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MihaiPop edited this page Aug 17, 2018 · 87 revisions

Welcome to the STAMPS2018 wiki!

Schedule and information for STAMPS 2018 #stamps2018

See these installation notes for help installing software needed for the course, and here are instructions for logging into the MBL servers.

Schedule STAMPS 2018

Workshop Instructors and Lecturers

Workshop TAs

  • Evan Bolyen
  • Jessica Chopyk
  • Michael Lee
  • Bryan Martin
  • Daniel Nasko
  • Michael Nute
  • Pauline Trinh


Code of Conduct and Accessibility

Course Communications and Notes

Installation notes

You will need various tools and software packages throughout the course. You can find installation instructions here.


All activities are in Loeb G70 unless otherwise noted

Sunday 29 July 2018

Time Activity
19:00 Opening Reception (Meigs Room on the second floor of the Swope building)

Monday 30 July 2018

Time Activity
09:00 Welcome & Code of Conduct (Mihai Pop and Tracy Teal)
09:15 Introduction to MBL and Microbiome Science (Mitch Sogin)
10:15 Break
10:30 Tutorial: Introduction to the command line & MBL infrastructure (Mike Lee)
12:00 Lunch
14:00 Tutorial: Introduction to R (Tracy Teal)
17:00 Dinner
19:00 Open lab tutorials: More R; More Unix

Tuesday 31 July 2018

Time Activity
09:00 Introduction to MBL (note: in Lillie auditorium)
10:15 Metagenomics approaches, course structure (Mihai Pop)
12:15 Promega Lunch (Swope private dining room)
14:00 Statistics & statistical thinking (Amy Willis)
17:00 Dinner
19:00 Guest Lecture: Jay Lennon
20:00 Intro to phyloseq pdf and hands-on Lab:html Susan Holmes

Wednesday 01 August 2018

Time Activity
09:00 Lecture: OTU Clustering and workflow (Tracy Teal); Generic amplicon pipeline overview pdf
10:00 Amplicon sequence variant assignment--DADA2 (Susan Holmes)
11:00 DADA2-Tutorial and lab
.... DADA2-Tutorial and lab Rmd
12:00 Lunch (Optional: 12:00 - 1:00 "How to Share and Promote Your Science Using Social Media" Meigs Room Registration required
14:00 Taxonomic annotation and phylogeny (Tandy Warnow); Link to tutorial github
17:00 Dinner
19:00 Project introductions

Thursday 02 August 2018

Time Activity
09:30 Statistical estimation: diversity, abundance, shotgun data (Amy Willis);
Diversity lab, (Amy Willis); Abundance tutorial R script, pdf (Bryan Martin)
12:00 Lunch
14:00 Documentation, notebooks and interaction with RStudio, Shiny (JJ)
15:00 Break
15:15 Exploratory multivariate visualization (Susan Holmes)
.... Exploratory multivariate pdf
A Lab to work through on your own: Multivariate Lab with R and ggplot
Download the "lakelike" dataset by copying and running this line of code in R: download.file("", "lakelike.tsv") ; download.file("", "lakelikeh.tsv") ; lakelike <- read.table("lakelike.tsv", sep="\t") ; lakelikeh <- read.table("lakelikeh.tsv", sep="\t") ; lakelike ; lakelikeh
17:00 Dinner
19:00 Heterogeneous Data, networks and tests. (Susan Holmes)
..... Workflow with networks, graphs and multiple tables
20:00 Open Lab

Friday 03 August 2018

Time Activity
09:00 Introduction to QIIME 2: presentation (Rob Knight, Evan Bolyen)
10:30 Short Break
10:45 QIIME 2 - Upstream processing (Rob Knight, Evan Bolyen)
12:00 Lunch
14:00 QIIME 2 - Downstream processing (Rob Knight, Evan Bolyen)
15:30 Short Break
15:45 QIIME 2 - Downstream processing cont. (Rob Knight, Evan Bolyen)
17:00 Dinner
19:00 Brief tour of Github
20:00 Friday Evening Lecture: Dianne Newman "Life without Oxygen" (Lillie Auditorium)

Saturday 04 August 2018

Time Activity
09:00 Network analysis (Christian Müller) presentation
10:15 Network analysis II (Christian Müller) presentation
11:30 Network analysis III (Christian Müller) presentation
12:00 Lunch
14:00 Introduction to shotgun metagenomics & metagenome assembly (Titus Brown)
... Notes & presentation (annotated PDF)
15:30 Evaluating shotgun metagenome assemblies (Todd Treangen)
17:00 Lobster boil (Meigs room in Swope)

Sunday 05 August 2018

Time Activity
Day Off

Monday 06 August 2018

Time Activity
09:00 Taxonomy independent binning
(Christian Müller)
10:15 Break
10:30 Assembly: Reference sequence databases and reference-guided metagenome assembly
Reference Databases
(Todd Treangen, Dan Nasko)
12:00 Lunch
14:00 Graph-based variant detection and strain-level analyses (Todd Treangen, Dan Nasko, Marcus Fedarko)
..... Slides, Command-Line MetagenomeScope Tutorial, Graph-based variant detection
17:00 Dinner
19:00 Automating workflows: shell scripts, and snakemake (Titus Brown)
20:00 Lightning talk on 'how to give a lightning talk'
20:15 Open Lab

Tuesday 07 August 2018

Time Activity
09:00 K-mers are awesome (Titus Brown)
... Tutorial/discussion: k-mers, minhash, and sourmash
... Presentation: more on k-mers (annotated PDF)
12:00 Photo outside Lillie!
12:30 Lunch with Optional 'Career Conversations' in Swope Cafeteria side room
14:00 Functional analysis of microbial communities (Curtis Huttenhower)
14:30 Functional profiling with HUMAnN2 and the bioBakery
15:00 HUMAnN2 lab
15:40 Break
15:50 Other microbial community analyses and reproducible workflows with the bioBakery
16:10 Reference-based strain profiling, StrainPhlAn, and PanPhlAn
16:30 StrainPhlAn lab
17:00 Dinner
19:00 The Human Microbiome Project (Curtis Huttenhower)
20:00 Course wrap up (Mike Lee) – Outline here
21:00 Open Lab and post-workshop survey

Wednesday 08 August 2018

Time Activity
09:00 Presentations by student groups
11:30 Final course close out
... Contact List
12:00 Lunch
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