HMS Laboratory of Systems Pharmacology

Oct 2nd - 3rd, 2019

9:00 am - 4:00 pm

Instructors: Jeremy Muhlich, Patrick Greene

Helpers: Mariya Atanasova, Greg Baker, Changchang Liu

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Armenise 108, 200 Longwood Avenue, Boston, MA 02115. Get directions with OpenStreetMap or Google Maps.

When: Oct 2nd - 3rd, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Important: Pre-workshop laptop setup is required!

To save time at the workshop, it is required to pre-install all necessary software on your laptop at the LSP Computational Forum. Simply drop in any Thursday at 11:30 in Warren Alpert 436. If you are unable to attend the forum, contact Jeremy Muhlich immediately to make alternate arrangements.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email jeremy_muhlich@hms.harvard.edu for more information.

Schedule

Day 1

09:00 Automating tasks with the Unix shell
10:30 Coffee
12:00 Lunch break
13:00 Building programs with Python
14:30 Coffee
16:00 Wrap-up
16:30 END

Day 2

09:00 Building programs with Python (cont.)
10:30 Coffee
12:00 Lunch break
13:00 Data analysis and visualization in Python
14:30 Coffee
16:00 Wrap-up
16:30 END

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Syllabus

The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things

Programming in Python

  • Variables and assignment
  • Data types
  • Built-in functions and documentation
  • Using libraries
  • Loading and plotting tabular data
  • Lists
  • For loops and conditionals
  • Writing your own functions
  • Understanding variable scope
  • Programming style

Data analysis and visualization in Python

  • Indexing, slicing and subsetting tabular data using DataFrames
  • Managing data of different types (numbers, strings, etc.)
  • Combining DataFrames
  • Visualizing data in DataFrames

Setup

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. Select "Use the nano editor by default" and click on "Next".
    3. Keep "Git from the command line and also from 3rd-party software" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Select "Use the native Windows Secure Channel library", and click "Next".
    6. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    7. Select "Use Windows' default console window" and click on "Next".
    8. Leave all three items selected, and click on "Next".
    9. Do not select the experimental option. Click "Install".
    10. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press Enter)
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press Enter, you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing Enter

This will provide you with both Git and Bash in the Git Bash program.

The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on Mac OS X and Linux is usually set to Vim, which, although very powerful, is not the most intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+q+! (colon, lower-case 'q', exclamation mark), then hit Return to return to the shell.

atom is a free, high-quality code editor and the default that instructors use in the workshop. Once you have installed atom (see below) you should be able to, from the shell, enter atom newfile.txt to start editing a file.

To install atom, go here and select the options for Windows installation. Follow all instructions, selecting defaults where there are choices.

Some other editors that you can use are Notepad++ or Sublime Text.

To install atom, go here and select the options for Mac installation. Follow all instructions, selecting defaults where there are choices.

Some other editors that you can use are Text Wrangler or Sublime Text.

To install atom, go here and select the options for your Linux (.deb for Ubuntu or similar, .rpm for Fedora or similar) installation. Follow all instructions, selecting defaults where there are choices.

Other editors that you can use are Gedit, Kate or Sublime Text.

Python

Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.7 is fine). Do not install version 2.7.

  1. Open https://www.anaconda.com/download/#linux with your web browser.
  2. Download the Python 3 installer for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window.
  4. Type 
    bash Anaconda3-
    and then press Tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with: 
    cd Downloads
    Then, try again.
  5. Press Return. You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.