After being steadfastly against anything in R beyond base, I’ve recently been indoctrinated into the tidyverse way of doing things. In particular, ggplot and extensions has made making complicated plots a lot easier than using base graphics (especially ggpubr’s ggarrange() function for labelling panels, which I used to do with mtext()). However, I’ve never been a huge fan of the ggplot aesthetic, being trained from a young age to eschew “chart junk“, like grid lines and unnecessary backgrounds. It’s fairly easy to do, with a few modifications of ggplot’s theme_bw(). Include this code before your ggplot commands:

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Knight lab does the University of Manchester Community Festival!  Live-action demos of evolution simulations and examples of antibiotic resistant E. coli.

This somewhat-ridiculous BASH one-liner will create a BibTeX database file (.bib) from a bunch of PDFs via the Crossref API for DOIs, providing the PDF has a DOI on the first page.  As DOI was introduced in 2000, this will probably not work on vintage PDFs.

 for pdfs in *.pdf; do pdftotext -f 1 -l 1 "$pdfs" - |tr -d "\n" | grep -oE "(doi|DOI):\s?[A-Za-z0-9./-\(\)-]+[0-9]" | tr '[:upper:]' '[:lower:]' | sed -r 's;doi:\s?;http://api.crossref.org/works/;g' | sed -r 's;$;/transform/application/x-bibtex;g' | xargs curl -fsS 2>/dev/null | sed -e '$a\'; done > allpdf.bib

Setting up a large selection experiment on antibiotic fitness landscapes. I’ve decided to use the Singer ROTOR HDA for consistency and repeatability. The Singer ROTOR HDA uses a pre-sterilized pad system (called RePads) to transfer bacteria between solid or liquid medium. RePads are available in 96, 384, 1536 or 6144 formats. Read more about the Singer ROTOR HDA.

Vented Petri dishes have a small lip on the top edge of the dish that allows the lid to sit a little up from the bottom, allowing for some air flow.  Non-vented Petri dishes allow the lid to sit more or less flat on the bottom.  I was wondering what the best applications are for triple, single and non-vented Petri dishes, and found this guide from Thomas Scientific:

• Triple vented: aids gaseous exchange. Ideally suited for short term work
• Single vented: limits gaseous exchange, minimizes evaporation and dehydration. Ideally suited for long term work
• Non-vented: most suitable for anaerobic and long term work