mblmicdiv / course2017

Genomics lessons for week 4 of the Microbial Diversity course at the Marine Biological Lab in Woods Hole, MA.

course2017

Microbial Diversity @MBL, Genomics lessons week 4

Instructors

• Titus Brown
• Scott Dawson
• Tracy Teal

TA:

• Lisa Johnson Cohen

Week 4

• 31 July 2017
  
• 1 August 2017
  
• 2 August 2017
  
• 3 Augusut 2017
  
• 4 August 2017
  

Monday 31 July 2017

Time	Activity	Location
09:00	Titus Brown: "Why Sequence Genomes?"	Candle House
10:30	Scott Dawson: Phylogenies	Candle House
1:00 - 3:00	Lab (Scott): Genome annotation, gene search and BLAST, IMG, and other resources	Groups 1 + 2, Candle House
7:00 - 9:00	Same Lab	Groups 3 + 4, Fishbowl

Tuesday 1 August 2017

Time	Activity	Location
09:00	Tracy Teal: "Soil microbial communities: A study with metagenomics"	Candle House
10:30	Titus Brown: "Shotgun metagenome assembly: how well does it work?"	Candle House
1:00 - 3:00	Lab (Tracy): UNIX command line, scripting, and automation	Groups 3 + 4, Candle House
7:00 - 9:00	Same Lab	Groups 1 + 2, Fishbowl

Wednesday 2 August 2017

Time	Activity	Location
09:00	Tracy Teal: "Computing Workflows for Biologists"	Candle House
10:30	Scott Dawson: Phylogenies (part 2)	Candle House
1:00 - 3:00	Lab (Titus): Use sourmash to search and compare genomes and metagenomes; understand a bit more about k-mers	Groups 1 + 2, Candle House
3:00 - 5:00	Same Lab	Groups 3 + 4, Candle House
6:00	2 min students miniproject pitch presentation - Pizza!	Everyone, Fish bowl
8:00	Termite guts at Fishbowl and lab	Everyone

Thursday 3 August 2017

Time	Activity	Location
09:00	Titus Brown: RNASeq and stats intro, static Jupyter notebook simulation	Candle House
10:30	Scott Dawson: A Giardia transcriptome story	Candle House
1:00 - 3:00	Lab (Tracy): Programming in R for plotting and community analysis	Groups 1,2, 3 + 4, Candle House
6:30	Swope Group photo

Friday 4 August 2017

Time	Activity	Location
09:00	Murat Eren: Anvi'o for visualization	Candle House
10:30	Titus Brown: Our data-intensive future and how to plan for it.	Candle House
1:00 - 5:00	Miniprojects; genomic & bioinformatics consultation with Titus and Lisa	Lab

Extra:

Thursday 10 August 2017

Time	Activity	Location
3:00 - 4:00	Lisa Johnson: Using External Compute Resources for Analyzing Large Sequencing Data Files	Candle House