Overview¶
This guide will introduce you to Nucleus Hub for accessing the Cell Development Kit (CDK) and collaborating with other Nucleus Developers. If you are looking for information to get started with Developer Notes (DevNotes), please refer to Getting Started Developer Notes
Nucleus Hub Registration¶
Currently, access to Nucleus Hub is available by request. If you are a Nucleus Contributor, you can gain access by following these steps:
Make sure you have a GitHub Account. Take note of your GitHub username.
Send an email to the Nucleus team (build@bnext.bio) asking for access to the Nucleus Hub. Please include your GitHub username. They will invite you through GitHub to join the Nucleus Engineering Hub Access GitHub Team. Please watch your email for the invite.
Once you accepted the invitation, you should be able to go to https://
hub .nucleus .engineering/ and login via your GitHub credentials.
Orientation¶
Upon entering Nucleus Hub you should see the the Nucleus Hub landing page. This section will describe a few key interfaces that are frequently used in common workflows. Since Nucleus Hub builds on JupyterLab, an exhaustive description of the interface can be found in the JupyterLab Docs.
Nucleus Hub landing page.
The file browser allows you to navigate your home directory to which notebooks, scripts, datasets, and other files can be saved.
The Launcher allows you quickly start a new activity such as creating a new template notebook or creating a new Developer Note.
File Browser¶
Nucleus Hub allows you with a home directory that allows you to save files. To learn more about your home directory and your filesystem, please refer to this documentation page from 2i2c. The file browser is the main interface for managing notebooks, scripts, datasets, and other file types. A few directories exist by default:
| Directory | Access | Permissions | Usage |
|---|---|---|---|
devnotes/ | private | read/write | A directory to organize DevNotes. When using the Create button from the Launcher, new DevNotes will appear here. |
projects/ | shared | read/write | A directory to that provides access to files for specific projects. |
sample-data/ | private | read/write | A directory that contains sample data for testing purposes. |
shared/ | shared | read | A shared directory that allows Nucleus Hub admins to make files available to all Hub users. |
work/ | private | read/write | A private directory to collect your individual work. |
Launcher¶
Common Nucleus Hub workflows can be initiated from the Launcher. The button on the Launcher window are organized into the following categories:
| Launcher Category | Function |
|---|---|
| Notebook | Create new blank or template notebooks associated with a specific kernel. |
| Console | Initiate an interactive console session associated with a specific kernel. |
| Other | Miscellaneous tools including the ability to initiate a terminal session. |
| Developer Notes | Tools for working with DevNotes. Some features will require setting API access, see Getting Started: Developer Notes for more details. |
| Nucleus | Links to other Nucleus resources. |
Accessing the Cell Development Kit¶
Nucleus Hub makes it easy to access the CDK to design and analyze experiments. This section will demonstrate a simple workflow for analyzing fluorescence time series data obtained from a microplate reader.
From the Launcher, click the Template button and select
/analysis/platereader_tutorial.ipynb, and click GO.Run the first cell to import the
platereaderlibrary from the CDK.If needed, modify the variables
data_pathandplatemap_pathin the second cell to reference the corresponding files in the/sample-data/directory and run the cell to load the data.Generate basic plots using the function
pr.plot_curves()These plots can then be incorporated into a Developer Note. See Developer Notes for more information.
For a closer look into the workflows supported by the CDK, take a look at the following tutorials:
If you are a newcomer to Python and Jupyter the following links may be helpful: