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” …
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 …
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 …
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 …
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 …
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 …