Mar 27-28, 2019
9:00 am - 4:30 pm Wed; 9:00 am - 12:30 pm Thu
Instructors: Sue McClatchy, Georgi Kolishovski
Helpers: Mandy Chen, Duy Pham
This workshop is open to those from neighboring institutions.
Where: The Jackson Laboratory, Breezeway Bioinformatics Training Room 1540, building 1, unit 5, 600 Main Street, Bar Harbor, Maine. Get directions with OpenStreetMap or Google Maps.
When: Mar 27-28, 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.). They should have a few specific software packages installed (listed below). They are also required to abide by Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers 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 susan.mcclatchy@jax.org for more information.
| 09:00 | Workshop Overview |
| 09:30 | Running and Quitting |
| 09:45 | Variables and Assignment |
| 10:05 | Data Types and Type Conversion |
| 10:30 | Coffee |
| 10:45 | Built-in Functions and Help |
| 11:15 | Libraries |
| 12:05 | Reading Tabular Data into DataFrames |
| 12:30 | Lunch break |
| 13:30 | Pandas DataFrames |
| 14:15 | Plotting |
| 15:00 | Coffee |
| 15:15 | Lists |
| 15:45 | For Loops |
| 16:15 | Wrap-up |
| 09:00 | Looping Over Data Sets |
| 09:30 | Writing Functions |
| 10:30 | Coffee |
| 10:45 | Variable Scope |
| 11:15 | Conditionals |
| 11:45 | Programming Style |
| 12:15 | Wrap-up |
| 12:30 | End |
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
To participate in a 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.
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., 3.6 is fine).
We will teach Python using the Jupyter notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).
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 DownloadsThen, try again.
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).