Intelligent Systems for Bioinformatics

Curricular Unit

Master in Bioinformatics, University of Minho, 2024-2025.

Description

A package of machine learning algorithms to grasp the concepts of the course. Students should implement essential algorithms from scratch using numpy and pandas. Implementations must follow a common and simple API.

Setup

To get started, fork the repository from GitHub and clone it to your local machine.

Fork the following GitHub repository: https://github.com/jcapels/si.git

Then, clone the repository to your local machine:

git clone https://github.com/YOUR_USERNAME/si.git

Open the repository in your favorite IDE and install the dependencies (if missing):

pip install -r requirements.txt

or

pip install numpy pandas scipy matplotlib

Note: You can also create a similar Python package and push it to your GitHub.

Make a change to the repository: Add your co-authorship to the __init__.py file (within the si folder):

__author__ = "YOUR_NAME" 
__credits__ = ["YOUR_NAME"]
__license__ = "Apache License 2.0"
__version__ = "0.0.1"
__maintainer__ = "YOUR_NAME"
__email__ = "YOUR_EMAIL"

Then, commit it to your local repository and publish it to your GitHub:

git add src/si/__init__.py
git commit -m "Adding my co-authorship to the package"
git push origin main

Note: you can also use the IDE Git tools.

Update you fork with the latest changes from the original repository

Option 1:

• Manually copy the changes from the original repository to your fork.

Option 2:

• You can perform a “Reverse Pull Request” on GitHub. A reverse pull request will follow the same steps as a regular pull request. However, in this case, your fork becomes the base and your colleague’s repo is the head. You can do it directly on GitHub by clicking on the “New pull request” button on your forked repo. Then, you need to change the base fork to your forked repo and the head fork to the original repo. Finally, you need to click on the “Create pull request” button. You can then merge the pull request.

Option 3:

• You can use the command line to update your forked repo with the original repo. First, you need to add the original repo as a remote. Then, you need to pull the original repo into your local repo. Finally, you need to merge the original repo into your forked repo.

git remote add upstream https://github.com/jcapels/si.git
git pull upstream main
git push origin main

Architecture

The package is organized as follows:

si
├── src
│   ├── si
│   │   ├── __init__.py
│   │   ├── data
│   │   │   ├── __init__.py
├── datasets
│   ├── README.md
│   ├── ...
├── scripts
│   ├── README.md
│   ├── ...
├── ... (python package configuration files)

A tour to Python packages:

• The src folder contains the source code of the package. It should contain an intermediate file called si (the name of the package) and the modules of the package. All python packages and subpackages must also contain a file called __init__.py.
• The datasets folder contains the datasets used in the scripts.
• The scripts folder contains the scripts used to test the package and include examples.

Note: It is also common to have a tests folder to include the unit tests of the package. However, we will not cover this topic in this course.

Note: A python package also contains many configuration files (e.g., setup.py, requirements.txt, etc.).

Datasets

All datasets are available at: https://www.dropbox.com/sh/oas4yru2r9n61hk/AADpRunbqES44W49gx9deRN5a?dl=0

Credits

This package is heavily inspired and adapted from:

• https://github.com/vmspereira/si
• https://github.com/cruz-f/si
• https://github.com/jcorreia11/si