Phaedra 2 – Getting Started

Documentation: Setting up a Project

Mon, 01 Jan 0001 00:00:00 +0000

The first thing you’ll want to do when you start using Phaedra, is setting up a new Project.

Note: to learn more about Projects, Experiments and Plates, check the Data Model section.

Creating a New Project

In the Navigator, select Projects. The projects browser will open.
In the top right corner of the table, click the blue + button (Create New Project)

Provide a name for the new project, and optionally a description. Also, select the team that will administer the project.

Viewing a Project

To view the contents of a project, open the Projects browser from the Navigator, and double-click on any project.

Editing a Project

You can modify the project’s name, description, tags and properties, if you have the appropriate permissions. The Access field shows the teams that have Read, Write or Admin access on the project. If you don’t have Write or Admin access, you will not be able to edit the project.

To edit the project name or description, click the Pencil button next to the project name.
To add a tag, click the + button next to the Tags field. A tag is a simple label that can be attached to any project.
To add a property, click the + button in the top right corner of the Properties table. A property is a Name-Value pair that can contain more detailed information than a tag.

Below the project’s general information section is another section listing the project’s Experiments.

Creating a New Experiment

To create a new Experiment, open a project and in the Experiments section, click on the blue + button (Create New Experiment) in the top right corner of the table.

Enter a name for the new experiment and select Create.

Note: when using Pipelines, experiments (and plates) are often created automatically, and you don’t need to create them by hand.

Viewing an Experiment

All available experiments for a project are listed in the Experiments section of the project. If you have Read access to a project, you will automatically be able to see all the experiments in that project.

Double-click on any experiment to open it and see more details.

Just like the project view, the experiment view contains two sections:

The first section displays general information about the experiment: the name, ID, creator info, description, tags and properties.
The second section lists the plates this experiment contains. There are different ways to visualize the plates, depending on which tab you select: Overview, Statistics and Heatmaps.

Overview

The Overview tab lists the plates in a tabular format, showing general plate information as well as the plate validation status:

L: Link status, showing a green checkmark if the plate has been linked with a plate definition
C: Calculation status, showing a green checkmark if the plate has been calculated by at least one protocol
V: Validation status, showing a green checkmark if the plate has been validated
A: Approval status, showing a green checkmark if the plate has been approved

Statistics

The Statistics tab also lists the plates in a tabular format, but adds statistical information about the feature data.

For each feature, several columns will appear displaying the primary statistics for that feature:

Heatmaps

The Heatmaps tab shows small heatmaps for all the plates in a grid layout, allowing you to scroll through resultdata heatmaps of all the plates at once.

Editing an Experiment

If you have Write permissions on the project, you can modify experiment properties and contents using the experiment view:

In the general section, you can rename the experiment, change the description, and add or remove tags and properties.
In the plates section, you can create new plates, as explained below. In addition, you can perform various actions on the plates by selecting one or more plates, right-clicking, and choosing an action from the menu:

Note: these actions are explained further in the section Working with Plates.

Documentation: Setting up a Protocol

Mon, 01 Jan 0001 00:00:00 +0000

If you want to perform any sort of calculations on the data you’ve imported into Phaedra (see Data Capture), you’ll need to set up a protocol that defines those calculations precisely.

To learn more about the concept of protocols and calculation in general, refer to Calculation.

Creating a New Protocol

In the Navigator, select Calculation to unfold its contents and then select Protocols. The protocol browser will open.
In the top right corner of the table, click the blue + button (Create New Protocol)

Provide a name and optionally a description for the new protocol, then click Create.

Viewing a Protocol

In the protocol browser, double-click on any protocol to open it.

The top section displays general information about the protocol such as the name, version, description, modification info, as well as tags and properties.

The bottom section shows a list of all the features that have been defined in this protocol. To view or edit features, see the sections Viewing a Feature and Editing a Feature below.

