World of Viruses “World of Viruses comics” from the University of Nebraska are available free on-line as PDF or for reading online. A nice way to educate oneself and younger ones while seemingly having fun! Just follow this link: worldofviruses.unl.edu/comics-apps Description of the series on Amazon: World of Viruses is a graphic novel that contains the …
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 …
I regularly roam the Internet in search of solutions to simple questions and often find the answers in sites such as stackoverflow.com, biostars.org or similar forums. Once in a while I find interesting, free materials, such as the FREE “Think” book series by Allen B. Downey on Green Tea Press. The premise of this series …
This textbook introduces the basics of protein structure and logically explains how to use online software to explore the information in protein structure databases.
PyMOL is a great program that runs natively on all 3 major platforms. However, I wanted to use a docker image that allegedly can run PyMOL (albeit an older version 1.8.2.) The reason might not be apparent at first but while the 3D interactivity would be slow, there can be other reason such a contraption …
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 …
In 1992 I attended a molecular graphics visualization and simulation somewhere in Texas, organized by Keck. One of the presenter had a movie of molecular dynamics of a protein that forever changed my mental view of the 3D structure of a protein: the atoms “wiggled” and it made clear with a stunning visual depiction that …
PyMOL license needs update Attention PyMOL users. The UW license is set to expire on January 15th, 2020. The license is required for running PyMOL starting with version 2.o and works for now on all updated 2.x versions (currently 2.3.4.) Edit: for Departmental computer Biochem IT is “pushing” the license to departmental computers, hence this …
Winter 2020 Programming Workshops on Campus In the past years I have offered python 3, R, and RStudio workshops within the Biochem Department (see links below.) R is both a language and a software environment for statistical computing and graphics. R (and other languages) can be used through the amazing RStudio interface for even more performance, ease …