C4M: Computing for Medicine Summer Exercises and Assignments

Overview

The Summer phase consists of two projects. Each project is supported by a series of three exercises. We encourage you to work in pairs when working on the projects. The exercises are to be submitted individually. You are encouraged to start working on the projects as soon as possible. Doing the exercises should help with working on the projects.

Course resources

• Ask questions on Piazza (sign up here).
• Submit assignments on MarkUs

Project 1: Medical Document Retrieval using TF-IDF

• Exercise 1 on PCRS (More on CSV files: video, med_nobel.py. The first ~7 minutes should explain the Anonymizing your Data exercise.) (due: Jun. 7 at 11PM)
• Exercise 2 Part 1: on PCRS; Part 2: handout, submit on MarkUs. (Video tutorial on writing to text and CSV files) (both due: Jun. 10)
• Exercise 3 Part 1: on PCRS; Part 2: handout, tester.py and sym_data1.txt. Submit on MarkUs. (both due: Jun. 17)
• Project: Handout, Starter code, wikipages.zip, Some basic tests (tester.py)

Project 2: Human Mobility and Epidemic Modelling

Project: Project description, cities.txt.

Starter code:

• dijkstra_starter.py
• simulation_starter.py
• e5_tester.py

Video tutorials —watch while reading the handout:

• Representing Travel Distances in Graphs — useful for understanding the description of Part 1
• Dijkstra's Algorithm — explains the core algorithm in Part 1/Exercise 5
• Simulation Intro; Implementing a Simulation with Python (code) — useful for Part 2

Project timeline

• Read the project description straight away to understand the exercises.
• Exercise 4: submit by Jul. 8, on PCRS
• Exercise 5: submit by Jul. 15 on PCRS and MarkUs (please remember to submit the output of e5_tester.py)
• Exercise 6: submit by Jul. 22 on PCRS
• Put together your earlier submissions and complete the simulation part of the project, and submit everything on MarkUs by Jul. 29.

Extra Session Materials

• bugs_pressure.py, xmart.csv

Submitting your work on MarkUs

The projects (and parts of some of the exrcises) will be submitted on MarkUs using the MarkUs system. You can log in to MarkUs using your UTORid.

To submit as a group, one of you needs to "invite" the other to be partners, and then the other student needs to accept the invitation. To invite a partner, navigate to the appropriate Assignment page, find "Group Information", and click on "Invite". You will be prompted for the other student's CDF user name; enter it. To accept an invitation, find "Group Information" on the Assignment page, find the invitation listed there, and click on "Join". Only one student must invite the other: if both students send an invitation, then neither of you will be able to accept the other's invitation. So make sure to agree beforehand on who will send the invitation!

To submit your work, navigate to the appropriate Assignment page, then click on the "Submissions" tab near the top. Click "Add a New File" and either type a file name or use the "Browse" button to choose one. Then click "Submit". You can submit a new version of any file at any time (though the lateness penalty applies if you submit after the deadline) — look in the "Replace" column. For the purposes of determining the lateness penalty, the submission time is considered to be the time of your latest submission.

Once you have submitted, click on the file's name to check that you have submitted the correct version.