This is a demo site for teaching purposes. It contains a small collection of tools that I use. The tools itself are contained in the bin/ folder. Some tools come from this repository where you can find more information on the philosophy.
This repository can be made interactive by launching it in mybinder.org. This will open a browser tab where the repository will be installed into a Jupyter Lab session. Please, be patient! This may take up to 10 minutes. But then the tools can then be used directly in a browser: Launch a terminal or open the Jupyter notebook:
When launching this repository in mybinder.org the Entrez Direct tools from NLM are installed (see the postBuild file). Please, act responsible when using resources of mybinder.org and NLM and do obeye their usage guidelines! For the Entrez API see here.
Currently, this is also a testbed on how to deploy a work environment.
This kind of setup is not recommended for repeated productive use. Install the tolls locally, see below.
The scripts in the bin/ folder and the Entrez Direct tools depend on a Unix-type shell. That is available on Linux/Unix and Macintosh computers, and under WSL or the Cygwin Unix-emulation environment on Windows PCs. Therefore, running the Jupyter notebooks in Jupyter installed on a pure Windows system will not work. I am happy with the Windows Subsystem for Linux (WSL).
The installation instructions for Entrez Direct are a good source for how to get started.
To use the tools in the bin/ folder they must be saved to a local folder. Download the GitHub repository as a zip file and unpack e.g. to your home folder. (Or clone with git from GitHub.)
Assuming you saved to a folder cli4es in your home directory you need then to add the cli4es/bin folder to your PATH so that the shell will find the tools.
This will do it for the current session:
export PATH=${HOME}/cli4es/bin:${PATH}Add it to your .bash_profile file for permanent use:
echo "export PATH=\${HOME}/cli4es/bin:\${PATH}" >> $HOME/.bash_profileThis notebook is a demo of a tool used to fetch MeSH entry terms via API from the commandline. You can try it out.
Not (yet?) possible within Binder: Once you have the scripts installed on your local computer, it is possible to use the functionality directly from within a (better) text editor:
