WIS Python programming course started in 2025.03

Course number: 20253072

• Direct link to course information

• Feinberg Moodle

• Location: Feinberg Room B

Students

Home page	Repo	Assignments	Project	Status
Aaron Finn	repo	repo
Abraham Zucker	repo	repo	Time evolution of deterministic card games
Amit Paz	repo	repo	Analysis of Visium HD: Combining Gene Expression and Morphological Features (private)
Anastasia Paz	repo	repo
Anat Ben-Yaacov	repo	repo
Andrei Sarenko	repo	repo	Root & Shoot Colour & Morphology Analysis Across Plant Genotypes
Aviel Rosenbaum	repo	repo	Predicting-Immunotherapy-Response-from-Tumor-Mycobiome-Composition
Beatrice Mereshensky	repo	repo
Benel Levy	repo	repo	Recipe Recommender – Smart Cooking From Your Fridge
Chen Bibi	repo	repo	Amplicon_analysis_for_SNP_detection
Chen Weller	repo	repo	Codon-Based Frameshift Translator
Coral Shalmoni	repo	repo	Genetic Art Generator
Dana Brosh	repo	repo	DNA-to-protein
Elizabeth Popov	repo	repo	Oligo-Barcode-Profiler
Emmanuel Amzallag	repo	repo	Determining aggregation propensity from proteomics data
Gal Hermelin	repo	repo	Baby Feeding Correlation Analyzer
Gaya Granot	repo	repo	Base Editor Design Assistant
Giulia Carradori	repo	repo	TissueGraph: Spatial Graphs for Tissue Microenvironments
Inbal Naveh	repo	repo	Diamond-polishing-directions-analyzer
Karen Waskewitz	repo	repo	Analyzing-Interview-Transcripts
Kedar Waychal	repo	repo	optogenetic-data-analysis
Lee Halevi	repo	repo	Codon Usage Analyzer and Optimizer
Maya Salomon	repo	repo	Movie-scan-correlation-viewer
Maya Skolozub	repo	repo	Automatic DMI Experiment Report
Michal Zamberg Elad	repo	repo	Neural Activity To Behavior
Noam Weil	repo	repo	Extract Scientific Article Text from PDFs
Paramita Manna	repo	repo
Priel Siman-Tov	repo	repo	Gibson Assembly Assistant
Ruthie Surujon	repo	repo	Image Reconstruction From Hdf
Sagi Maor	repo	repo	Particle-by-Particle Aerosol Analysis
Shani Rochell	repo	repo
Sophie Piwko	repo	repo	Preprocessing of Proteomic Data
Sun Terletsky	repo	repo	Trajectory Visualization for Virtual‑Arena Experiments
Uri Monsonego	repo	repo
Yotam Yaniv	repo	repo	Gene Interactions and Machinary
Yovel Edri	repo	repo

Lecturer

• Gábor Szabó

Teaching Assistants

• Hadar Klimovski
• Liron Hoffman

Plan

SYLLABUS

Schedule

• Day 1 2025.03.27 9:00-12:00
• Day 2 2025.04.03 9:00-12:00
• Day 3 2025.04.10 9:00-12:00
• Passover
• 2025.04.24 9:00-12:00 cancelled
• Independence day
• Day 4 2025.05.08 9:00-12:00
• Day 5 2025.05.15 9:00-12:00
• Day 6 2025.05.22 9:00-12:00
• Day 7 2025.05.29 9:00-12:00
• Day 8 2025.06.05 9:00-12:00
• Day 9 2025.06.12 9:00-12:00
• Day 10 2025.06.26 9:00-12:00

Assignments

There will be assignments after every lecture. You will submit them via GitHub. I'll explain the details during the lectures.

Extensions

Each assignment and the project will have dead-lines. If you need to ask for extensions, do it up-front asking your TA. Make their life easier and ask specify the new dead-line you need.

Project

Towards the end of the course you'll be asked to do a project. First you will need to submit a proposal for the project and when it is accepted then implement it. The project should be something that is useful for your studies or at least it is fun for you to make. Ask in the lab where you work what needs are there that you might implement as your final project. You can get inspiration from the projects listed here and the projects of the 2023 autumn semester or those of 2024 spring semester and 2024 autumn semester.

The idea of the project is that you write something that is going to be useful for you beyond the course. e.g. There is some manual work in your lab and this project will automate it. It can be also a tool to help you with your research. etc. It can also be useful in your private life. e.g. we had projects trying to register for visa applications at the USA embasy and we also had games.

You can even take an existing project and make some valuable improvements to that project. (e.g. one project from one of the previous courses).

How to submit your proposal?

• Create a separate repository for the project. Its name should reflect the project: (e.g. Gene-Amplification-and-SNP-Analysis) and not the the course. If someone looks at this repository they should see it as a real application and not "some stuff you wrote just to get the grade".

• The proposal should be the README.md file of the repository. If you need to include images or data files, those should be also included in the repository. It should be a description that will help any future visitor of the project to understand

1. What does this project do?
2. What kind of input data it expects and what kind out output the user might expect?
3. The technicalities: How to download it, install the dependencies, run the tests, and run the project?

It would be nice if at the end of the README you mention that this was written as part of the course and link to the course repository.

We understand that the project and thus the description might evolve during the implementation. That's fine. You can update the README with the new information. In the proposal we would like to see your understanding of the project before you start implementing it.

Before you submit it for approval it is recommended that you send it to another student and ask if the description is clear. If that student has any questions then you probably will need to update the README to answer those questions so the next person won't need to ask.

Once you are ready, open an issue on our repository linking to you project to get it approved.

Once the project is approved you will implement it in the same repository. Open a new issue when you'd like the project to be graded.

Expected workload

In addition to the lectures you will spend about 2-4 hours / week on the assignments and 20-40 hours on the project.

The actual time spent will greatly depend on your previous experience with programming in general and Python in particular.

The time you spend on the project will also depend on the availability of the data you work on. If you pick a project that you would want to do anyway then this is basically time you would spend anyway.

Grades

• Each assignment counts as 5% (we will have 10 of them).

• The project proposal is 15%.

• The project is 35%.

• The project is a requirement. Without that you won't get a passing grade.

Slides

During the course I'll use some of the slides that can be found here. These slides are publicly available and will remain on the web site after the course is over.

Videos in English

There are recording of this course from 3 years ago.

There are also recordings from the 2023 autumn semester.

There are also recordings from the 2024 spring semester.

You can watch those, but be also warned, this semester the order of the material will be different.

There are many more videos in my English-language YouTube channel. You are invited to check them out and to follow the channel.

Videos in Hebrew

Some of the material is also available in Hebrew. You can find them on my website and in my Hebrew-language YouTube channel. You are invited to follow that channel as well.

Language

The default teaching language of WIS and of this course is English.

In writing please stick to English.

If and when we have one-on-one conversions I'd be happy to speak in Hebrew, Hungarian, Spanish, or Ladino as well.

Bring your own computer!

You are expected to bring your own computer to the lectures.

Installations

There is no need to install anything up front. We'll do that during the lectures.

Videos

Login to Moodle and you should be able to see the video recordings on the right hand side.

Day 1

• Self introduction
• Overview of the course
• Programming
  • The language: Python
  • 3rd party libraries on PyPI e.g. Biopython.
  • On GitHub
• Version control
• GitHub
• GitHub pages

Assignment (day 1)

• Watch

• Create web site for yourself using GitHub pages. Remember to use the repository name USERNAME.github.io. Get ideas from the pages of the students in the previus courses.

• Watch the 2nd video.

• Create a separate public repository for all the assignments of the course. (e.g. call it python-course-assignments)

  • Create a folder called day01
  • In the folder create a program that will print "Hello World!"

Once they are ready open an issue on the GitHub repository of the course. The title of the issue should contain your full name and name of the assignment e.g. "Day1 by Foo Bar", in case your name is Foo Bar. In the issue include the link to the site, the link to the repository of the site, and the link to the repository of the assignment.

Dead-line: April 1, 23:00 April 3, 23:00

Day 2

• Biopython project, issues.

• Computer architecture (memory vs hard-disk), filesystem

• Continue the First Steps chapter (till Floating point limitations)

• Someone should have mentioned in class that I mistakenly let co-pilot write weight instead of width and that's why it wanted to compute my BMI intead of the area of the rectangle.

Assignment (day 2)

• In the repository of your assignments create a folder called day02 and put your solutions in that folder.

• Write a program called circle.py that will ask the user for the radius of the circle and will print the area and the circumeference of the circle.

• Write a program called rectangle.py that will ask the user for height and width and calculate the area and the perimeter of the rectangle.

• You will have to use the int() or the float() function to convert tha data you received from the user to an int or float in your program.

• Once you are done, open an issue on our repository in whch the subject includes your full name and the number of the assignment so the TAs will be able to handle it. Include a link to the repository of your assignments.

Dead-line: April 8, 23:00

Day 3

Covered chapters

• End of "First steps"
• "Second steps"
• Numbers

Assignment (day 3)

Task 1

• Open issues on the repository of the web site of 2 students. In order to make sure every student receives issues, first open for student who do not yet have issues or only have 1 issue opened. In the issue write down what you like and what improvement you'd like to see. Mention the TAs and my by including our GitHub user ideas with an @ mark. E.g. @szabgab will notify me about the issue.
• When you receive an issue, comment on it. Decide if you'd like to implement the suggestions and one you implemented it or if you decide you don't want to do that, close the issue.
• The goal here is to have some experience with GitHub issues and to improve your web sites.
• I recommend you collaborate with each other. Feel free to pick a random student and ask her/him to work on this together in-person or via a zoom session.

Task 2

In a folder called day03

• Level 0 of the number guessing game

Task 3

• Copy the circle.py and rectangle.py from day02 to day03 and change both of them to get the values one the command line (using sys.argv) intead of waiting for input.

Dead-line: April 23, 21:00

Day 4

Covered chapters

• Comparison and Boolean
• Strings
• Loops

Assignment (day 4)

• Number guessing game

Dead-line: May 15, 21:00

Day 5

Covered chapters

• Formatted strings
• Lists
• Tuples

Assignment (day 5)

• dna sequences
• Count digits
• Count words

Dead-line: May 22, 21:00

Day 6

Covered chapters

• Files
• YAML
• JSON
• beginning of the Biopython chapter

Assignment (day 6)

• ROT13 of a file
• Count digits
• Color selector

Dead-line: June 4, 21:00

Day 7

Covered chapters

• Dictionaries
• Sets
• Code-reuse
• Functions

Assignment (day 7)

• count words from a file
• Count Amino Acids
• Refactor previous solutions to use functions

Dead-line: June 8, 21:00

Day 8

Covered chapters

• Modules
• Regular Expressions part 1 and 2

Assignment (day 8)

• Take one of your solutions to one of the earlier assignments. Split up the code into functions. Move the functions to a module. Submit the new script and the module.
• parse hours log file and create report

Dead-line: June 15, 21:00

Day 9

Covered chapters

• Regular Expressions part 3
• math, sys, os, pathlib, shutil, time, datetime, subprocess, argparse
• Testing Demo
• A few words about classical machine learning.

Assignment (day 9)

• Take one your earler solutions. Convert the code into functions and move the functions to a separate module.
• Write documentation for the non-I/O functions with examples and run doctest.
• Write tests using assert and use pytest to run the tests.

Dead-line: June 22, 21:00

Project

For detailed desciption see above.

Project proposal dead-line: June 12, 21:00

Project submission dead-line: July 3, 21:00