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Schedule EDAMAME 2016
Ashley Shade edited this page Jul 20, 2016
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#Schedule EDAMAME 2016
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10 July 2016
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11 July 2016
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12 July 2016
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13 July 2016
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14 July 2016
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15 July 2016
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16 July 2016
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17 July 2016
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18 July 2016
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19 July 2016
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20 July 2016
##Etherpad Here
| Time | Activity | Location |
|---|---|---|
| 15:00 | Check in after 3 pm | Front Desk at McCrary Dining Hall |
| 19:00 | Meet & Greet (optional) - PC download and install MoBaxTerm | Carriage House Classroom |
| Enjoy the summer solstice at the lake! |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 09:00 | Welcome & Introductions | Carriage House Classroom |
| 09:30 | Assessment: Front-end (Ashley) | Carriage House Classroom |
| 10:00 | Lecture: Overview of microbial ecology and tutorial dataset (Ashley) | Carriage House Classroom |
| 10:30 | Break | GO OUTSIDE! |
| 10:45 |
Discussion/Group Exercise: Experimental Design (Adina) Scribe: Jin Choi |
Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:00 |
Tutorial: Introduction to the Shell and cloud computing with EC2 Handout(Tracy) Co-Instructor Jackson, Scribe: Taylor |
Carriage House Classroom |
| 14:30 | Break | SUNSHINE! |
| 14:45 |
Tutorial: Transferring data to the AMI (Tracy) Co-Instructor Jackson, Scribe: Taylor |
Carriage House Classroom |
| 16:00 | Afternoon Break | Frolic in nature |
| 18:00 | Dinner | McCrary Dining Hall |
| 20:00 | Lightning get-to-know-you presentations | Carriage House Classroom |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 09:00 |
Discussion/Lecture: Computing workflows for biologists (Ashley) Lecture Demo tutorial: Subsampling a large dataset |
Carriage House Classroom |
| 09:30 |
Tutorial: Intro to GitHub (Jackson) Co-Instructor: John, Scribe: Siobhan |
Carriage House Classroom |
| 10:30 | Break | Carriage House Classroom |
| 11:00 | Continue with GitHub (John) Co-Instructor: Jackson, Scribe: Siobhan |
Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 |
Lecture: Overview of amplicon analysis (Ashley) Co-Instructor: John, Scribe: Taylor |
Carriage House Classroom |
| 14:00 |
Tutorial: Quality checking your (Illumina) data - plus Automation and installing software on an EC2 (Siobhan) Co-Instructor: Taylor, Scribe: Fan |
Carriage House Classroom |
| 16:00 | Break | Fresh air, coffee! |
| 18:00 | Dinner | McCrary Dining Hall |
| 20:00 | Guest lecture Sarah Evans, Kellogg Biological Station | Carriage House Classroom |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 09:00 | Parallel Tutorials: QIIME Intro, QIIME0 and [QIIME1] (https://github.com/edamame-course/Amplicon_Analysis/blob/master/final/2016-07-13-QIIME1.md) (Jackson and John) and mothur (Pat Schloss and Tracy) | Terrace Room (QIIME) and Carriage House Classroom (mothur) |
| 10:30 | Break | Tea and coffee, please |
| 10:45 | Tutorial: Continue amplicon analysis QIIME2 (Jackson and John) and mothur (Pat Schloss and Tracy) | Terrace Room (QIIME) and Carriage House Classroom (mothur) |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 | Tutorial: Continue amplicon analysis QIIME3 (Jackson and John) and mothur (Pat Schloss and Tracy) | Terrace Room (QIIME) and Carriage House Classroom (mothur) |
| 16:00 | Afternoon Break | Swim! |
| 18:00 | Dinner | McCrary Dining Hall |
| 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 | McCrary Dining Hall |
| 08:30 |
Lecture: Comparative and within-sample diversity(Ashley) Subsampling Exercise Diversity is not the answer preprint Co-Instructor John, Scribe: Jackson |
Carriage House Classroom |
| 09:30 |
Tutorial: Introduction to ecological analysis in R Git clone repo for data files(Stuart) Co-Instructor Ashley; Scribe: John |
Carriage House Classroom |
| 10:30 | Break | Yes! |
| 10:45 |
Tutorial: More R (Stuart) Co-Instructor Ashley; Scribe: John |
Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 |
