Bioinformatics Course Schedule

Overview

Day 1 Introduction and Overview of Microbial Single Cell Genomics
Day 2 Exploring Microbial Genomes
Day 3 Use of SAGs in Quantitative Microbial Ecology
Day 4 Integration of SAG and Other ‘omics Data with anvi'o
Day 5 Data Workshop

Speakers

Ramunas Stepanauskas (Bigelow Laboratory for Ocean Sciences)
Phil Hugenholtz (University of Queensland)
Stephen Giovanonni (Oregon State)
Katherine McMahon (University of Wisconsin)
Murat Eren (University of Odenburg)
Maria Dzunkova (University of Valencia)

Instructors

Maria Pachiadaki (WHOI)
Florian Trigodet (University of Chicago)
Jacob Munson-McGee (Bigelow Laboratory for Ocean Sciences)
Julia Brown (Bigelow Laboratory for Ocean Sciences)
Melody Lindsay (Bigelow Laboratory for Ocean Sciences)
Gregory Gavelis (Bigelow Laboratory for Ocean Sciences)

Expanded Schedule

Day 1 Introduction and Overview of Microbial Single Cell Genomics

• 7:00 AM - 8:00 AM Continental Breakfast for non-Bigelow participants
• 8:30 AM Ice Breaker
• 9:00 AM Expert Lecture: Ramunas Stepanauskas
• 9:30 AM - 11:00 AM Hands-on Introduction to the course computational environment
  • Lead by Julia Brown
• 11:00 AM - 12:00 PM Tour of SCGC
  • Lead by Ramunas Stepanauskas
• 12:00 PM - 1:00 PM Catered Lunch
• 1:15 PM - 4:30 PM Hands-on: Understanding the SCGC workflow and data structure
  • Lead by Greg Gavelis, Ramunas Stepanauskas, Julia Brown
• 5:15 PM Catered dinner for all instructors and participants

Day 2 Exploring Microbial Genomes

• 7:00 AM - 8:00 AM Continental Breakfast for non-Bigelow participants

• 8:00 AM Expert Lecture: Phil Hugenholtz

• 8:30 AM - 12:00 PM Hands-on: Tools for taxonomic assignment of microbial SAGs

  • Lead by Jacob Munson-McGee, Greg Gavelis

• 12:00 PM - 1:00 PM Catered Lunch

• 1:15 PM Expert Lecture: Stephen Giovanonni

• 1:45 PM - 4:30 PM Hands-on: Functional annotation of SAG Data

  • Lead by Maria Pachiadaki, Melody Lindsay

• 5:15 PM Catered dinner for external instructors and external participants only

Day 3 Use of SAGs in Quantitative Microbial Ecology

• 7:00 AM - 8:00 AM Continental Breakfast for non-Bigelow participants

• 9:00 AM Expert Lecture: Trina McMahon

• 9:30 AM - 12:00 PM Hands-on: Meta'omic read recruitment to SAGs

  • Lead by Julia Brown, Maria Pachiadaki

• 12:00 PM - 1:00 PM Catered Lunch

• 1:15 PM - 4:00 PM Hands-on: Taxonomic and Functional characterization of meta’omics data using SAGs

  • Lead by Jacob Munsun-McGee, Ramunas Stepanauskas, Julia Brown

• 5:15 PM Catered dinner for external instructors and external participants only

Day 4 Integration of SAG and Other ‘omics Data with anvi'o

• 7:00 AM - 8:00 AM Continental Breakfast for non-Bigelow participants
• 9:00 AM Expert Lecture: Murat Eren
• 9:30 AM - 12:00 PM Hands-on: Integration of multi-‘omic datasets with anvi’o
  • Lead by Florian Trigodet
• 12:00 PM - 1:00 PM Catered Lunch
• 1:15 PM - 4:00 PM Continued Integration of multi-‘omic datasets with anvi’o
• 5:15 PM Catered dinner for all instructors and participants

Day 5 Data Discussion and Exploration

• 7:00 AM - 8:00 AM Continental Breakfast for non-Bigelow participants
• 9:00 AM Expert Lecture: Maria Dzunkova
• 9:30 AM - 12:00 PM Research Vignettes: Presentation and discussion of small project ideas
• 12:00 PM - 1:00 PM Catered Lunch
• 1:15 PM - 4:00 PM Independent data exploration and open discussion
• 5:15 PM Catered dinner for external instructors and external participants only