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This page is the central hub for all things STAMPS 2022 🙂 (#stamps2022)
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 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 MikeLee@bmsis.org 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.
Links to accessing our cloud computers can be found on this page: https://hackmd.io/@astrobiomike/STAMPS2022-cloud-links
- 21 July – Thursday
- 22 July – Friday
- 23 July - Saturday
- 24 July – Sunday
- 25 July – Monday
- 26 July – Tuesday
- 27 July – Wednesday
- 28 July – Thursday
- 29 July – Friday
- 30 July – Saturday
- Mihai Pop, University of Maryland
- Tracy Teal, Rstudio
- Titus Brown, University of California Davis
- Ben Callahan, North Carolina State University
- Curtis Huttenhower, Harvard University
- Mike Lee, NASA Ames Research Center
- Todd Treangen, Rice University
- Amy Willis, University of Washington
- 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.
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 10:20–10:40
- Afternoon session break will be 3:20–3:40
- Evening break (if we're all together) will be 8:20-8:40
| 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 |
|---|---|
| 9 am – 12 pm |
Orientation/Introductions (Tracy Teal) Sequencing Type and Sequence Quality (Ben Callahan) assembly exercise (Titus Brown) |
| 12 – 2 pm | Lunch |
| 2 – 5 pm |
5 Things I wish I knew when getting into bioinformatics Accessing our cloud computers A Unix Crash Course An introduction to scripting in Unix (Mike Lee) |
| 5 – 7 pm | Dinner |
| 7 - 10 pm |
Getting started with R (Tracy Teal) |
| Time | Activity |
|---|---|
| 9 am - 10 am | Continuing getting started with R (Tracy Teal) |
| 10am - 12 pm |
OTUs and ASVs DADA2 workflow: Slides and Rmarkdown (Ben Callahan) |
| 12 – 2 pm | Lunch |
| 2 - 5 pm |
Long-read amplicon sequencing DADA2 lab: Illumina paired-end 16S or Pacbio HiFi 16S Contamination and decontam (Ben Callahan) |
| 5 – 7 pm | Dinner |
| 7 - 10 pm |
How to give a lightning talk (Tracy Teal) Attendee lightning talks Open lab |
| Time | Activity |
|---|---|
| 9 am - 12 pm |
Statistics Bootcamp (Amy Willis) |
| 12 – 2 pm | Lunch |
| 2 - 5 pm |
Modeling Microbiome Data RadEmu Shiny App (Amy Willis) Labs |
| 5 – 7 pm | Dinner |
| 7 - 10 pm | Statistics Day Spillover Attendee lightning talks Open lab |
| Time | Activity |
|---|---|
| 9 am - 12 pm |
Metagenomic sequencing and sequencing quality (Todd Treangen) QC Tutorial Squeegee Tutorial ONT QC |
| 12 – 2 pm | Lunch |
| 2 - 5 pm |
Assembly and binning Tutorial Answers to learner questions (Taylor Reiter) |
| 5 – 7 pm | Dinner |
| 7 - 10 pm | Attendee lightning talks Open lab |
| Time | Activity |
|---|---|
| All day | Free day! |
| Time | Activity |
|---|---|
| 9 am - 12 pm | Assembly-free analysis - presentation and tutorial (Titus Brown) |
| 12 – 2 pm | Lunch |
| 2 - 3 pm |
Annotation (Mihai Pop) |
| 3 - 5 pm |
Functional annotation tutorial (Taylor Reiter) |
| 5 – 7 pm | Dinner |
| 7 - 10 pm |
Microbial community function Curtis Huttenhower |
| Time | Activity |
|---|---|
| 9 am - 12 pm | Strain-level analysis (Todd Treangen / Mike Nute / Titus Brown) Bespoke Strain-level Analysis Strain-level analysis with ParSNP Chasing strain variation (PDF) Optional tutorial - reads vs assembly containment of known genomes |
| 12 – 3 pm | Lunch / Longer break for tour |
| 1 - 2 pm | MRC tour 1 |
| 2 - 3 pm | MRC tour 2 |
| 3 - 5 pm |
Statistics with metagenomics data (Amy Willis) Labs |
| 5 – 7 pm | Dinner |
| 7 - 10 pm | Attendee lightning talks Open lab |
| Time | Activity |
|---|---|
| 9 am - 10:20 am |
An introduction to phylogenetics and phylogenomics (Mike Lee) Gene-tree exploration (Sarah Teichman) Important considerations of multiple sequence alignment (Mike Nute) Gene-tree exploration lab (Sarah Teichman) |
| 10:40 am - 11:20 pm |
Phylogenomics with GToTree (Mike Lee) |
| 11:20 am - 12 pm |
Experimental design (Mihai Pop) |
| 12 – 2 pm | Lunch |
| 2 - 5 pm | Attendee lightning talks High-level review of amplicon sequencing and metagenomics (Mike Lee) Wrap-up / summary (Mihai Pop / all) Open lab |
| 5 – 7 pm | Dinner |
| 7 - 7:30 pm | Graduation ceremony (in the Loeb tent area where we've been hanging out!) |
| 8 - 9 pm | Friday Evening Lecture: Carrie Harwood "50 Years of Microbial Diversity: What a Ride!" |
| Time | Activity |
|---|---|
| All day | Departure day! |
| 9 am - 12 pm | Open lab / say goodbye :( |