Programming Foundations

1.       Theoretical background on computers and programming (algorithms and algorithmic thinking, libraries, types of programming languages, etc.).

2.       Basic usage of command line, version control software (Git), and an integrated development environment (VS Code).

3.       Troubleshooting/debugging, asking the right questions, and good coding practices.

4.       Effectively using AI in computer programming.

5.       Variables, data types, working with arrays (indexing, slicing, performing mathematical operations, etc.).

6.       Flow control, Boolean logic to combine logical conditions, and loops.

7.       Using functions from libraries and creating own functions.

8.       Reading and writing data files and plotting data.

9.       Using graphical library to draw on computer screen.

10.   Applying acquired programming skills to design and implement Python code that simulates the behavior of biomolecules.

NB1420 is a practical course. For the assessments, one of the two trajectories must be chosen in the first week of the course. The choice made in the first week on the course will be considered a final choice and cannot be changed in later weeks. The exact deadline for making a choice will be communicated during the first lecture. If a student doesn’t communicate a choice, as a default they will be assessed according to trajectory I. We will provide a pre-test on the first day of the course, such that students can make an informed choice.

Overall passing final grade is 5.8. The three assignments and the final project must each have a minimum grade of 5.0 to pass the course.

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Trajectory I "The training schedule": This trajectory helps with the planning of the course and allows the student to get credits for in-class quizzes. Participation in peer feedback is a prerequisite for doing the related assignment. It is designed for those who have no prior experience or do not feel confident with programming.

 In trajectory I, the final grade will be composed of:
- 60 % assignments, each counts 20% of the grade.
- 10 % quizzes
- 30% final project
- mandatory peer feedback
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Trajectory II "Experienced programmer": This trajectory is designed for those who feel confident with programming. Taking part in the peer feedback sessions and quizzes is still recommended but is not obligatory.

 In trajectory II, the final grade will be composed of:
- 70 % assignments, each counts 23.3% of the grade, participating in peer feedback is optional
- 30 % final project
--Quizzes do not contribute to grade

Assignments

There will be 3 graded assignments completed in class.

Students will have one opportunity to redo 1 or 2 assignments in week 2.9 (repair session).

- Students will not be able to repair all three assignments.
- Missing an assignment during class will limit a student’s opportunities for repairing the results on other assignments, since they will need to do the one they missed during the repair session.
- Students must enroll for the repair session via BrightSpace, before week 2.9.
- If a student attempts an assignment more than once, the best grade will be used in final grade calculations.
- Being present at the assignment session (i.e., signing the presence sheet) counts as an attempt.

Peer Feedback

There will be 3 peer feedback moments during the course, scheduled prior to each graded assignment. Completion of peer feedback prior to the related graded assignment is mandatory in trajectory 1. Peer feedback is not graded (i.e., formative assessment).

Quizzes

There will be 7 quizzes, the best 5 will each count for 2 % of the final grade. The quizzes will be offered in class. There are no repair options for quizzes.

Final Project

The final project consists of Python code for a biomolecular simulation. The assessment will consist of an individual oral exam. Students need to enroll for this oral exam via BrightSpace, in week 2.8. One day before the scheduled oral exam, the code of the final exercise must be handed in via student’s GitLab.

Students will have one opportunity to resit the oral exan in week 3.10
The schedule of the quizzes and assignments is posted in Brightspace no later than the first day of class.
- Students can update the code of their project and then redo the oral exam to resit this portion of the course.