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 …
In some instances we start a container, but it will default to immediately running a program within and prevent immediate shell access. This is possible since Docker version1.3 Assuming that the container is already running (for example serving a web browser) and you can’t access the shell commands we can gain shell (bash, ssh) through …
Programming for Biology 2019 The famous Cold Spring Harbor Laboratory offers many courses, the course Programming for Biology 2019 was held in October 2019 and this specific course generously offers the course materials online on this site: programmingforbiology.org The course materials covers basics and advanced methods using Unix & Python and provides tutorial materials that include …
When activated by the docker run command, some docker container immediately start a software within. This can be useful for the author of the image, but for others it may cause issues. Here is one example amongst many, from a series: Bioinformatics Docker Images Project which may be difficult for some users due to the use of …
As I am creating the docker tutorials “for biologists” I find that having some notes here could be useful. This is therefore a bit like a Frequently Asked Questions (FAQ) that I answer to myself at first! For general info it would be best to refer to the tutorials themselves when they are online. Remove …
Docker Containers I don’t remember how exactly I discovered Docker containers a bit over a year ago, but it seemed a very good system and I immediately saw the potential, then I thought that it would be very good tutorial material. As I am now creating those tutorials “for biologists” I discover a lot of …
R Workshops on Campus R is both a language and a softwware environment for statistical computing and graphics. R can be used through the amazing RStudio interface for even more performance, ease and Reproducible Research. In the past years I have offered R and RStudio workshops within the Biochem Department (see links below.) However, multiple …
A small chapter At the turn of the Century (from XX to XXI) I was invited to write a small chapter on the visualization of virus structure for a book that would be published in Spanish called “Principios de Virología” by Professor Jorge Ossa Londoño (CV) from the Universidad de Antioquia. (His UW Alumni Profile “Jorge Ossa …
Blog series This June 2019 marked my 33 years at UW–Madison when I joined Prof. Paul Kaesberg‘s lab as a PostDoc to learn the then new methods of “cloning and sequencing” (i.e. Sanger sequencing.) In this blog I will share memories and stories, images and perhaps (probably useless) software code… as often people ask me …