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 …
Year: 2019
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 …
Docker notes – Shell Access to Running Container
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 …
Programming for Biology – Cold Spring Harbor
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 …
Docker notes – Bypass entrypoint
When activated by docker run 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, …
Docker notes – Remove stopped containers
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 …