Schedule EDAMAME 2018

Taylor Dunivin edited this page Jun 30, 2018 · 83 revisions

Schedule EDAMAME 2018

Workshop Instructors and TAs

  • 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

Sunday 24 June 2018

Time Activity Location
15:00 Check in after 3 pm Front Desk at McCrary Dining Hall
19:00 Meet & Greet Carriage House Classroom

Monday 25 June 2018

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

Tuesday 26 June 2018

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

Wednesday 27 June 2018

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

Thursday 28 June 2018

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

Friday 29 June 2018

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

Saturday 30 June 2018

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
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