Monthly Archives: January 2020

TableConvert.com – free tabular data formats converter

This is a repost of my post on the Biochemistry department: tableconvert-com-free-tabular-data-formats-converter Tabular formats When I first came to Madison in 1986 as a postdoc with Biochemistry professor Paul Kaesberg to learn cloning and sequencing, I was surprised when he said that the most important program to work with sequences was the (now defunct GCG) program… Read More »

Bioawk for handling bioinformatics formats

Today I found a new tool: bioawk that was written by Heng Li who also wrote samtools and bwa. I first discovered it ont this blog: bioawk-basics (Bioinformatics Workbooks) There is also a short tutorial on GitHub: github.com/vsbuffalo/bioawk-tutorial I also found a recent docker image, and in fact there are only 2 images on docker hub: lbmc/bioawk updated 2 months ago,… Read More »

A Boy And His Atom: The World’s Smallest Movie

Moving atoms For some reason a paper copy of “Chemical and Engineering News” (November 11, 2019 – Vol 97 Issue 44) ended up in my hands, and I almost missed this fun section named: “30 years of moving atoms: How scanning probe microscopes revolutionized nanoscience” (link.) The article is progressing over time from 1993 til… Read More »

GREP was written overnight – Birth and Name

I use grep very often, and I made-up and acronym that made sense to me: Get REgular ExPression But I discovered this YouTube video that gives an accurate historical recounting of its birth and where its name came  from. See video below, titled “Where GREP Came From – Computerphile” Summary: this comes from the command g/re/p… Read More »