Welcome to the EDAMAME course!

EDAMAME happened already for 2014, if you're interesting in being on our mailing list for EDAMAME 2015, please provide us your name and email by going here.

For more about this course, see edamame-course.org.

edamame header image

Our Mendeley reading list is located here. PDF copies of readings can be found here

Our Etherpad is located here and is a shared note-taking space.

Handouts from tutorials are here


Tutorials by topic

Getting around at the command line
  • Terminal basics
  • Automation and text matching tips ##### Cloud computing
  • Amazon EC2 start-up
  • File transfer to the EC2 ##### Amplicon analysis
  • Assessing sequencing quality
  • Subsampling a large amplicon dataset for developing an analysis workflow
  • Paired end merging (with PANDASeq)
  • QIIME workflow: rarefaction, building an OTU table, diversity analysis
  • mothur workflow: rarefaction, building an OTU table, diversity analysis ##### Shotgun metagenome analysis
  • Subsampling a large metagenome dataset for developing an analysis workflow
  • Quality Trimming
  • Digital normalization
  • Assembly with MEGAHit
  • Annotation of assembled reads ##### R
  • R basics
  • Advanced R
  • R visualizations ##### Using Databases
  • Local BLAST
  • Using APIs to access NCBI and MG-RAST data

Tutorials by 2015 Schedule

Sunday 21 June 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!

Monday 22 June 2015

Time Activity Location
08:00 Breakfast McCrary Dining Hall
09:00 Welcome & Introductions Carriage House Classroom
09:30 Assessment: Front-end (STEM, 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 Cloud Computing: Starting an EC2 instance (Jackson) Carriage House Classroom
12:00 Lunch McCrary Dining Hall
13:15 Tutorial: Introduction to the Shell (Josh) Carriage House Classroom
14:00 Tutorial: Transferring data to the AMI (Jackson) Carriage House Classroom
14:30 Break SUNSHINE!
14:45 Lecture: Field guide to next generation sequencers (Josh) Carriage House Classroom
15:15 Tutorial: Quality checking your (Illumina) data (Siobhan) 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

Tuesday 23 June 2015

Time Activity Location
08:00 Breakfast McCrary Dining Hall
09:00 Tutorial: Merging paired-end reads and Introduction to QIIME (Ashley) Carriage House Classroom
10:30 Break Fresh air, coffee!
10:45 Lecture/Tutorial: Within-sample Diversity in QIIME (Ashley) Carriage House Classroom
12:00 Lunch McCrary Dining Hall
13:15 Lecture/Tutorial: Comparative diversity in QIIME (Ashley) Carriage House Classroom
16:00 Afternoon Break Volleyball!
18:00 Dinner McCrary Dining Hall
20:00 Guest Lecture: Vince Young, University of Michigan Carriage House Classroom

Wednesday 24 June 2015

Time Activity Location
08:00 Breakfast McCrary Dining Hall
09:00 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

Thursday 25 June 2015

Time Activity Location
08:00 Breakfast McCrary Dining Hall
09:00 Lecture: Computing workflows for biologists (Ashley) Carriage House Classroom
09:30 Lecture: Why metagenomics is flawed and why you want to do it (Josh) Carriage House Classroom
10:30 Break Tea and coffee, please
10:45 Tutorial: Metagenome quality trimming (Josh) Carriage House Classroom
12:00 Lunch McCrary Dining Hall
13:15 Tutorial: Metagenome digital normalization and assembly (Josh) Carriage House Classroom
15:00 Tutorial: Making and using local BLAST databases (Josh) 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

Friday 26 June 2015

Time Activity Location
08:00 Breakfast McCrary Dining Hall
09:00 Tutorial: Using APIs to access data in NCBI and MG-RAST (Jin) Carriage House Classroom
10:30 Break STRETCH
10:45 Tutorial: Continued metagenome assembly (Josh) Carriage House Classroom
12:00 Lunch McCrary Dining Hall
13:15 Discussion: Experimental design in microbial ecology (Jay) Boat Dock
14:00 Tutorial: Continued metagenome assembly (Josh) 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

Saturday 27 June 2015

Time Activity Location
08:00 Breakfast McCrary Dining Hall
09:30 Tutorial: Introduction to ecological analysis in R (Stuart) Carriage House Classroom
10:30 Break Yes!
10:45 Tutorial: More R (Stuart) Carriage House Classroom
12:00 Lunch McCrary Dining Hall
13:15 Tutorial: Even more R! (Stuart) 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

Sunday 28 June 2015

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

Monday 29 June 2015

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 Carriage House Classroom
16:00 Afternoon Break Volleyball
18:00 Dinner McCrary Dining Hall
20:00 Lecture: The wooly world of non-16S amplicon analysis (Josh) Carriage House Classroom

Tuesday 30 June 2015

Time Activity Location
08:00 Breakfast McCrary Dining Hall
09:30 Tutorial: Metagenome annotation wrap-up(Josh) Carriage House Classroom
10:30 Break Tea and coffee, please
10:45 Independent Study: TAs and Instructors available for troubleshooting Carriage House Classroom
12:00 Lunch McCrary Dining Hall
13:15 Guest lecture: Vincent Denef (University of Michigan) Carriage House Classroom
14:15 Independent Study: TAs and instructors available Carriage House Classroom
16:00 Afternoon Break Interpretive dance
18:00 Dinner McCrary Dining Hall
20:00 Guest Lecture: Sarah Evans (Kellogg Biological Station) Carriage House Classroom

Wednesday 01 July 2015

Time Activity Location
08:00 Breakfast McCrary Dining Hall
09:30 Demo: Data visualization (TBD) 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
14:00 Depart KBS Check out at Front Desk, McCrary Dining Hall