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Mike Lee edited this page Aug 1, 2019 · 108 revisions

Welcome to the STAMPS 2019 wiki!

This page is the central hub for all things STAMPS 2019 πŸ™‚ (#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)

Before the course

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.

Schedule links for STAMPS 2019


Link to cloud instance info


Workshop Instructors and Lecturers

Workshop TAs

Information

Code of Conduct and Accessibility

  • 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.

Course Communications and Notes

  • Slack
  • Course etherpad for notes:
  • Relevant papers:
  • Additional resources
  • Course presentations

Schedule

All activities are in Loeb G70 unless otherwise noted. All times in EDT (UTC-4).

Monday, 22 July

Time Activity
7 pm Opening Reception
(in Meigs Room on second floor of the Swope building)

Tuesday, 23 July

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 :)

Wednesday, 24 July

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 :)

Thursday, 25 July

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

Friday, 26 July

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

Saturday, 27 July

Time Activity
All day Free day

Sunday, 28 July

Time Activity
9 am – 12 pm Network analysis
(Christian MΓΌller)
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

Monday, 29 July

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 **

Tuesday, 30 July

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

Wednesday, 31 July

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)

Thursday, 1 August

Time Activity
9 am – 12 pm Presentation/Lecture
12 pm Lunch and departure