Nucleus Hub Guide

Overview
Nucleus Hub Registration
Orientation
Accessing the Cell Development Kit
Collaboration options

Overview

This guide will introduce you to Nucleus Hub for accessing the Cell Development Kit (CDK) and collaborating with other Nucleus Developers.

Nucleus Hub Registration

Currently, access to Nucleus Hub is available by request to build@bnext.bio.

Navigate to hub.nucleus.engineering.

Follow the prompts to make an account.

After clicking Create User , send an email to build@bnext.bio to approve the account.

Orientation

Upon entering Nucleus Hub you should the following screen.

File directory.
Launcher window.
Make a new empty Jupyter Notebook.
Make a new template Jupyter Notebook.
Preview a Developer Note.
Open a terminal window.
View a draft of a Developer Note.

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.

Open the /sample-data/ directory.

Click the Template icon, select /analysis/platereader.ipynb, and click GO.

Run the first cell to import the platereader library from the CDK.

Modify the variables data_path and platemap_path in 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 Note Guide for more information.

If you are a newcomer to Python and Jupyter the following links may be helpful:

Beginner Python tutorial [link].
Introduction to the Pandas library [link].
Introduction to JupyterLab and Jupyter Notebooks [link].

Collaboration options

Currently, Nucleus Hub supports two options for collaborating with other developers:

Option 1: share your entire workspace by generating a shared link. Any existing Nucleus Hub user will be able to read and write to documents in your workspace.

Click to the Generate a Shared Link icon at the top right corner of the workspace.

Option 2: create a collaborative workspace. This will create a special workspace to which a select group of authorized users will have read and write access to documents within that workspace. This option allows users to ensure that their personal workspace remains private.

Request a collaborative workspace by reaching out to build@bnext.bio.