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Schedule
Ashley Shade edited this page Jul 1, 2015
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#Schedule EDAMAME 2015
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21 June 2015
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22 June 2015
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23 June 2015
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24 June 2015
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25 June 2015
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26 June 2015
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27 June 2015
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28 June 2015
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29 June 2015
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30 June 2015
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01 July 2015
| Time | Activity | Location |
|---|---|---|
| 15:00 | Check in after 3 pm | Front Desk at McCrary Dining Hall |
| 19:00 | Meet & Greet (optional) | 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 (STEM Ed, LLC) | Carriage House Classroom |
| 10:00 | Lecture: Overview of microbial ecology and tutorial dataset (Ashley) | Carriage House Classroom |
| 10:30 | Break | GO OUTSIDE! |
| 10:45 |
Tutorial: Introduction to the Shell (Paul) Co-Instructor Sang-Hoon, Scribe: Jackson |
Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:00 |
Tutorial: Introduction to Cloud Computing: Starting an EC2 instance (Jackson) Co-Instructor Siobhan, Scribe: Ashley |
Carriage House Classroom |
| 13:30 |
Tutorial: Transferring data to the AMI (Jackson) Co-Instructor Siobhan, Scribe: Ashley |
Carriage House Classroom |
| 14:30 | Break | SUNSHINE! (cancelled) |
| 14:45 | Movie!: How sequencing works (Siobhan) | Carriage House Classroom |
| 15:00 |
Tutorial: Introduction to tmux (Jackson) Co-Instructor Ashley, Scribe: Sang-Hoon |
Carriage House Classroom |
| 15:30 |
Tutorial: Quality checking your (Illumina) data (Siobhan) Co-Instructor Jackson, Scribe: Paul |
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 |
Tutorial: Introduction to tmux (Jackson) Co-Instructor Ashley, Scribe: Sang-Hoon |
Carriage House Classroom |
| 09:30 |
Tutorial: Merging paired-end reads and Introduction to QIIME (Ashley) Co-Instructor Jackson, Scribe: Siobhan |
Carriage House Classroom |
| 10:30 | Break | Fresh air, coffee! |
| 10:45 | Lecture (here)/Tutorial: Within-sample Diversity in QIIME (Ashley) Co-Instructor Siobhan, Scribe: Sang-Hoon |
Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 | Lecture (here)/Tutorial: Comparative diversity in QIIME (Ashley) Co-Instructor Sang-Hoon, Scribe: Jackson |
Carriage House Classroom |
| 16:00 | Afternoon Break | Volleyball! |
| 18:00 | Dinner | McCrary Dining Hall |
| 20:00 | Keynote Lecture: Vince Young, University of Michigan | Carriage House Classroom |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 09:00 |
Lecture Tutorial: mothur (Schloss lab) |
Carriage House Classroom |
| 10:30 | Break | Tea and coffee, please |
| 10:45 | Tutorial: More mothuring (Schloss lab) | Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 | Tutorial: Even more mothuring! (Schloss lab) | Carriage House Classroom |
| 16:00 | Afternoon Break | Swim! |
| 18:00 | Dinner | McCrary Dining Hall |
| 20:00 | Guest Lecture: Schloss Lab, University of Michigan | Carriage House Classroom |
| 21:30 | Evening firepit | outside Carriage House |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 09:00 | Discussion/Lecture: Computing workflows for biologists (Ashley) | Carriage House Classroom |
| 09:45 | Discussion: Metagenomics 2.0 - McMahon 2014; Overview of metagenome analysis - Sharon et al. 2013 (Siobhan) | Carriage House Classroom |
| 10:30 | Break | Tea and coffee, please |
| 10:45 |
Tutorial: Install updates to EC2(Jackson) Co-Instructor Ashley, Scribe: Jin |
Carriage House Classroom |
| 11:00 |
Tutorial: Metagenome quality trimming (Jackson) Co-Instructor Aaron, Jin, Scribe: Siobhan |
Carriage House Classroom |
| 11:15 |
Tutorial: Start: Metagenome digital normalization (Jackson) Co-Instructor Aaron, Jin, Scribe: Paul |
Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 |
Tutorial: Continue: Metagenome digital normalization (Jackson) Co-Instructor Aaron, Jin, Scribe: Siobhan |
Carriage House Classroom |
| 15:45 |
Tutorial: Assembly (Jackson) Co-Instructor Aaron, Jin, Scribe: Paul |
Carriage House Classroom |
| 16:00 | Afternoon Break | Swim! |
| 18:00 | Dinner | McCrary Dining Hall |
| 20:00 | Guest Lecture: Ariane Peralta, East Carolina University and Kellogg Biological Station | Carriage House Classroom |
| 21:30 | Evening firepit | outside Carriage House |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 09:00 |
Tutorials: Making and using local BLAST databases/Benefits of Assembly and Using APIs to access data in NCBI and MG-RAST (Jin) Co-Instructor Jackson, Scribe: Paul |
Carriage House Classroom |
| 10:30 | Break | STRETCH |
| 10:45 |
Tutorial: Continue: Assessing metagenome assembly (Jackson) Co-Instructor Jin, Scribe: Siobhan |
Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 | Discussion: Misconceptions about 'Omics in microbial ecology - Prosser 2015 (Jay) | Boat Dock |
| 14:30 |
Tutorial: Start metagenome annotation using Prokka(Jackson) Co-Instructor: Jin; Scribe: Sang-Hoon |
Carriage House Classroom |
| 15:00 | Guest Lecture: Jay Lennon, Indiana University | Carriage House Classroom |
| 16:00 | Afternoon Break | Hike! |
| 18:00 | Dinner: Bell's Brewery | Meet outside McCrary Dining Hall to car pool |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 09:30 |
Tutorial: Introduction to ecological analysis in R (Stuart) Co-Instructor Ashley; Scribe: Siobhan |
Carriage House Classroom |
| 10:30 | Break | Yes! |
| 10:45 |
Tutorial: More R (Stuart) Co-Instructor Ashley; Scribe: Jackson |
Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 |
Tutorial: Even more R! R script (Stuart) Co-Instructor Ashley; Scribe: Sang-Hoon |
Carriage House Classroom |
| 16:00 | Afternoon Break | Volunteers needed to plan BBQ dinner |
| 18:00 | Dinner: BBQ | Near Carriage House |
| 20:00 | Guest Lecture: Stuart Jones, University of Notre Dame | Carriage House Classroom |
| 21:30 | Evening firepit | outside Carriage House |
| Time | Activity | Location |
|---|---|---|
| 09:30 | Brunch | Carriage House Classroom |
| 10:00 | Guest Lecture: Informal Q&A with Jim Tiedje (Michigan State) | Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 | Day of rest and reflection | As you wish |
| 18:00 | Dinner: Thai Take-out? | Carriage House |
| 20:00 | Panel Discussion: Ask your burning questions about analysis | Carriage House Classroom |
| 21:30 | Evening firepit | outside Carriage House |
| 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 (Jim Cole and Qiong Wang) | Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 | Guest lecture: Introduction to computing clusters (Matt Scholz, MSU iCER/HPCC) | Carriage House Classroom |
| 15:00 | Independent Study: TAs and instructors available; Intro to GitHub | Carriage House Classroom |
| 16:00 | Afternoon Break | Volleyball |
| 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 |
| 09:30 | Tutorial: Metagenome annotation wrap-up(Jackson, Aaron) | Carriage House Classroom |
| 10:00 | Demo/Tutorial: Uploading data to and using MG-RAST (Aaron) | Carriage House Classroom |
| 10:30 | Break | Tea and coffee, please |
| 10:45 | Summative assessment: STEM Ed, LLC | Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 13:15 | Guest lecture: Vincent Denef (University of Michigan) | Carriage House Classroom |
| 14:15 | Choose your own adventure! Independent Study with TAs and instructors available OR demonstration/discussion of GitHub use | Carriage House Classroom |
| 16:00 | Afternoon Break | Interpretive dance |
| 18:00 | Dinner | McCrary Dining Hall |
| 20:00 | Lecture: Deciphering temporal patterns of rarity (Ashley) | Carriage House Classroom |
| Time | Activity | Location |
|---|---|---|
| 08:00 | Breakfast | McCrary Dining Hall |
| 09:30 | Demo: Data visualization (Ashley, Rachel) | Carriage House Classroom |
| 10:30 | Break | Tea and coffee, please |
| 10:45 | Group exercise: Exploring and comparing databases(Ashley) | Carriage House Classroom |
| 12:00 | Lunch | McCrary Dining Hall |
| 14:00 | Depart KBS | Check out at Front Desk, McCrary Dining Hall |
EDAMAME : Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology at Michigan State University