Update 1: reported in the CALS eNewsletter on April 17 [Archived May 2, 2020] Update 2: I compiled a table with more Covid-19 coloring books from other inspired sources. Friday, April 10, 2020 (“Good Friday”) I have created a booklet titled “SARS-CoV-2 – COVID-19 | A Coloring Book” that parents who are spending a lot …
This is a list of R material that I found online that I think can be useful as reference or as working material to learn R / RStudio / Mardkown. I’ll try to separate the links between “Classic” and “Tidyverse” versions, but that is not always possible… “Tidyverse” would include plotting with ggplot2 R package which …
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 REFORMAT. And “boy” was he right, as in my 30+ years …
Reproducible research Docker is a great tool to provide methods for reproducible research that should allow other researchers to reproduce any advanced calculations that you, as a researcher have done, most likely in association with publishing a paper. However, there are many caveats along the way, the first one being explanations on how to launch …
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 …
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 …
Edit: April 8, 2025 Images were updated to remove the error that presented the roadmap in a mirror image. Docker saves the day! Here is a great example of how Docker can help save a NATURE paper! Summary: Problem: Professor wants to use a specific virology program called rivem (links below.) However, this only works on …
As biochemists and biologists, like all scientists we convey results in the form of graphs. We also read papers that present results. More generally graphs are used in many aspects of every day news… The following YouTube video from Ted-Ed shows stunning examples on how our perception can be manipulated when graphs are created with obvious …
In the past years I have focused on what seemed to be the most useful bioinformatics tools for biologists that need to analyze data with software that does not have a graphical interface. The final result is that I created tutorials for bash, R and python. It seems that others agree, and I think this youtube …