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This page is the central hub for all things STAMPS 2019 🙂 (#stamps2019)
If you are participating in the course in any way, please review our Code of Conduct, and visit our Expectations page.
For any help on the MBL campus, you can dial 0 from any of the campus phones and they'll direct you to the resource you need. A campus accessibility map, shuttle schedule, hours for facilities and more is available through the MBL App.
Emergency phone numbers: 911; x7911 (from MBL phones); 508-289-7217 (security); x7217 (security from MBL phones)
You will need to bring a laptop to actively participate in this course. Please see here for information on computer requirements, help installing software needed for the course, and how to get onto the MBL wifi network.
- 22 July – Monday
- 23 July – Tuesday
- 24 July – Wednesday
- 25 July – Thursday
- 26 July – Friday
- 27 July – Saturday
- 28 July – Sunday
- 29 July – Monday
- 30 July – Tuesday
- 31 July – Wednesday
- 1 August – Thursday
- Mihai Pop, University of Maryland
- Tracy Teal, The Carpentries
- Yana Bromberg, Rutgers University
- Titus Brown, University of California Davis
- Ben Callahan, North Carolina State University
- Susan Holmes, Stanford University
- Curtis Huttenhower, Harvard University
- Adina Howe, Iowa State University
- Rob Knight, University of California San Diego
- Mike Lee, NASA Ames Research Center
- Christian Müller, Simons Foundation
- Todd Treangen, Rice University
- Tandy Warnow, University of Illinois at Urbana–Champaign
- Amy Willis, University of Washington
- Evan Bolyen
- Bryan Martin
- Mike Nute
- Ryan Peek
- Taylor Reiter
- Nidhi Shah
- Pauline Trinh
- We operate under a Code of Conduct, and expect cooperation from everyone involved in any capacity to help ensure a professional and positive learning environment.
- If you have any accessibility needs or need designated time or space for nursing, contact Tracy Teal or MBL's Equal Employment Opportunity Coordinator Carol Hamel chamel@mbl.edu.
- Slack
- Course etherpad for notes:
- Relevant papers:
- Additional resources
- Course presentations
All activities are in Loeb G70 unless otherwise noted. All times in EDT (UTC-4).
| Time | Activity |
|---|---|
| 7 pm |
Opening Reception (in Meigs Room on second floor of the Swope building) |
| Time | Activity |
|---|---|
| 9 am – 12 pm |
Orientation: Metagenomics approaches, course structure (Mihai Pop) |
| 12 – 2 pm | Lunch |
| 2 – 5 pm |
Unix and R introductions (Mike Lee/Tracy Teal) |
| 5 – 7 pm | Dinner |
| 7 – 8 pm | dplyr in R (Tracy) |
| 8 – 10 pm |
Open lab Unix and R Phyloseq and friends :) |
| Time | Activity |
|---|---|
| 9 am – 12 pm |
Data visualization in R and workflows (Tracy Teal) Titus Brown On Workflows |
| 12 – 2 pm | Lunch |
| 2 – 5 pm |
Statistics Bootcamp (Amy Willis) |
| 5 – 7 pm | Dinner |
| 7 – 10 pm |
Open lab Phyloseq and friends :) |
| Time | Activity |
|---|---|
| 9 am – 12 pm |
Concept of OTUs and DADA2 (Ben Callahan) |
| 12 – 2 pm | Lunch |
| 2 – 5 pm |
Heterogeneous data structures and phyloseq (Susan Holmes) Heterogeneous data slides download.file("http://web.stanford.edu/class/bios221/stamps/Phyloseq_Lab.Rmd", "Phyloseq_Lab.Rmd")
|
| 5 – 7 pm | Dinner |
| 7 – 8 pm |
Using positive and negative controls (Ben Callahan) |
| 8 – 10 pm | Open lab |
| Time | Activity |
|---|---|
| 9 am – 12 pm |
Metagenomic assembly (Titus Brown/Adina Howe) Trimming Assembly |
| 12 – 2 pm | Lunch |
| 2 – 5 pm |
Taxonomic annotation and phylogenetics and PASTA (Tandy Warnow/Mike Nute) tutorial link |
| 5 – 6:30 pm | Dinner |
| 6:30 – 7:30 pm |
Lecture – From field to figures (Adina Howe) - Speck Auditorium |
| 7:30 pm - .. | Game night in the courtyard outside Loeb |
| 8 – 9 pm | MBL Friday Night Lecture The Future of Ocean Conservation Ayana Elizabeth Johnson, New York University; Ocean Collectiv |
| 9 - 10 pm | Open lab |
| Time | Activity |
|---|---|
| All day | Free day |
| Time | Activity |
|---|---|
| 9 am – 12 pm |
Network analysis (Christian Müller) Lecture slides 1 Lecture slides 2 Lecture slides 3 Tutorial |
| 12 – 2 pm | Lunch |
| 2 – 5 pm |
Estimating abundance and diversity (Amy Willis) |
| 5 – 7 pm | Dinner |
| 7 – 8 pm | Working with remote computers (ssh) |
| 8 – 10 pm | Open Lab |
| Time | Activity |
|---|---|
| 9 am – 12 pm |
Exploratory statistics (index of links) Multivariate slides pdf (Susan Holmes) |
| 12 – 2 pm | Lunch |
| 2 – 5 pm |
QIIME 2 (Evan Bolyen) Slides Tutorial start |
| 5 – 6 pm | Reception - Meigs Room |
| 6 – 8 pm | **Evening Reception Dinner - Meigs Room ** |
| Time | Activity |
|---|---|
| 9 am – 12 pm |
Metagenomics workflows/Bringing it all together (Taylor) Assembly graph visualization and assembly variants lecture (PDF) (Todd) MetagenomeScope tutorial |
| 12 – 2 pm | Lunch |
| 2 – 5 pm |
Reference-guided metagenomic assembly lecture (PDF) (Todd) MetaCompass tutorial Strain-level analyses lecture (PDF) ParSNP tutorial |
| 5 – 7 pm | Dinner |
| 7 – 8 pm | Panel (Professional development) |
| 8 – 10 pm |
Open Lab Optional discussion/overview of amplicon/marker-gene sequencing and metagenomics in microbial ecology |
| Time | Activity |
|---|---|
| 9 am – 12 pm |
Functional analysis (Yana Bromberg) |
| 12 – 2 pm | Lunch |
| 2 – 3 pm | Microbial community multi'omics (Curtis Huttenhower) |
| 3 – 3:15 pm | Break |
| 3:15 – 4 pm | bioBakery overview (Curtis Huttenhower) |
| 4 – 5 pm | Lecture (Rob Knight (remote)) |
| 5 – 7 pm | Dinner |
| 7 – 10 pm | bioBakery labs (StrainPhlAn, HUMAnN2, MaAsLin2: Curtis Huttenhower) |
| Time | Activity |
|---|---|
| 9 am – 12 pm | Presentation/Lecture |
| 12 pm | Lunch and departure |
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