Lab Meetings - meyermicrobiolab/Meyer_Lab_Resources GitHub Wiki

Agenda:

• Quick "state of the lab" by JM
• Everyone will give a quick update to the group of what they are working on
• Review lab expectations and best practices
• Discuss frequency/content of upcoming lab meetings.

zoom recording

Discussion of Nearing paper on microbiome study biases

zoom recording

Potential follow-up papers to read:

• Pratte & Kellogg 2021 preservation & extraction in coral microbiome

• Salter et al 2014 kit contaminants

• Gloor et al 2017 compositional data

• McMurdie & Holmes 2014 Waste not, want not (don't do subsampling of reads)

Emilee will give a presentation on her internship

Zoom recording

Monica & Rachel gave early practice talks of their ICRS presentations

Zoom recording

Bioinformatics Workshop III: Making publication-ready figures using R and Inkscape

Get Inkscape here

Zoom recording

Riffomonas youtube channel (Pat Schloss)

Thank you, Sara! ---> how to export plots as .svg, .png, .jpeg, .tiff, etc.: the link (toward the bottom of the page) has other options for tweaking your exports, in my example below, I have only dictated the width, but the link shows how to add a background color, size of the page, etc. This turns out to be very similar to exporting a pdf.

# name the pdf to be exported
pdf("kor.pdf",width=11)

#plotting commands
p2<-ggplot(KORmetadat,aes(Date,CopyPERng))+
  geom_boxplot()+
  geom_jitter(aes(color=HealthState))+
  facet_grid(.~Treatment)+
  theme(axis.title.x=element_blank())+
  theme_bw()+
  theme(text=element_text(size=24,face="bold"))+
  ylab("copies of korormicin per ng DNA")+
  scale_color_manual(values=palette)
p2

#close the graphics device
dev.off()

# name the svg to be exported (for inkscape)
svg("kor.svg",width=11)

#plotting commands
p2<-ggplot(KORmetadat,aes(Date,CopyPERng))+
  geom_boxplot()+
  geom_jitter(aes(color=HealthState))+
  facet_grid(.~Treatment)+
  theme(axis.title.x=element_blank())+
  theme_bw()+
  theme(text=element_text(size=24,face="bold"))+
  ylab("copies of korormicin per ng DNA")+
  scale_color_manual(values=palette)
p2

#close the graphics device
dev.off()

Bioinformatics Workshop II: Genome Assembly, following the Basic Genomics Workflow

List of Probiotic Genomes to Assemble

Zoom recording 1 (group meeting)

Zoom recording 2 (follow-up steps)

Bioinformatics Workshop I: Amplicons

Working on small dataset from a tank-based probiotics trial

Zoom recording

Outdoor potluck at Depot Park

Monica will present on the disease outbreak in the coral nursery in Little Cayman

Alli lead discussion of sea star wasting disease preprint

Julie presented seagrass microbiome data

Discussion of two related papers:

• Claar paper
• Roitman paper

Send-off for Anya

Anya presented her recent work on the disease outbreak (summer 2019) in the coral nursery in Little Cayman

Jessica led us in trying out elevator pitches

DeVante' led discussion on Aiptasia paper: https://www.frontiersin.org/articles/10.3389/fmicb.2019.00975/full

Recent paper on microbiomes of new Australian lineages of Aiptasia: https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-020-00029-5

Rachel led discussion on symbiosis/microscopy paper: https://mbio.asm.org/content/11/2/e02626-19

Julie led discussion on temporal variation in Acropora: https://www.frontiersin.org/articles/10.3389/fmicb.2019.01775/full

Writing Science Chapters 13-18 (end)

Minor lab notes: EtBr, gloves, lab computer End of year goal: finish IDPs, plans for 2020 updates on wiki: funding for grad students Writing Science Chapters 9,10,11,12

Jessica will talk about the importance of lab notebooks & standard practices in industry Writing Science Chapters 5,6,7,8

Lab safety, Gator Tracs login, protocols check Register for Florida Genetics Symposium Writing Science Chapters 2,3,4

lab meeting agenda