Category: bash

Learn X in Y minutes

Learn X in Y minutes In the past we had “flash cards” to memorize and review materials. This site Learn X in Y minutes has one-page reminders that can be used to re-learn material or get some idea of what the subject is about. For example I wrote a series of 4 posts titled  Do …

1to3 and 3to1 peptide sequence conversion

Summary 1. How to easily convert a string of character to appear one character per line> Either of: echo "abcdefg" | fold -w1 echo "abcdefg" | grep -o . 2. How to convert amino acid sequence from one-letter to three-letter or vice versa? Easiest is on a listed web site. 3. How to write the …

Reformat every other line with paste

  Sometimes a very simple command can accomplish amazing tasks. Recently I had a list with alternating entries on every other line with about 200 lines, and lots of uneven text. But  I wanted to have 2 columns instead. A quick online search let me find a new way of using a familiar command called …

PowerShell – an opinionated primer

PowerShell One day I discovered that there was a Windows App called “PowerShell” while searching on my Windows 10 installation. I did not pay much attention to it even if I stumbled upon it a few times since. It seems that the early versions were present already in Windows 7, so in that sense it …

csvkit command-line spreadsheet can convert and compute multiple Excel files

(Last edit: April 11, 2023) Summary How to deal with many Excel files If  I had had the information I was looking for within a single Excel spreadsheet I would not have found csvkit because I would simply have copied the column containing the data I wanted, in that case a list of email. But …

Data Analysis Workshops Fall 2020

SUMMARY: Check calendar for Free "R" and "Python" workshops (Steenbock Library.) "Introduction to R with RStudio," "Data Wrangling in R" (SSCC - Social Science Computing Cooperative.) "Automating Tasks with the Unix Shell," "Data Management with SQL," "Introduction to Docker" (Software Carpentry through UW-Madison Data Science (fees apply).)

bioinformatics tutorials

  June 26, 2020. I have added a new entry under the “Tutorials” menu for “bioinformatics” to provide a place for tutorials that are more than just about one subject. “bioinformatics is the science of collecting and analyzing complex biochemical and biological information using computers.” It may provide the tools to “look under the hood” …

A great Unix tutorial suitable for beginners

...provides a wonderfully well done, easy to understand set of small tutorials, with exercises, each with an accompanying video that should make it easier for beginners that want to learn Unix command line / bash.... To make is faster to navigate the lessons and videos I have combined both into a simple table...

Finding alternate software

A couple years ago I wrote a short note on another blog (DNA.today – link below) about a web site that can be quite useful: it provides the name of alternate software. The site is: alternativeto.net For example, if you cannot afford Adobe PhotoShop you would be glad to find an alternative in “Gimp” (GNU Image Manipulation Program.)  The …

Survival command line

The built-in Terminal in MacOS and Linux and in Windows with added software provides access to the core of the computer. They are simply a software version (an emulation) of what used to be a hardware terminal (as the one shown above) user to connect to a computer when these were the size of multiple washing …