Academic Reading on Protolyst – Quick Start Guide

If you’ve signed up to Protolyst to support your academic reading, here’s a workflow to get you started!


We’ve organised this guide into different sections based on your experience with digital notetaking apps and connected notes:

  • Beginner – if this is your first time using a connected note-taking app
  • Intermediate – if you’re familiar with notetaking, having used apps like Notion, EverNote, OneNote and are ready to use more features of Protolyst

Academic Reading Workflow – Beginner #

As a researcher, you’ll read a huge number of papers. So many that it can be hard to remember WHERE you read about a new characterisation method, an interesting system behaviour or to refind a partly remembered quote you want to use.

On Protolyst your highlights are lifted out the page as Atoms, so any details that caught your eye while reading are saved outside of the PDF. So that method, behaviour or quote is just a quick search away!

This 4 step workflow will get you familiar with using Protolyst to read your papers, collect your highlights and capture your ideas and annotations.

1. Add a Table to your Workspace

Protolyst interface showing the left hand sidebar and highlighting a blue plus button labelled 'Add New Page'. The Create Table button is also labelled in the list of Page Type Options on a New Page
Use the Blue Plus Button at the top of your Left Hand Sidebar to add a New Page into your workspace. Then select the Table option from the 4 different Page Type Options in your New Page to create a Table in your workspace


Tables have 2 properties by default – Atoms (which will display the highlights you save as Atoms) and Sub-Pages. For this flow let’s change the Sub-Pages property to a Citation Property.

Protolyst for Academic Reading. In a Table you can make use of a Citations Property to automatically extract reference information. Here 2 Images of a Table are shown, the first shows the Properties Name, Sub Pages and Atoms and the second shows Name, Citation and Atoms with further info on using dropdowns to change between Property types.
Tables have Name, Sub Pages and Atoms as the 3 Standard Properties when you create a Table. To swap Property Type, click on the Property Title and then choose from the different Options in the Dropdown Menu. Here Citations has been chosen.

Citations are automatically generated here for each paper you upload into a Table. (More on Citations below!)

Citations are automatically added into the Citations Property when you upload a Paper into your Table.

2. Upload a Paper

You can upload Papers by using the New Button above the Table. The Dropdown arrow will give you a list of Page Types to choose From. Select File to choose a File to upload to Protolyst.

Use the Dropdown arrow next to New to select File to upload your Files one by one

You can also batch upload files into your Table by Drag and Drop. Select the Files you want to upload and drag them onto your Table.

3. Capture Highlights while Reading
Highlight interesting text and hit ‘Capture Atom’. This saves your highlighted text as an Atom. Atoms are searchable (and viewable) without you needing to have the PDF open. (For more on what you can do with Atoms, take a look at the Beginner Plus info below)

When you highlight text a ‘Capture Atom’ button will appear. Choose this to create an Atom from your highlighted text. This will bring up the Atom Box

When you Capture an Atom, a text box appears. You can type to add your annotations in here, so if there are any ideas or further thoughts you want to add, just pop them in.

4. Return to your Table

All the highlights you have captured as Atoms are visible in the Atoms Column of your Papers table

You can also view all the Atoms captured within a particular Paper when you have it open. Use the Atoms button on the top right of the screen to open the Atoms Menu. All the Atoms captured from the Page will display in a list here.

Finding your Atoms #

Now your highlights are saved as Atoms, they are accessible and viewable outside of the source file. You can browse through all your highlights in the Atoms column of a Table, without having to open each paper up separately. To search through all your Atoms from all of your Papers, you can use All Pages search, which will search by Keyword across your workspace, and help you locate a particular Atom.

At the top of your Left Hand Sidebar, there’s an All Pages Search option. Here you can search through all your Pages and Atoms by keyword

Click on the Source Tag to view the Atom in the Source PDF. The Source Tag is a link between your Atom and it’s original location, it’s indicated by the Shield shaped icon next to the Page Title underneath your Atom in List View.

The Atom Box displays the Source Tag above the Atom Text (green encircled text). Click this to open the Source PDF and original location of your Atom

If you open up your Atom then the Source Tag is indicated by an encircled upward arrow in the Linking Bar area above your Atom Text.

Beginner Plus #

Organising notes from papers you are reading can fuel your research direction and also give you a headstart on academic writing. Here are some additional steps to help you with using your Atoms to write and how to make use of Citations and Referencing features on Protolyst.

Automated Bibliography Information #

Reference information can be automatically extracted from papers you upload onto Protolyst. In your Table, you can add a Citations Property. When Papers are added into the Table, the Reference information will be automatically added here.

The Citation Property in a Table automatically extracts citation information from Papers that you add into your Table

Reference Style can be editted in the Citations Property Options. Click the Property Title to open the Property Options, and then choose from the available referencing styles.

Let us know if there’s a style you want us to add!

Using Atoms from your Academic Reading #

Atoms can be added into Text Editor Pages, so you can use them in your writing. See how in 3 steps:

1 Add a New Page for your Written Piece

Add a New Page using the Blue Plus Button at the top of your Left Hand Sidebar. To create a Notes Page select Text Editor from the available Page Type Options in the New Page.

2 Open up your Papers Table in Split Screen

To open Pages side by side in Split Screen use ‘CTRL+Click’ on the second Page you want open. Alternatively you can right click on a Page and then select ‘Open in Splitscreen’ from the options that appear.

