Turing Centre for living systems's "Introduction to biological data analysis" course

This is the repository for the introduction of the CENTURI "Introduction to biological data analysis" course.

This first day is split in 2 main parts:

1. Introduction to coding with Turing patterns
2. Data handling and visualisation

0. Requirements for the course

0.1 Recommended software

This course is made on a jupyter notebook running on Python 3.8 or newer.

You can either run the notebooks using google colab.

From there you can open the notebooks by selecting the GitHub tab then typing GuignardLab/Centuri-Course:

If you don't want to use google colab you can run the software directly on your computer by first cloning this repository:

git clone https://github.com/GuignardLab/CenTuri-Course.git

Then, to install Python and the required dependencies we strongly recommend to use conda, mamba or pipenv (the teachers will use conda)

0.2 Installing conda

Conda can be installed multiple ways. We do not have any recommendations about how to but one can read there for a likely exhaustive list on ways to install conda.

Note that we do not necessarily recommend installing Anaconda, we do have a slight preference towards Miniconda but that's just us.

Moreover, we advise to start jupyter notebooks from a shell/terminal/prompt to be able to better see the error messages.

0.3 Dependencies

To install them one can for example run the following command lines in a terminal, assuming that conda is installed:

conda create --name CenTuri-Course python=3.10

to create the environment for the course. Then:

conda activate CenTuri-Course

to activate the course environment. And finally:

pip install centuri_course

All dependencies should now be installed!

You can then start the notebooks by running:

jupyter notebook 1-Introduction-to-Python

Enjoy!