Applied Python Programming for Biomedical Sciences

ECTS

7,5 ECTS

Type of assessment

Written assignment

Type of assessment details

The exam is an individual project where the student in collaboration with the supervisor chooses a subject and the data to analyze. The end result consists of three parts:
1: The code developed during the project in the form of a Jupyter notebook, one or more scripts or libraries.
2: A report describing the projects (pdf format).
3: Any input files necessary to run the code, which have not been provided by the supervisor.

The code can be written either as one or more terminal scripts, or as a Jupyter notebook.
If the project is written as a terminal script the code must be in one or more `.py` files, and it you must use `argparse` to parse the commandline.
If the project is written as a Jupyter notebook then the notebook should focus on presentation of analysis and the results, the code should be mostly imported from one or more `.py` files. The Jupyter notebook must import at least one `.py` file written.

It is important that the Python code can run, is free of significant errors, and that all functions have docstrings. Nontrivial code lines should be commented.

The report (max 10 pages) should have the following sections:
1: Introduction. A brief background and motivation to the problem addressed
2: Documentation. A guide to the user. Here it should be documented how the code/Jupyter notebook is to be used. All options should be documented. What is the purpose of the option and what kind of value is expected (type and range) if any. All input files and their formats should be documented, and the expected output should be described.
3: Code architecture. Explain the overall structure of the program. Explain the flow of data through the program. How is the input data parsed? How is the data stored in the code. What are the main elements of the code, like classes and functions.
4: Reflections. What are your thoughts about the code. What important design decisions did you make while writing the code? Are there any problems with the current code? How could the code be improved if you had more time?
5: References. If you copied more than one or two lines of code from any source, it should be documented. For websites include the data and time of access. If Large Language Models are used then include name of the model, version, and the promts used must be included.

It is allowed to use Large Language Models, LLMs, (like ChatGPT) or similar methods to write small parts of the code for the exam project. The sections of the code where these methods have been used to write all or parts of the code must be clearly marked. It is the student’s responsibility that the code is not plagiarized and does not violate any copyrights.

It is not allowed to use Large Language Models or similar methods to write any part of the report.

Aid

All aids allowed except Generative AI

GAI is not allowed at the exam.

Marking scale

passed/not passed

Censorship form

No external censorship

More than one internal examiner

Criteria for exam assessment