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- Python tutorial setup instructions
- MD tutorial setup instructions
- Homology modelling tutorial setup instructions
- Docking tutorial setup instructions
The Oxford Computational Biochemistry course contains 4 self-contained tutorials which each have different software installation requirements. These instructions can be found in the respective tutorial's folder. Here we provide some basic instructions on the base setup requirements common to these tutorials and how to obtain a local copy of the materials.
In order to ensure that you have everything ready in advance of the workshop, we ask that you follow these setup instructions before attending each tutorial. Q&A sessions will be setup on the two days preceeding the course to help you with any issues you might encounter during the setup process.
1. Anaconda
All tutorials in this course rely heavily on the Anaconda package manager. This cross platform tool allows you to install other software packages in an easy and controllable manner. We require all attendees to install this prior to starting any of the tutorials. Please see the follow the Anaconda install instructions to get started.
The Anaconda package manager, is named conda. Throughout the tutorials you will see several invocations of conda, including to create environments and install software. If you are unfamiliar with this tool, it is heavily recommened that you go through the getting started guide.
Throughout the tutorials we will be interacting with various software through the use of a terminal interface. Terminals are a powerful means by which to navigate through files and quickly execute various programs.
On linux/macOS this is generally done though a bash/zsh shell.
- In linux this can be accessed by searching for terminal in the startup menu. See below for an example in the ubuntu gnome shell.
- On macOS this is done by searching for terminal in the Launchpad (see the following for more details).
On Windows (unless using WSL, the Windows Subsystem for Linux, in which case please follow the linux instructions), this will be done via the Anaconda prompt. The Anaconda prompt can be opened by searching for it in the startup menu after having installed Anaconda (see the step above).
There are substantial differences in the way in which the terminal works between Windows and linx/macOS. We will give a quick overview of the the basics below, including some links for extra resources you can look at to get more familiar with using the shell. We recommend that you have a look through these before attempting the tutorials.
Note: in the MD tutorial you will eventually be required to access a remote HPC machine to run a Molecular Dynamics simulations. This will require use of the linux terminal. If you are using Windows you will therefore also need to look at the instructions for the linux terminal before attempting this tutorial.
This section only provides a very basic overview of using the bash/zsh shell in linux/macOS. For more information please see the following tutorials:
- Ubuntu's terminal tutorial
- MacOS terminal beginners guide (youtube video)
On first opening the terminal
Generally upon opening the terminal you will be placed in your $HOME directory. This is the base directory where all the documents for your login account are placed. If you ever need to return to this directory enter the following command:
cd $HOME
or even just
cd
Seeing and navigating the contents of folders
One of the main uses of the terminal is to allow users to quickly see and navigate through the various files and folders on your computer.
You can see what files are in the current folder you are accessing using:
ls -lrt
You can change from one folder to another (in this case named 'newfolder') by doing:
cd newfolder
To go back out of the folder, you can do:
cd ..
If you want to know where you are amongst all your folders you can do:
pwd
This will give you the full path to the current folder.
If you want to delete (remove) a file do:
rm file
If you want to rename a file do:
mv file newfilename
If you want to view the contents of a file do:
more file
This section only provides a very basic overview of using the Anaconda terminal. For more information please see the following tutorials:
- Windows command line tutorial (youtube video) Note: this uses the standard windows command line, but the instructions should carry over to the Anaconda terminal. Disclaimer: we have not watched all 9 videos in the tutorial series and do not take responsibility for any of the contents.
On first opening the terminal
Generally upon opening the terminal you will be placed in your %HOMEPATH% directory.
This is the base directory where all the main folders (My Documents, Downloads, etc...)
for your login account are placed, which is usually C:\Users\username. If you ever
need to return to this folder enter the following command:
cd %HOMEPATH%
Seeing and navigating the contents of folders
One of the main uses of the terminal is to allow users to quickly see and navigate through the various files and folders on your computer.
You can see what files are in the current folder you are accessing using:
dir
You can change from one folder to another (in this case named 'newfolder') by doing:
cd newfolder
To go back out of the folder, you can do:
cd ..
If you want to know where you are amongst all your folders you can do:
cd
This will give you the full path to the current folder.
If you want to delete (remove) a file do:
del file
If you want to rename a file do:
rename file newfilename
If you want to view the contents of a file do:
more file
At several points during the tutorials you might be asked to edit a file.
There are several editors available and generally we recommend you use the one that you are most accustomed with (if possible).
Here are our recommendations for editors that can be invoked directly from the command line:
- gedit (recommended for linux, usually pre-installed)
- nano (recommended for linux & macOS, pre-installed)
- TextEdit (for macOS, pre-installed. From the terminal prompt you can issue
open -a TextEdit) - vim
- notepad (recommended)
Built into Windows, just type notepad filename in your terminal. This will open a
window where you can edit the file, save and then close the window to get back to
your terminal.
In order to carry out the exercies presented in the tutorials you will need to download a local copy of the course materials. Our recommended way is to do the following:
Go to the tutorial github page: https://github.com/bigginlab/OxCompBio
On the top left-hand side of the page you will see a green button titled "Code".
Click on it and then click on "Download ZIP".
This will download a copy of the course materials to your computer. Then simply move the zip file to some convenient folder (ideally easily accessible through your terminal), and extract it (macOS: double click, windows: right-click and extract all).
This will create a folder named OxCompBio-master.
Note: there are other more complex way to obtain these materials, such as through
the use of git, however in the interest of easy of use, we shall not discuss them
here.
The tutorials rely on the use of Jupyter notebooks to provide an interactive experience, particularly when dealing with python code. The install instructions for each tutorial will install a copy of the jupyter notebook interface where required. We recommend that you start by setting up the python tutorial and then look at some of the following resources on how to use notebooks:
- The jupyter notebook beginners guide
- Codeacademy's jupyter notebook tutorial
- Quick introduction to jupyter notebooks (youtube video)
Briefly, one usually starts a jupyter notebook session by opening a terminal,
navigating to the folder where ipynb (notebook) files are present, and
typing the following:
jupyter notebook
This should automatically open an interactive session in your browser.
You can then click on the .ipynb (notebook) file to start it.
Jupyter notebooks are composed of cells, some of which contain normal text (with a white background), and code blocks (shaded in grey):
Code blocks are meant to be interactive, you can type in them and press
shift+Enter to run the contents of the cells.
You can exit a notebook by clicking "File"->"Close and Halt":
Sometimes when too many things are running, notebooks can start to behave erratically, when this happens clicking on the "interrupt" button may help:
Alternatively, using one of the "Kernel"->"restart" options can be very useful. Particularly, the "Restart & Clear Output" can be useful in cleaning up the notebook's outputs and starting again:
Note: In a Jupyter notebook you can run cells in any order you like. This might create problems in the long run, therefore we suggest to run the cells sequentially (from top to bottom). If you start to get strange results within a Jupyter notebook, you can use "Kernel"->"Restart & Run all" to run clean everything up and re-run the notebook from scratch.
The next step is to do the individual setup steps for each tutorial.
These can be found at the following links: