Included here are instructions to help you get started with the Oxford Computational Biochemistry Python course. The instructions are split into two parts:
- Setup
These instructions should be followed prior to the tutorial. These will walk you through creating the appropriate conda environment for the tutorial and testing that everything works as expected.
- Starting the tutorial
These instructions should be followed on the day of / when starting the tutorial. We assume here that you have completed the setup instructions on the same machine and that testing passed as expected.
Here we assume you have completed the main setup instructions (see setup.md and have done the following:
- You have installed an anaconda distribution
- You have access to a terminal
- You have downloaded the contents of this tutorial locally.
Open a terminal and type the following:
conda --version
This should print out the current version of your conda install.
On my machine this returns conda 4.9.0.
Should this not happen, it means that you may not have installed anaconda properly. If you are having any issues please get in contact with one of the demonstrators.
From your terminal navigate to the OxCompBio/tutorials/Python folder.
Note: depending on how you downloaded the data, OxCompBio may also be called
OxCompBio-master.
Assuming you opened the terminal in the OxCompBio folder, on linux/macOS
this would mean doing the following:
cd tutorials/Python
and on Windows:
cd tutorials\Python
Then do the following in your terminal:
conda env create -f oxpython-env.yml
The above step may take some time, it will fetch all the required python packages required for the tutorial and install them within a conda environment named "OxPython"
Once completed, we then need to activate this conda environment:
conda activate OxPython
As part of the setup process, we will need to activate some jupyter notebook extensions, to do this write the following instructions in your terminal:
jupyter-nbextension enable nglview --py --sys-prefix
jupyter contrib nbextension install --user
jupyter nbextension enable exercise2/main
At this point, you should have completed the installation of the software required to run the Python tutorial.
To make sure that everything is installed properly, let's run a jupyter notebook
and open Verify.ipynb.
Type:
jupyter notebook
And in the resulting window click on Verify.ipynb
In the top row click on "Cell" -> "Run All", you should see the following:
- A code output with a y=x graph
- A code output with an interactive protein representation
Try to move the protein around with the cursor, you should be able to rotate it.
If all this works the installation has been successful.
Click on "File" -> "Close and Halt" and then "Quit" of the jupyter notebook instance.
Finally, you will need to deactivate the conda environment:
conda deactivate
You can now move on to the setup phase for the other tutorials.
Assuming everything went well with the Setup, open a terminal and navigate back to the Python tutorial (see the instructions above if you need a reminder on how to do this).
Then activate the conda environment for the Python tutorial:
conda activate OxPython
You can now start the tutorial by typing:
jupyter notebook
From there, navigate to 00_Introduction to open the notebooks within.
Don't forget to close down the session ("File" -> "Close and Halt" and then "Quit") and deactivate your environment when you are done!
conda deactivate