KTH course: Applied Programming for Life Sciences III

The second mandatory course from the KTH semester is the Applied Programming in Life Sciences III. This aim of this part of the programming course is to impart knowledge in using Git-hub and managing various shared projects on Git-hub. This course is conducted by Olav Vahtras.

The course consists of 2 main parts , just like previous two parts of APLS (Applied Programming for Life Sciences).

1. Theory

There are 3 theory classes, each class covers one module i.e. Introduction to Git-hub, testing of user built functions, and usage of various scientific libraries.

We explored each of the modules in detail during the lab exercises.

Theory class on function testing

2. Lab exercises

The lab exercises are very detailed and complement the theory courses very well. In the first exercise we created our own Git-hub accounts and learned to move, download and copy folders from local system to the server, as well as the other way round. As a part of the exercise we forked the given directory and cloned it to our local system. Then we completed the incomplete code in the file, added and committed changes to the local system and pushed it to the individual accounts on git-hub and then submitted a pull request to allow the changes in the provided original directory as a user.

Git-hub accounts with different projects

In the second lab exercise we wrote new functions along with new set of codes that can test for the accuracy of the function i.e. if the function does what is expected or if it gives an incorrect output. If the function gives an incorrect output then the testing part of the function will give an error and an indication.

The third lab was an optional lab, were the main idea was to learn to implement various forms of python interface such as Jupyter, Anaconda, etc and usage of scientific libraries.