Overview

Welcome to the webpage for the 2018 Computing for Medicine workshops.

Contents

Course Staff

Installation

Installation involves installing Python 3, setting up your local environment and testing that it works. The following steps walk you through this.

Install Python

MacOS / Linux

First, open your terminal.

On MacOS, you can do this by going to Applications/Utilities/Terminal or, using Spotlight by pressing the command + space keys, and searching for “Terminal”).

Copy & paste the following into your terminal and press the return key:

MacOS

curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh --output ~/miniconda.sh

Linux

curl https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh --output ~/miniconda.sh

Once this has finished, copy & paste the following and hit the return key:

bash ~/miniconda.sh

Agree to the terms of service.

Press return, space, and then return keys.

Hit return when you are asked to accept the default install location.

Enter “yes” when prompted by “Do you wish the installer to prepend the Miniconda3 install location to PATH in your ~/.bashrc?”

Windows

Download the installer from here.

If you are running a 32-bit version of Windows, download the installer from here. If you don’t know, you can check which version you are running here.

Double click the .exe file to start the installation. Accept the terms of service, and leave all the default values when installing.

Setup your environment

We need to create a virtual environment and install jupyter. Note, you only have to do this ONCE!

The instructions here are almost identical for MacOS / Linux and Windows.

First, lets create an environment called C4M

conda create -n C4M python=3.6

When conda asks you to proceed, type y

proceed ([y]/n)? y

Activate this environment that you just created with

source activate C4M

Then copy & paste the following to install jupyter

conda install -c conda-forge jupyterlab

Answer y if prompted. This might take a little bit.

And finally, run

conda install nb_conda

Again, answer y if prompted.

Using the jupyter notebooks

Everything in this class will happen through the jupyter notebooks. Notebooks are somewhere we can mix code and english, and run the code right in our browsers. Every time you wish to open a notebook, you need to

First, activate your environment

MacOS / Linux

source activate C4M
(C4M) # you should notice your command prompt change when the environment is active!

Windows

conda activate C4M
(C4M)

Then, run jupyter

(C4M) jupyter lab

This will open a page in your browser. Click Python [default] in the top right corner and select Python [conda env:C4M].

To make sure everything is working, use this window to find hello_world.ipynb on your computer and follow the instructions in the notebook to make sure you installed everything correctly.

You can download the hello_world.ipynb notebook from here.

Schedule

Phase 1 (Fall 2018)

Level 1

Sessions Date Time Location Resources Homework
Session 1 Wednesday September 19, 2018 9:30 – 12:30 pm MS 3281
Session 2 Wednesday October 3, 2018 9:30 – 12:30 pm MS 3287 Phase I: Level 1 Session 2 Homework on PCRS
Due date: Oct. 18, 2018, 11:59 p.m
Session 3 Wednesday October 17, 2018 1:00 – 4:00pm DSC Innovation Lab, Gerstein Library Phase I: Level 1 Session 3 Homework on PCRS
Due date: Nov. 22, 2018, 11:59 p.m
Session 4 Wednesday November 21, 2018 1:00 – 4:00pm MS 3281 Phase I: Level 1 Session 4 In Class Assignment on PCRS
Due date: Dec. 7, 2018, 11:59 p.m
Homework Help Session Tuesday December 18, 2018 4:00 – 6:00pm MS 3281
Homework Help Session Wednesday December 19, 2018 9:30 – 12:30pm MS 3281

Level 2

Sessions Date Time Location Resources Homework
Session 1 Wednesday October 17, 2018 1:00 – 4:00pm | DSC Innovation Lab, Gerstein Library PRE-WORK FOR LEVEL 2 STUDENTS: MATERIAL COVERED: Phase I: Level 2 Session 1 Homework on PCRS
Due date: Nov. 22, 2018, 11:59 p.m
Session 2 Wednesday November 21, 2018 1:00 – 4:00pm | MS 3281 Phase I: Level 2 Session 2 Homework on PCRS
Due date: Dec. 20, 2018, 11:59 p.m
Session 3 Wednesday December 19, 2018 9:30 – 12:30 pm MS 3281
  • Python Memory Model [html]
Phase I: Level 2 Session 3 Homework on PCRS
Due date: Dec. 27, 2018, 11:59 p.m
Homework Help Session Tuesday December 18, 2018 4:00 – 6:00pm MS 3281
Homework Help Session Wednesday December 19, 2018 9:30 – 12:30pm MS 3281

Phase 2 (Winter 2019)

Sessions Date Time Location Resources Homework
Session 1 Wednesday January 23, 2019 1:00 – 4:00 pm MS 3281
  • Project 1 preparation exercises
  • Session 2 Wednesday February 27, 2019 1:00 – 4:00 pm MS 3281
    Session 3 Wednesday March 20, 2019 1:00 – 4:00 pm MS 3281 Work on projects.
    Session 4 Wednesday March 27, 2019 1:00 – 4:00 pm MS 3281 Project 2
    Session 5 Wednesday April 3, 2019 1:00 – 4:00 pm MS 3281 Work on projects.
    Session 6 Wednesday April 17, 2019 1:00 – 4:00 pm DSC Innovation Lab, Gerstein Library Work on projects.

    Phase 3 (Fall 2018 - Winter 2019)

    Sessions Speaker Date Time Location Resources
    Session 1 Fanny Chevalier Tuesday, October 9, 2018 4:00 – 6:00 pm DSC Innovation Lab, Gerstein Library
    Session 2 Jared Simpson Tuesday, October 16, 2018 4:00 – 6:00 pm DSC Innovation Lab, Gerstein Library
    Session 3 Frank Rudzicz Tuesday, November 20, 2018 4:00 – 6:00 pm DSC Innovation Lab, Gerstein Library
    Homework Help Session Tuesday December 18, 2018 4:00 – 6:00pm MS 3281
    Homework Help Session Wednesday December 19, 2018 9:30 – 12:30pm MS 3281
    Session 4 Chris J. McIntosh Tuesday, February 12, 2019 4:00 – 6:00 pm DSC Innovation Lab, Gerstein Library
    Session 5 Michael Brudno Tuesday, March 26, 2019 4:00 – 6:00 pm DSC Innovation Lab, Gerstein Library
    Session 6 Marzyeh Ghassemi Tuesday, April 9, 2019 4:00 – 6:00 pm DSC Innovation Lab, Gerstein Library