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I visited the one and only microbe museum-, Micropia in Amsterdam in August, following the ESEB meeting in Groningen.  Highly recommend for anyone with an interest in microbes or science in general.  Very interactive.

BibTeX database from PDFs via DOI

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

Experimental evolution with the Singer ROTOR HDA

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.