Computing Basics
While using the Jupyter Notebooks in this lesson, you’ll encounter quite a few different tools for computing. Here are a few useful things to know.
Software Development Kits
In these Jupyter Notebooks, we’re interacting with the Allen Institute’s Software Development Kit (SDK). SDKs provide a set of tools, libraries, documentation, code samples, processes, and or guides that allow developers to create software applications. The AllenSDK is really useful because it enables us to interact with their raw data as well as any computed metrics they’ve already computed and saved.
Python
Python is a coding language that is widely used in research, data science, and more. You might use Python in a "distribution" such as Anaconda. Distributions such as this are useful because they contain various tools to help you code as well as many pre-installed coding packages. You might also encounter Python within a Jupyter Notebook, or directly in the Terminal of your computer.
Jupyter Notebooks
Jupyter Notebooks are great ways to collaborate on coding projects and learn how to code. Usefully, they contain both markdown (helpful text describing what is happening in the notebook) and blocks of code. Jupyter Notebooks can be used with multiple coding languages.
If you’ve never used a Jupyter Notebook before, I’d recommend starting with the Introduction to Jupyter Notebooks, otherwise, feel free to move on to the Cell Types Notebook.
There is a full tutorial on how to use Jupyter Notebooks here.
Cell Types Lesson Roadmap
Understand how the data was collected.
Access the Allen Cell Types Database on their website. In this part, you can use the web interface to look at raw electrophysiology recordings and biocytin fills from mouse and human cells.
Learn about the basics of coding & using Jupyter notebooks. If you'd like to learn a bit of Python, this is a great chance to do so!
Analyze data through the Allen Software Development Kit (SDK)