Splitscreen View of 2 pages on the left, a Text Editor page and on the Right a Table. Here you can make use of the insights and ideas gathered from your academic reading

3 Drag and Drop Atoms from your Table into the Page

To use an Atom in your new Page, drag and drop your chosen Atom into your Page.

Drag and Drop Atoms in a Table into a Text Editor Page to add the Atom Text into your Page.

When you add an Atom into your Page, a numbered citation next to the Atom text appears. You can edit the Atom text to integrate it into your paragraph and write a flowing piece. This Citation links you directly to the original Atom in the Source PDF.

Atoms can be dragged into a Page. Once dropped into the Page, a Numbered Citation is generated and a Reference appears at the bottom of the Page

References Section #

When you drop your first Atom into the Page, a References Section will automatically appear at the bottom of your Page. This Section can be removed and the Referencing Style and Information can be edited to your preferences.

Hover over a reference until the 3 dot button apperas to access the Reference Options; Edit, Copy and Extract. Edit Reference opens a Pop Up where you can add or edit reference information and Import Reference Information.

These additions allow you to start using the Atoms collected during your academic reading, to write referenced pieces, so you’re only ever one click away from the source information!

Academic Reading Workflow – Intermediate #

As you collect your highlights and save them as Atoms in your workspace, you may want to categorise them further by Research Themes, Structural Concepts or Specific Keywords. These further categories allow you to pool related information together from across your library of papers, so that you can unlock the knowledge acquired from your academic reading. With categories you can view a collection of Atoms relevant to a theme from many different sources.

On Protolyst you categorise your Atoms by adding Tags. To access and use Tags across your workspace, they should be set up as Pages in your Workspace.

Take the following steps from the Beginner workflow:

1 Create a Table for your Tags

Add a new Table into your Workspace and then add in your chosen Tags. These Tags should related to the information you want to remember from your academic reading. Tags could be Research Themes or Keywords like hydrogel, acoustics, gelation mechanisms, or Structural Concepts like Abstract, Methods, Key Results.

A Table with several Tags added

Add the Tags you would like to use to categorise your Atoms as rows in this Table

2 Capture Atoms as you read

Read your papers and highlight the important and interesting parts to save them as Atoms in your workspace.

3 Add Tags to your Atom

After you hit ‘Capture Atom’ the Atom box appears. Here is where you add your Tags.

The Linking Bar is above the Atom text. A Source Tag has already been added when you captured your Atom and this links you back to the Atom’s Source Location in you academic reading list. Type in the Bar next to this Tag, and a list of all the Pages in your workspace will appear. Start typing the Tag Name or scroll to the Tags Table to select a Tag. Repeat for all the Tags you want to add to your Atom.

Capture Atoms by highlighting text. Once the Atom Box opens you can add Tags to your Atom using the Linking Bar.

Your Atom will display for all of the Pages it has been Tagged to in your workspace.

4 In the Tags Table, the Atoms property will display all the Atoms that have been Tagged to each of your Tags.

All the Atoms that have been Tagged to a Page in the Tags Table will display in the Atoms property column.

Every Atom displays all it’s Tags, with the Source Tag first so you can always get back to the original source of your Atom.

You can always see information about your Atom when you view it. In List View, underneath your Atom text there’s a list of #Page to show you the Tags added to your Atom. In the Atom Box, the Tags display above the Atom Text.

Atom Overviews #

You can use Atom Filters to separate out your Captured Atoms into a grid overview based on the different Tags that have been added. In this way you can see a breakdown of the Atoms collected by Keyword or Concept from each of your Papers.

1 Add an Atoms Property to your Papers Table

Use the ‘+ Property’ option next to the last column on display in your Table to add a new Property

2 Add a Filter to the Atoms property,

Select one of your Tags as the Filter. Once added this will Filter all the Atoms to display only the Atoms that have been Tagged to the Filter Page such as Key Results.

Add a Property to your Table using the +Property button. Swap the Property Type to Atoms and then underneath there are further options for the Atoms Property. One of the options is to add a Filter, here you can scroll through all the Pages in your workspace and select the Tag from your Tags Table to add it as a Filter.

3 Repeat for the Tags of interest

Here is the Papers Table with 2 Filtered Atom Properties for Key Results and Methods

You can also add multiple Tags to a Filter to further refine the Atoms that display.

Table Views can be used to save different combinations of Properties so that you can quickly move between different information overviews, without having to update the Properties each time. These views allow you to see particular information inside all of the papers uploaded into your academic reading list.

Atom Import #

As you continue with your academic reading, you will build your collection of Atoms in your workspace.

To access and use collections of Atoms, you can Import them into New Pages in your workspace. Import will display all of the Atoms from a particular Page (Tag) in your workspace in the current Page.

To Import Atoms, open the Atom menu in the top right of a Page, and select the Add Atom Plus Button.

Open the Atoms Menu using the Atoms Button in the Top Right of a Page.

Select ‘Import Atoms from Page’ then select the desired Page. All of the Atoms of this Page will then appear in the Atom list for your current Page.

Use the Plus Button in the Atoms Menu and Select Import Atoms from a Page. You then select a Page in your workspace to Import Atoms from. The Atoms will be imported and display in the Atom List for the Current Page.

Using Atom import means you can access the Atoms you have already organised and want to use most from your entire library of academic reading, without using Splitscreen to browse them in your Table.

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