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This page is the central hub for all things STAMPS 2025! 🙂
If you are participating in the course in any way, please review our Norms and Code of Conduct pages.
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 which is available for Apple and Android devices.
Emergency phone numbers
- 911; x7911 (from MBL phones)
- 508-289-7217 (security); x7217 (security from MBL phones)
Course communication
We will be using Slack for communication during the course. You should have received an email with an invite to our Slack group, but if not, please email Titus Brown at [email protected] for access.
You will need to bring a laptop to actively participate in this course. The MBL Wifi supports both eduroam and MBL Guest access (name: mblguest; password: mblguest).
The page with links to our cloud computers can be found here.
- Titus Brown, University of California Davis
- Amy Willis, University of Washington
- Christina Boucher, University of Florida
- Ben Callahan, North Carolina State University
- Mike Lee, NASA Ames Research Center
- Todd Treangen, Rice University
- Iva Veseli, Helmholtz Institute for Functional Marine Biodiversity
- Maria Valdez (UW)
- Sarah Teichman (UW)
- Natalie Kokroko (Rice)
- Jorden Rabasco (NC State)
- Hugo Monteiro (UC Davis)
- Sarah Tucker (MBL)
- 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.
- Questions? Concerns? Please contact Amy Willis or Titus Brown or MBL’s Equal Employment Opportunity Coordinator at 508-289-7378 / [email protected] immediately.
| Date | Theme | Morning (9am-noon) | Arvo (2-5pm) | Evening (7pm+) - Candle House | 7pm+ - library | Notes |
|---|---|---|---|---|---|---|
| Mon 7/14 | arrival | - | - | reception &c (location TBD) | ||
| Tues 7/15 | intro | welcome & intro: Amy; sequencing: Ben | topics & techniques: Titus; intro stats: Amy | hands-on: (Sarah VT & María) |
||
| Wed 7/16 | 16s | 16S (Ben) | More 16S (Ben) | hands-on: Ben | ||
| Th 7/17 | mgx | intro metagenomics (Titus) | more metagenomics (Titus) |
hands-on: Titus | ||
| Fri 7/18 | mgx | metagenomics (Todd) | metagenomics (Christina) | hands-on: mgx | ||
| Sat 7/19 | mgx | anvio / metabolism (Iva) | anvio / pangenomics (Iva) | hands on: Iva | ||
| Sun 7/20 | free day | - | - | - | ||
| Mon 7/21 | stats | stats (Amy et al) | stats (Amy et al) | hands-on: Amy | ||
| Tues 7/22 | adv | metatranscriptomics (Sarah JT) / phylogenomics (María) |
misc (Ben) + stat misc (Amy) | open lab | ||
| Wed 7/23 | adv | Review (Titus) | A data story (Hugo); open lab | graduation + party | ||
| Th 7/24 | departure | head out | - |
All daytime activities are in Candle House room 104/105 unless otherwise noted. Most evenings we also have the Bay Reading Room for small group and individual work.
All times in EDT (UTC-4).
"Open Lab" periods are times to practice something we've covered, work on your own things, talk with other folks, ask specific questions about data you may have, etc. Basically anything you'd like to do with the time 🙂
Breaks
There will be 20-minute breaks in the middle of each 3-hour block 👍
- Morning session break will be 10:30–10:50
- Afternoon session break will be 3:30–3:50
- Evening break (if we're all together) will be 8:30-8:50
Meal times
Daily dining hall sessions in the Swope Cafeteria:
- Breakfast: 7:30am – 9:30am
- Lunch: 11:30am – 1:30pm
- Dinner: 5:00pm – 7:30pm
Daily Schedule
| Time | Activity |
|---|---|
| All day | Arrival day! |
| 5 - 7 pm | Dinner in Swope (Swope is our regular meal location, and dinner hours are 5:00-7:30pm) |
| 7 - 9 pm | Evening welcome reception at MBL Club (100 Water St., park side entrance, map here) + activities |
| Time | Activity |
|---|---|
| 9am - noon |
Welcome to STAMPS! - Amy and Titus Intro to Microbiome Sequencing - Ben |
| 2pm - 5pm |
Getting started with our computing environment! - Titus Statistics primer - Amy |
| 7pm - 9pm |
R workshop - Sarah VT & María R workshop keys |
| Time | Activity |
|---|---|
| 9am - noon |
16S: ASVs and OTUs - Ben DADA2 Workflow Click on link then download to render - Ben |
| 2pm - 5pm |
DADA2 WalkThrough Activity: Illumina - Ben |
| 7pm - 9pm |
16S: Long Read - Ben DADA2 WalkThrough Activity: Pacbio - Ben |
| Time | Activity |
|---|---|
| 9am - noon | Titus - metagenomics! slides PDF; morning 1; morning 2 |
| 2pm - 5pm | Titus - metagenomics more! slides; afternoon 1; afternoon 2 |
| 7pm - 9pm | Titus |
| Time | Activity |
|---|---|
| 9am - noon | Metagenomic Assembly, slides_one - Todd Nanopore - Mike Emu_tutorial - Todd/Natalie More Assembly, slides_two - Todd Mystery Metagenomic Game - Todd Metagenomic Strains - Mike Strain_Level_Tutorial - Mike |
| 2pm - 5pm |
Resistome (Metagenomics) - Christina AMR++_tutorial - Christina |
| 7pm - 9pm | open lab |
| Time | Activity |
|---|---|
| 9am - noon | Iva - anvi'o basics and metabolism. Slides. Morning tutorial |
| 2pm - 5pm | Iva - pangenomics. Slides. Afternoon tutorial |
| 7pm - 9pm | Iva - anvi'o-related free work + discussion time |
| Time | Activity |
|---|---|
| 9am - noon | Statistics Foundation Lecture - Regression lab |
| 2pm - 5pm | Inference and abundance Lecture - Differential abundance lab |
| 7pm - 9pm |
| Time | Activity |
|---|---|
| 9am - noon | Sarah Tucker - Metatranscriptomics. María Valdez Cabrera - Slides, Lab |
| 2pm - 5pm |
Feline Bile Slides, Contamination_Slides - Ben Decontam_lab - Ben Diversity slides - Amy |
| 7pm - 9pm |
| Time | Activity |
|---|---|
| 9am - noon | Integration activity! |
| 2pm - 5pm | Hugo talk Slides; STAMPS closeout talk |
| 7pm - 9pm | Graduation @ Loeb Tent |