Programming Course: Python (MSc Bioinformatics)

Dear all,

the points for the project part 2 are available and you can find the feedback as your submission for Project part 2 feedback.

The possible points are

• 0 (part 2 failed)
• 0.5 (minor mistakes, in most cases missing red crosses that should indicate which region was used to estimate the slope)
• 1 (your slope estimate was correct for the 12 samples)

If you got 0.5 points you don't need to modify your code in estimate_afm.py, but the problem should be solved for part 3. In some submission the --show option did not work as expected, but since this does not effect part 3, it is not mandatory to fix this issue.

If you got 1 points, this means that your method worked on the provided samples. However, since the complete data is more complex and noisy, it might not work on all samples, in which case you also need to revisist your code.

Here are some more general remarks that are also important for part 3:

• The slope estimation should be independent of the plotting part, in particular for computing the heatmap don't create/store all lineplots.
• The estimate should be based on the lower part of the linear region, many of you used a sliding window approach to find the most linear region. This worked for the provided samples, but might not work on all samples, e.g., the sample given in the slides for part 3.

Regarding assignment 06, please use the most recent tests, since there was a mistake in the first version.

Dear all,

part 3 of the project is now online. For simplicity, you can download preprocessed measurement series as a pickled Python dict. A partial program (that loads the data) is also available. Please read the slides with the task. Writing the streamlit app (a basic version) should be simple, so please spend your time on robustifying your slope estimation. It should work at least for all 128 * 128  series-0 measurements. Good luck! (Deadline is in 2 weeks from today.)

Unfortunately, part 3 of the project turned out to be more difficult than we anticipated, and until we have reduced its complexity, it will be delayed. We hope to publish. the task tomorrow (Thursday). You will have the full 2 weeks to work on it. We apologize and suggest you work on the other assignments in the meantime.

Dear all,

the results and feedback for project part 1 are now online in the CMS. The feedback is visible in the submission section (the message You did not submit in time. The submission is closed. is the same for everyone).

These are the possible points:

- 1 point: you passed part 1 and everything was fine, except some minor things like plot titles, empty legends, etc.

- 0.5 points: you passed but there are major revisions required so that you will be able to pass part 2, e.g., some missing plots, etc.. Please solve these problems directly in the new file estimate_afm.py

- 0 points: you failed, because you either did not submit on time, the code did not work or you plagiarized

If you got zero points, this means that you failed the project and cannot qualify for the exam anymore.

We also ran plagiarism checks for the project and the old assignemnts and you can see on your personal status page if you passed the plagiarism tests or not.

Remeber that it is not allowed to copy solutions from other students, ChatGPT or other internet sources.

If you have any further questions, please come to the tutorials.

Hello everyone, here are a couple of important bits of information!

1. Please be sure to submit project parts ONLY via your git fork by commiting and pushing. We will automatically download and test your code on the sample.txt file. If it doesn't work (or we cannot get your code automatically), you have a problem. Please follow the instructions very carefully (and read the last news, too).

2. Today, part 2 of the project is released. Please continue from your old codebase and implement the new funcitonality. Please COPY the final part1 file into `estimate_afm.py` and ONLY work on that for part 2. Remember: We will auto-download `plotafm.py` to test it, so it should always be in working condition. Do not modify your part 1 solution further. 

3. One of you pointed out that numpy 2.0 was just released (after many years of development). Please DO NOT yet switch to numpy 2.0 but continue with the 1.26 branch. There may be some early bugs and incompatibilities, and we may run into problems when testing code (with our version 1.26) that was developmed for 2.0; so please do not update numpy.

4. As usual, there is also a new weekly quiz (on numba).

Happy coding!

Dear all,

the deadline for assignment 4 and project part 1 is tomorrow.

For the assignment, the submission is as usual in the CMS. The submission for the project is in your git repository.

Please follow the instructions in the project description and create in git a new folder project-afm/ and push the two files sample.txt and plotafm.py (with your changes) to this directory (and not project_01 with the partial file).

 

Tomorrow (Wednesday), a new assignment AND part 1 of the programming project will go online (at 6am). Please be sure to read both and submit both on time. The programming project will consist of several parts; in the end, the whole application must work and produce reasonable results. Part 1 is relatively easy: parsing the actual data from a text file and plotting it. Data and a stub Python file are provided as well.

The written exam for the Python Course takes place on Tuesday 30.07.2024, 09:00 - 12:00.

This is an ungraded exam (pass/fail only), but since in the future, the course will be graded (new study regulation), you may optionally apply for a graded exam IF you plan to switch to the new regulations.

The re-exam takes place on Tuesday 08.10.2024, 09:00 - 12:00.

The rooms are yet to be determined, probably E2.1, 0.01.

Dear all, the points for assignment 02 are now entered in the CMS. Here are some general remarks for all assignments:

- Only submit your function implementations and do not include function calls. If you include function calls with local files we cannot run your code.

- Your submission must be self-contained. All functions that you need must be implement in the file. For example, imports from old assignments do not work.

- If not stated otherwise, all tasks should be solvable in a few seconds with a naive approach. We therefore timeout the tests if your code takes very long (after around 30s per test).

For assignment 03, there was an update to one of the test, so please update your fork again.

Good morning,

please make sure your code runs from the terminal. IDEs sometimes change your code or run it under conditions that aren't reproducible when do automated tests. Your code must run in the terminal with pytest and pass the tests. You can and should try it out. Also, if you have not read the Missing Semester info or done the git/bash/shell tutorials, etc., you'll have problems in the future.

 

Dear all,

we decided to change the passing status of assignment 00. You can find your passing status at your personal status page.

Now everyone passed who submitted a "reasonable" solution for task 2 in the CMS and correctly adjusted the README.  The assignment was supposed to be very easy with simple print statements, you shouldn't have added any additional spaces, tabs, typos or require user input in your code.

For the following assignments, we will only grade your assignments based on our automatic tests, so you will get no points if you do not conform with the specified format that you can test yourself with the provided example tests. 

Dear all,

the second quiz and the next programming assignment is now available in the CMS. Due to some problems with the CMS, the quiz was not available this morning, so everyone who did the quiz before 11:50 has to redo the quiz.

For the programming assignment, we added a template file and tests to the git repository. For more information about testing in python, extra slides are now available in the tutorials section.

Dear all,

you can start the doing the first quiz online at your personal status page, you have time to complete it until Friday, 19.04. 23:59. In addition, the mandatory assignment 00 is online, you can find it in the Materials section. Please note, that the final submission of the programming assignments (.py file only) is via the CMS, but you should still work on the assignment in your forked git repository. You will need the git repository mainly for the two programming projects.

We also added a link to the MIT missing semester if you are unfamiliar with git, shell or other basics that we highly recommend you work through this week.