Schedule EDAMAME 2017

JacksonSorensen edited this page Aug 11, 2017 · 71 revisions

Schedule EDAMAME 2017

Workshop Instructors and TAs

  • Jin Choi
  • Phil Colgan
  • Taylor Dunivin
  • Jared Flater
  • Nicole Ricker
  • Schuyler Smith
  • Jackson Sorensen

Course notes

EDAMAME etherpad

Sunday 06 August 2017

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

Monday 07 August 2017

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

Tuesday 08 August 2017

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

Wednesday 09 August 2017

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

Thursday 10 August 2017

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

Friday 11 August 2017

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

Saturday 12 August 2017

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
You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.