Accessing the Allen SDK

We could spend all day going through the cells in the website database to find some interesting comparisons. But, it’s much quicker to do these comparisons by accessing the entire database directly, through the Allen Software Development Kit (SDK).

If you’re at UC San Diego, you should run this code on the UCSD Data Hub (Option 2 below). Otherwise, you can run it on Binder, or locally on your computer.

Option 1: From Binder

This is the easiest option (if you’re not at UCSD), though the code itself will run more slowly. Simply click the button below to launch a dashboard containing both notebooks. Once you’re done with the Introductory notebook, open CellTypesNotebook.

Option 2: From the UCSD Data Hub

1. While either on campus or connected via VPN, go to http://datahub.ucsd.edu and log in.

2. You’ll land on a page where you’re asked to choose a container to spawn. Choose the container with your course name.

3. On the Jupyter home page, go to New > Terminal (upper right corner).

4. Type (all in one line): git clone http://www.github.com/ajuavinett/CellTypesLesson.git to clone the necessary codebase into your folder.

5. Close the Terminal window. On the Jupyter dashboard, you should now see a folder CellTypesLesson. Click into it, and open “Introduction to Jupyter Notebooks” From here, you can follow the directions in the Jupyter Notebook.

6. Once you’re done with the introductory notebook, open the CellTypesLesson notebook.

   • Note: When you’re done, go to the Running tab and Shutdown all of your terminal & notebook processes (see orange “Shutdown button”:
     
     

Option 3: From a local computer

If you’d like to access the SDK locally, follow these steps. Note: If you’re in BIPN145, you should do this lab through the Data Hub (Option 1 above).

1. Make sure that you have the Anaconda Python 3.7 distribution installed on your computer.
2. If necessary, install Git on your computer. You can click “Next” through all of the options.
3. If you’re using Windows. Open an Anaconda Prompt window. This will open a new Python terminal. If you’re using a Mac, simply open a Terminal window.
   • Hint: Search for “Anaconda” in Windows and you should see come up as an option. Similarly, you can search for Terminal in Mac.
4. Change directories into your Documents folder by typing cd Documents
5. Make a new folder for your Python notebooks by entering mkdir PythonNotebooks
6. Check that your folder is there with the command dir. You should see PythonNotebooks in the list.
7. Move into your PythonNotebooks folder by using > cd PythonNotebooks
8. Next, we’ll clone the necessary Python notebooks into your Documents directory.
9. Type git clone http://www.github.com/ajuavinett/CellTypesLesson.git to clone the lab codebase into your folder.
10. Next, we need to install the allenSDK tools. Open a new Terminal window (if you’re in Windows, it needs to be an Anaconda terminal window) and type pip install --user allenSDK Note: If you receive an error, try pip install allenSDK
11. After the AllenSDK package has installed, you can open Jupyter Notebook in two ways:
    • In Terminal, type jupyter notebook
    • Open the Anaconda Navigator, and click on Jupyter Notebook.
12. A Jupyter Notebook landing page (the Dashboard) should open.
13. On the dashboard, you should now see a folder CellTypesLesson. Click into it, and open “Introduction to Jupyter Notebooks” From here, you can follow the directions in the Jupyter Notebook.
14. Once you’re done with the introductory notebook, open the CellTypesLesson notebook.