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Notebooks

Notebooks are versatile canvases for capturing and organizing multiple types of content. The notebook canvas is equipped with a rich text editor that enables you to input and style text and headings. Additionally, you can incorporate several types of advanced blocks within your notebooks. This includes tables, images, videos, audio, file attachments, embedded databases, and even executable code and its results.

Example use cases​

Notebooks are suitable for a wide range of use cases, such as:

  1. Experimental protocols: Create and maintain detailed experimental protocols, outlining step-by-step procedures, necessary materials, and equipment.
  2. Notebooks for recording experiments: Use notebooks as digital documents for recording experiments, including text descriptions, data tables, images, and file attachments.
  3. Project documentation: Use notebooks to document projects by organizing information into sections, using headings and subheadings for navigation, and including tables and images.
  4. Knowledge base articles: Notebooks are well-suited for creating knowledge base articles or guides. You can structure the information using headings, bulleted list, and numbered lists, making it easy for readers to follow along and find the information they need.

Getting started​

Follow these steps, to use notebooks with a database:

  1. Enable notebooks for the database.
    1. Open the actions (…) menu for the database at the top-right of the data grid for the database.
    2. In the popup that opens, enable the "Enable document" toggle.
  2. Create a row , open the page for the row, and navigate to the bottom of the page for the row.
  3. Insert a block into the notebook: Type "/" and then use the window that pops up to select the type of block you'd like to insert.

Basic formatting blocks​

Notebooks supports multiple types of basic blocks:

  • Paragraphs: Create distinct paragraphs to organize your text.
  • Headings: Use headings to structure your notebook and create a hierarchical outline.
  • Ordered and unordered lists: Present information using numbered lists or bullet points.
  • Check lists: Use checklists to keep track of the progress of experiments.
  • Tables: Insert tables to display structured data or create comparisons.
  • Code: Capture code used to process and/or visualize your data.
  • Quotes (coming soon): Highlight important quotes or excerpts.

Image blocks​

Image blocks enable you to insert images into notebooks. Simply upload an image file or provide a URL for an image. The editor will embed the image into the notebook canvas at the desired location. Once an image is inserted, you can customize its appearance. When the block is selected, formatting options will be shown at the top left of the block. Formatting options include resizing, aligning (left, center, right), and adding captions.

Video blocks​

Video blocks enable you to insert videos into notebooks. Simply upload a video file or provide a URL from supported platforms (e.g., YouTube, Vimeo). The editor will embed the video into the notebook canvas at the desired location. Once a video is inserted, you can customize its appearance and playback options. When the block is selected, formatting options will be shown at the top left of the block. Formatting options include renaming the video, adding a caption, replacing the video, deleting the video, downloading the video, and aligning the video block within the notebook.

Audio blocks​

Audio blocks enable you to insert audio content into notebooks. Upload an audio file or provide a URL for an audio file. The editor will embed the audio into the notebook canvas at the specified location. Once an audio block is inserted, you will be able to start and stop the audio, change the volume and playback speed, and download the audio.

File attachment blocks​

File attachments block enable you to insert multiple types of files into notebooks. This is useful for including supplementary materials, such as PDFs, spreadsheets, or presentation slides. When the block is selected, several options will be shown at the top left of the block. This includes options for adding a caption for the file and downloading, renaming, replacing, and deleting the file.

Executable code blocks​

Executable code blocks enable you to run Python code and explore its results directly within your notebooks.

Our code blocks support several biology and data science libraries:

Code blocks are particularly useful for performing data analysis directly in your notebooks, creating interactive data visualizations, calculating properties of rows and adding them to databases, and documenting code used in your projects.

To add a code block, type "/" and select "Executable code" from the block menu.

To execute a code block, click the execute button (play symbol) on the top right corner of the block.

Global database blocks​

Views of global databases can be inserted into notebooks, enabling you to integrate data created within in the context of a notebook into your central databases.

Follow these instructions to add a view of a global database to a notebook and add rows to the view:

  1. Add a view of a database to a notebook: Position your cursor where you want to insert the database view. Type "/" to open the block menu and choose the desired global database from the "Database" section. A grid for the selected database will then be added to your notebook. Initially the grid will not have any rows.
  2. Add a row to the database view: Use the "New" button to add a row to the grid. Each row added to the grid will be automatically synchronized to the global database. To help you track the provenance of your data, the context (the parent notebook) in which each row is created is automatically recorded.

Local database blocks​

Local database blocks enable you to create databases scoped to a specific notebook, providing a way to organize and manipulate structured data within the context of a single notebook. Databases defined within notebooks are not available outside the notebooks in which they're defined. Local database blocks are useful for capturing the intermediate results of experiments.

Mentions​

Within text blocks, you can also use mentions to create references to specific rows, databases, and folders. These references enable you to create graphs of your knowledge.

Follow these steps to mention an item:

  1. Type "@" at the location in your notebook that you want to create a mention.
  2. Type the ID or name of the row, database, or folder that you want to reference.
  3. Select the desired item from the dropdown menu that appears. This will insert a tag into your notebook with the ID and name of the referenced item. When you click the tag, you will be navigated to the referenced item.