OSCOVIDA Tutorial: installation

Use OSCOVIDA in the cloud

To use OSCOVIDA in the cloud, you can go to this link, and can see all available Notebooks (most of which analyses one region, but you can also find the tutorial notebooks that start with the name tutorial). Or you can create your own notebook at that point.

What technically happens is that (through the binder project) a container (a bit like a small virtual machine) is created just for you at that point on a server somewhere on the planet. You can use this container from your browser, but any commands you execute are actually executed on this server somewhere else (i.e. "in the cloud"). You can use this container as long as you like, but there is a time-out: after 10 minutes of inactivity, your session will be closed.

This way of using OSCOVIDA in the cloud is very convenient, because you don't need to install any software on your own computer/tablet etc.

However, there are a number of limitations to be aware:

  • any interactive session you have, will be deleted after 10 minutes of inactivity
  • at that point, your notebooks is also lost
  • if you want to keep the notebook, you can go to File -> Download as -> Notebook (.ipynb) before your session expires
  • if you have have saved such a notebook, you can upload it and then continue to work on it in your next session.

Use OSCOVIDA on your own computer

Alternatively, you can install OSCOVIDA on your own computer, and then all the files you create and modify are saved locally on your computer.

OSCOVIDA is a python package, and makes use of other Python libraries such as matplotlib for creation of plots and numpy and pandas for data handling.

If you know Python and have Python (version 3.6 or newer) installed already, then you can install oscovida using pip install oscovida.

If you have no Python installation, or are new to Python, then we recommend to download and install the Anaconda Python distribution. Some more detailed instructions are available here. Once this is installed, you need to install the oscovida package within this Python environment. To do this, type pip install oscovida at a prompt.

Then start a Jupyter Notebook. Within than type

In [1]:
import oscovida

The next line is not required: it instructs Jupyter notebook to use vector plots instead of bitmaps, and thus produces generally nicer graphs:

In [2]:
%config InlineBackend.figure_formats = ['svg']

If no error message is printed, your system is working. in that case, try a first command, for example:

In [3]:

If you can see the plot, you have successfully installed oscovida, and are ready to use it.

Other tutorials

You can find more tutorials here.