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 …
Blog
GENESIS – All-atom Molecular Dynamics Simulation
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 …
PyMOL 2.x License and updates
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 …
R/Python/Reproducible Research Workshops on Campus – Winter 2020
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 …
Dockerization – details needed
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 …
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, …
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 …
Docker saves the day – Roadmaps – rivem
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 …
How to spot a misleading graph?
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 …
Bioinformatics – which computer language should I learn first?
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 …