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This page is the central hub for all things STAMPS 2023! 🙂
If you are participating in the course in any way, please review our Norms, 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 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 ctbrown@ucdavis.edu for access.
You will need to bring a laptop to actively participate in this course. Please see here for information on computer requirements and how to get onto the MBL wifi network.
The Web page locations for our cloud computers can be found here!
- Titus Brown, University of California Davis
- Amy Willis, University of Washington
- Ben Callahan, North Carolina State University
- Mike Lee, NASA Ames Research Center (remote)
- A. Murat Eren (Meren), Helmholtz Institute for Functional Marine Biodiversity
- Curtis Huttenhower, Harvard School of Public Health
- Tessa Pierce-Ward, University of California Davis
- Tracy Teal, Posit
- Alexander Henoch
- Hanna Houts
- Jia Liu
- Bryshal Moore
- Anneliek ter Horst
- Nicolae Sapoval (github, blog), Rice University
- Sarah Teichman
- 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 / eeo@mbl.edu immediately.
- 19 July - Wednesday
- 20 July - Thursday
- 21 July – Friday
- 22 July – Saturday
- 23 July - Sunday
- 24 July – Monday
- 25 July – Tuesday
- 26 July – Wednesday
- 27 July – Thursday
- 28 July – Friday
- 29 July – Saturday
| (theme) | morning (9-noon) | afternoon (2-5pm) | evening (7-9pm) | |
|---|---|---|---|---|
| Wed 19 July | - | - | welcome reception | |
| Thu 20 July | intro | Introductions and expectations | Data analysis in UNIX (Titus, Tessa) | Data analysis with R (Hannah and Sarah) |
| Fri 21 July | basics 16S | Analyzing 16S data (Ben) | Analyzing 16S data (Ben) | Lightning talks! |
| Sat 22 July | basics 16S | Data analysis with R (Hannah, Sarah, and Bry) | Contamination (Ben) | Lightning talks! |
| Sun 23 July | free day | - | - | - |
| Mon 24 July | shotgun metagenomics | Genome-resolved metagenomics(Meren) | Pangenomics in theory and practice (Meren) | Assembling shotgun data (Titus); open lab time |
| Tue 25 July | shotgun metagenomics | Analyzing shotgun data with k-mers (Tessa + Titus) | Topics in metagenomics (phylogenomics w/ Titus) + anvi'o lab (Meren) |
Lightning talks! + open lab |
| Wed 26 July | stats | Statistics! (Amy & Sarah) | Bias lecture (Ben) Statistics! (Amy & Sarah) |
Lightning talks! + open lab |
| Thu 27 July | adv | Experimental design (Amy) | BioBakery et al (Curtis) | BioBakery et al (Curtis) |
| Fri 28 July | closing thoughts | Wrap up topics; student questions | Wrap up summary + faculty panel | Farewell party |
| Sat 29 July | (clean up and goodbyes) |
All activities are in Candle House room 104/105 unless otherwise noted. 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
| 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 Loeb Quad |
| Time | Activity |
|---|---|
| 9am | Welcome and Orientation! - Amy and Titus |
| 9:45am | A brief history of everything - Tracy |
| 10:30am | break |
| 10:50am | Overview of microbial ecology data generation and analysis - Titus |
| noon | lunch! |
| 2pm | Intro to remote computing & UNIX command line - Titus and Tessa |
| 3:30pm-3:50pm | break |
| 3:50pm | (UNIX continued) - remote computing slides intro to shell |
| 4:45pm | Lightning talks intro! - Tracy - SIGN UP HERE |
| 5pm | dinner! |
| 7pm | R and RStudio - Hannah and Sarah R lesson materials slides |
| Time | Activity |
|---|---|
| 9am - noon |
OTUs and ASVs DADA2 workflow: Slides and Rmarkdown (Ben Callahan) |
| 2pm - 5pm |
Long-read Amplicon Sequencing DADA2 lab: Illumina paired-end 16S or Pacbio HiFi 16S (Ben Callahan) |
| 7pm - 10pm | Lightning talks Sign up here! |
| Time | Activity |
|---|---|
| 9am - noon | More data analysis skills (Hannah Houts, Bry Moore, and Sarah Teichman) Working w CSVs phyloseq and ggplot2 lecture and lab |
| 2pm - 5pm |
Contamination in Microbiome Sequencing decontam lab: Feline bile (Ben Callahan) |
| 7pm - 10pm | Lightning talks
Sign up here!|
No course activities!!
Activities to consider -
- Go to Falmouth and explore main street, or go see a movie! (The Whoosh Trolley will take you there)
- Rent a bike and go up the Shining Sea Bikeway!
- Go to Martha's Vineyard
| Time | Activity |
|---|---|
| 9am - noon | * A brief introduction to anvi'o :: slides * Introduction to shotgun metagenomics and read recruitment :: slides * Introduction to core concepts in genome-resolved metagenomics :: slides |
| 2pm - 5pm | * Introduction to pangenomics :: slides * Tutorial on pangenomics :: online resource |
| 7pm - 10pm | Assembly Exercise & Assembly Hands-On; Tutorial on pangenomics (continued) |
| Time | Activity |
|---|---|
| 9am - noon | K-mer-based Analyses slides & hands-on |
| 2pm - 5pm | Details to come... |
| 7pm - 10pm | Lightning talks Organization in RStudio Running workflows |
| Time | Activity |
|---|---|
| 9am - noon | Statistics bootcamp slides |
| 2pm - 5pm | Metagenomic bias* lecture slides Estimation lecture slides labs |
| 7pm - 10pm | Details to come... |
| Time | Activity |
|---|---|
| 9am - noon | Statistical estimation of diversity slides labs |
| 2pm - 5pm | BioBakery link to slides and labs |
| 7pm - 10pm | more delicious BioBakery work |
| Time | Activity |
|---|---|
| 9am - noon | Parting thoughts on shotgun metagenomics (Titus); open lab with Curtis, Amy, Tessa, Ben, et al. |
| 2pm - 5pm | Connecting data types to questions with tools (Tessa); course faculty Q&A |
| 6:30pm - 7:45pm | Refreshments and graduation ceremony! (Loeb tent; where we did our welcome) |
| 8pm - 9pm | MBL-wide Friday night lecture: "Blindspots to Inclusion in Environmental and Ocean Sciences" - Karlisa Callwood (Lillie Auditorium) |
| 9pm onwards | Grab more refreshments! |