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Tracy Teal edited this page Jul 12, 2019 · 28 revisions

Welcome to the STAMPS 2019 wiki!

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.

Before the course

You will need to bring a laptop to actively participate in this course. Please see [this information(installation-help) for information on computer requirements, help installing software needed for the course and on how to get onto the MBL wifi network.

Schedule links for STAMPS 2019

Workshop Instructors and Lecturers

Workshop TAs

Information

Code of Conduct and Accessibility

  • We operate under a Code of Conduct, and expect cooperation from all attendees 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 (in-progress)

All activities are in Loeb G70 unless otherwise noted.

Monday, 22 July

Time Activity
17:00 Opening Reception (Mihai)
(In Meigs Room on second floor of the Swope building)

Tuesday, 23 July

Time Activity
9:00–12:00 Orientation: Metagenomics approaches, course structure
(Mihai Pop; Takes places in Lillie building)
12:00–14:00 Lunch
14:00–17:00 Unix and R introductions
(Tracy/Mike Lee)
17:00–19:00 Dinner
19:00–22:00 Open lab (Unix and R)

Wednesday, 24 July

Time Activity
9:00–12:00 More R and workflows
(Tracy/Titus)
12:00–14:00 Lunch
14:00–17:00 Statistics and Statistical thinking
(Amy)
17:00–19:00 Dinner
19:00–22:00 Open lab (Unix and R)

Thursday, 25 July

Time Activity
9:00–12:00 Concept of OTUs and DADA2
(Ben)
12:00–14:00 Lunch
14:00–17:00 Heterogeneous data structures and phyloseq
(Susan)
17:00–19:00 Dinner
19:00-20:00 Open
20:00–22:00 Open lab

Friday, 26 July

Time Activity
9:00–12:00 Metagenomic assembly
(Titus/Adina)
12:00–14:00 Lunch
14:00–17:00 Taxonomic annotation and phylogenetics
(Tandy/Mike Nute)
17:00–19:00 Dinner
19:00–20:00 Lecture – From field to figures
(Adina)
20:00-22:00 Open lab

Saturday, 27 July

Time Activity
All day Free day

Sunday, 28 July

Time Activity
9:00–12:00 Network analysis
(Christian)
12:00–14:00 Lunch
14:00–17:00 Statistical estimation: alpha/beta diversity and differential abundance
(Amy)
17:00–19:00 Dinner
19:00–20:00 Panel (OTU/ASV)
20:00-22:00 Open Lab

Monday, 29 July

Time Activity
9:00–12:00 Exploratory statistics
(Susan)
12:00–14:00 Lunch
14:00–17:00 QIIME2
(Evan)
17:00–19:00 Dinner
19:00–22:00 Evening Reception

Tuesday, 30 July

Time Activity
9:00–12:00 Assembly - reference-guided, strain resolution, etc.
(Todd)
12:00–14:00 Lunch
14:00–17:00 Strain-level analyses (Titus/Todd)
Metagenomics workflows/Bringing it all together (Titus)
17:00–19:00 Dinner
19:00–20:00 Panel (Professional development)
20:00-22:00 Open Lab

Wednesday, 31 July

Time Activity
9:00–12:00 Functional analysis
(Yana)
12:00–14:00 Lunch
14:00–17:00 Lecture (Rob/Curtis)
17:00–19:00 Dinner
19:00–22:00 Lecture (Rob/Curtis)

Thursday, 1 August

Time Activity
9:00–12:00 Presentation/Lecture
12:00 Lunch and departure
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