adina Howe) | Carriage House Classroom |
| 16:00 | Afternoon Break | Frolic in nature |
| 18:00 | Dinner | McCrary Dining Hall |
| 19:30 | Lightning get-to-know-you presentations | Carriage House Classroom |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 09:00 |
Tutorials: Making and using local BLAST databases (Tracy) TA: Jared Flater |
Carriage House Classroom |
| 10:30 | Break | Tea and coffee |
| 10:45 |
Fetching data from NCBI (Adina Howe) Co-Instructor: Schuyler Smith |
Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 |
Data visualization (Adina Howe) Co-Instructor: Jared Flater |
Carriage House Classroom |
| 16:00 | Afternoon Break | Swim! |
| 18:00 | Dinner | McCrary Dining Hall |
| 19:00 |
Open office hours: Taylor: targeted gene assembly from metagenomes Jackson: Metagenome-assembled genomesJackson's Workflow |
Carriage House Classroom |
| 20:30 | Evening firepit | outside Carriage House |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 08:30 | Discussion: Sequencing workflows - Chalk Talk (Adina Howe) | Carriage House Classroom |
| 10:00 |
Tutorial: Introduction to tmux (Jackson Sorensen) Co-Instructor Taylor Dunivin |
Carriage House Classroom |
| 10:30 | Break | Tea and coffee, please |
| 10:45 |
Tutorial: metaG sequencing preprocessing, quality control, and trimming (Jin Choi) Co-Instructor: Jackson |
Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:00 |
Tutorial: metaG assembly (Jin Choi) Co-Instructor Jackson |
Carriage House Classroom |
| 14:00 |
Tutorial: Evaluating Assemblies (Jin Choi) Co-Instructor: Jackson |
Carriage House Classroom |
| 15:00 |
Tutorial: Continue: Counting abundances with mapped reads ; Slide(Jin Choi) Co-Instructor Jackson |
Carriage House Classroom |
| 16:00 | Afternoon Break | Swim! |
| 17:00 | Dinner | Kalamazoooooooo |
| 18:00 | Evening out: Arcadia | Kalamazoo |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 08:30 |
Lecture: Comparative and within-sample diversity(Ashley) Diversity is not the answer |
Carriage House Classroom |
| 09:30 | Tutorial: Introduction to ecological analysis in R Git clone repo for data files(Stuart) | Carriage House Classroom |
| 10:30 | Break | Yes! |
| 10:45 | Tutorial: More R (Stuart) | Carriage House Classroom |
| 11:45 | Group photo | Meet outside Carriage House |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 | Tutorial: Even more R! (Stuart) | Carriage House Classroom |
| 16:00 | Break | Relax! |
| 16:15 | Guest Lecture: Stuart Jones, University of Notre Dame | Carriage House Classroom |
| 17:00 | Dinner | McCrary Dining Hall |
| 18:00 | Evening out: Bell's (optional) | Kalamazoo |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 09:00 | Tutorial: mothur (Pat Schloss) Slide | Carriage House Classroom |
| 10:30 | Break | Tea and coffee, please |
| 10:45 | Tutorial: mothur (Pat Schloss ) | Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 | Tutorial: mothur (Pat Schloss) | Carriage House Classroom |
| 16:00 | Guest Lecture: Q&A with James Tiedje (Michigan State) | Carriage House Classroom |
| 17:30 | Break! | Smile! |
| 18:00 | Dinner with Jim | Carriage house classroom |
| 20:00 | Guest Lecture: Pat Schloss, University of Michigan | Carriage House Classroom |
| 21:30 | Evening firepit | outside Carriage House |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast with Dr. Heather Allen | Carriage House Classroom |
| 09:00 | Keynote Speaker: Dr. Heather Allen, USDA Agricultural Research Service | Carriage House Classroom |
| 10:30 | Break | STRETCH |
| 10:45 | Course Close Up - Post-Assessment | |
| 12:00 | Lunch | McCrary Dining Hall |