Tutorial: Even more R! (Stuart) Co-Instructor Ashley; Scribe: John |
Carriage House Classroom |
| 16:00 | Afternoon Break | Volunteers needed to plan BBQ dinner |
| 18:00 | Dinner | McCrary Dining Hall |
| 20:00 | Guest Lecture: Stuart Jones, University of Notre Dame | Carriage House Classroom |
| 21:30 | Evening firepit | outside Carriage House |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 08:30 | Discussion: [Metagenomics analyses and workflows] (https://github.com/edamame-course/Metagenome/blob/master/edamame_metagenomics_overview.pdf?raw=true) (Adina) | |
| 10:00 |
Tutorial: Introduction to tmux (Tracy or Jackson) Co-Instructor Siobhan, Scribe: Taylor |
Carriage House Classroom |
| 10:30 | Break | Tea and coffee, please |
| 10:45 | Presentation: Overview, Tutorial: metaG sequencing preprocessing, quality control, and trimming (Jin Choi) | Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:00 |
Tutorial: metaG assembly (Jin Choi) Co-Instructor TBD, TBD, Scribe: TBD |
Carriage House Classroom |
| 14:00 |
Tutorial: Evaluating Assemblies (Jin Choi) Co-Instructor TBD, TBD, Scribe: TBD |
Carriage House Classroom |
| 15:00 |
Tutorial: Continue: Counting abundances with mapped reads ; Slide(Jin Choi) Co-Instructor TBD, TBD, Scribe: TBD |
Carriage House Classroom |
| 16:00 | Afternoon Break | Swim! |
| 17:00 | Lecture: Tracy Teal | Carriage House Classroom |
| 18:00 | Dinner | Kalamazoooooooo |
| 21:30 | Evening firepit | outside Carriage House |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | Carriage House Classroom - no weekend breakfast at KBS |
| 09:00 | [Tutorials: Making and using local BLAST databases] (https://github.com/edamame-course/BLAST-tutorial/blob/master/running-BLAST.md) (Tracy) Co-Instructor Taylor, Scribe: Siobhan Additional Tutorial |
Carriage House Classroom |
| 10:30 | Break | STRETCH |
| 10:45 | [Lecture: Binning Assemblies] (https://github.com/edamame-course/metagenome_binning/blob/master/metagenome_binning.pdf) [Tutorial] (https://github.com/edamame-course/metagenome_binning/blob/master/binning_tutorial.md) (Fan Yang) Co-Instructor TBD; Scribe: TBD |
Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:00 | Break / Independent Study / Impromptu Awesomeness in Computing | Hike! |
| 18:00 | Dinner: Bell's Brewery or Arcadia | Meet outside McCrary Dining Hall to car pool |
| Time | Activity | Location |
|---|---|---|
| 09:30 | Catered Breakfast | Carriage House Classroom |
| 10:00 | Guest Lecture: Informal Q&A with Jim Tiedje (Michigan State) | Carriage House Classroom |
| 12:00 | Brunch | McCrary Dining Hall |
| 13:15 | Day of rest and reflection; dinner on your own | As you wish |
| 17:00 | BBQ - Please volunteer to help cook or shop! | Windmill Island |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 09:30 | Lecture/Demo: Ribosomal Database Project (Jim Cole, Michigan State) | Carriage House Classroom |
| 10:30 | Break | Tea and coffee, please |
| 10:45 | Tutorial: Xander: assembling targeted genes from metagenomes (Taylor) Co-instructor: Fan; Scribe: Siobhan | Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 | Tutorial: Advanced R: More ecological statistics and visualizations (Ashley) | Carriage House Classroom |
| 15:00 | Independent Study: TAs and instructors available | Carriage House Classroom |
| 16:00 | Afternoon Break | Volleyball |
| 18:00 | Dinner | McCrary Dining Hall |
| 20:00 | Keynote Lecture: Rich Lenski, Michigan State University | Carriage House Classroom |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 09:30 | Fetching data from NCBI (Fan) | Carriage House Classroom |
| 10:30 | Break | Tea and coffee, please |
| 10:45 | Demo/lecture: High Performance Computing (Pat Bills, ICER) | Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 | Summative Assessment | Carriage House Classroom |
| 14:15 | Choose your own adventure! Independent Study with TAs and instructors available | Carriage House Classroom |
| 16:00 | Afternoon Break | Interpretive dance |
| 18:00 | Dinner | McCrary Dining Hall |
| 20:00 | Panel Discussion: TAs, instructors, and friends | Carriage House Classroom |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 09:30 | Group exercise: Exploring Databases (Adina, Ashley) | Carriage House Classroom |
| 10:30 | Break | Tea and coffee, please |
| 10:45 | Group exercise: Concept mapping (Adina, Ashley) | |
| 12:00 | Lunch | McCrary Dining Hall |
| 14:00 | Depart KBS | Check out at Front Desk, McCrary Dining Hall |