Editing a Protocol

Note: Protocols are visible to all users, but only a protocol’s creator (or an administrator) can edit it.

You can modify the protocol’s name, description, tags and properties:

To edit the name or description, click the Pencil button next to the protocol name.
To add a tag, click the + button next to the Tags field. A tag is a simple label that can be attached to any protocol.
To add a property, click the + button in the top right corner of the Properties table. A property is a Name-Value pair that can contain more detailed information than a tag.

Adding a New Feature

To add a new feature to the protocol, click on the blue + button (Add a New Feature) in the top right corner of the features list.

A dialog will appear where you can enter the details of the new feature:

Provide a name for the new feature, and optionally an alias, description and format, then click Continue

In the Calculation section, choose one of the available formulas
Depending on the selected formula, you must specify one or more formula variables
For each variable, choose the Source and the Value that the formula should use

Note: For a more detailed explanation of formulas and their variables, refer to the Calculation Formulas section.

Optionally, a dose-response curve fit can be configured on this feature
When all relevant settings have been made, click Add to create and add the new feature to the protocol

Viewing a Feature

In the features list of a protocol, double-click on any feature to view its details.

The top section displays general information about the feature, such as its name, description, formatting, tags and properties.

The bottom section is divided into multiple tabs, with each tab showing a different aspect of the feature’s configuration:

Calculation

This tab lists the settings related to the calculation of the feature:

Sequence: this field determines whether a feature is calculated before or after another feature. This setting is important if a feature’s calculation depends on the value of another feature.
Formula: this field displays the formula that is used during calculation of the feature, as well as the list of variables this formula needs.

Statistics

This tab lists the statistics that will be calculated on the feature. For example, if you define a “CellCount” feature that computes the cell count for each well in the plate, you can additionally compute the min, median, max CellCount as well, both for the entire plate and for each well type group in the plate.

Dose-Response Curve

If the feature has been configured with dose-response curve fitting, you’ll find the relevant settings in this tab. The exact fields that are shown here, depend on which curve fitting Model you selected.

Editing a Feature

To edit a feature, click on the Pencil button next to the feature’s name:

A dialog will open, taking you through the same configuration sections as when creating a new feature (see section Adding a New Feature above).

Documentation: Setting up a Pipeline

Mon, 01 Jan 0001 00:00:00 +0000

Creating a Pipeline

In the Navigator, select Pipelines.
The folder will expand. Select New Pipeline…

Provide a name for the new pipeline, and select Create to complete the creation.

Viewing a Pipeline

In the Navigator, select Pipelines to view a listing of all available pipelines.
Click on any pipeline to view its details.

In the top section, you can view pipeline properties such as its name, description, creator info, and current status.
In the bottom section, you can view the pipeline definition, which is expressed in JSON notation.

Editing a Pipeline

Pipelines start off in the Disabled state, which means they will not be executed under any circumstances. To enable a pipeline, click on the slider button behind the status label.

To edit the pipeline definition, select the Edit button to the right of the pipeline definition JSON.

Make any changes as desired, then select Save to apply the changes.

Documentation: Data Capture

Mon, 01 Jan 0001 00:00:00 +0000

In order to view and analyse data with Phaedra, you will need to import some data measurements into Phaedra. This can be achieved by using the Capture Jobs feature.

Browse to Phaedra navigator:

Browse Capture Jobs

In the Data Capture navigator menu item, select Capture Jobs..
An overview of previously created/executed Capture Jobs will be shown

Capture Jobs Details

By clicking on the Details button in the Capture Jobs* overview table a pop-up dialog will appear containing the information about the selected Capture Job

Here you can find all the information about the capture job like the Status or the Events executed during the capture job

Submit a new Capture Job

By clicking on the SUBMIT NEW JOB… button in the left upper corner of the capture jobs overview page a dialog will pop up

Set Measurement source type to FolderScanner, S3 Bucket or Colombus. By default the Measurement source type is set to FolderScanner
Next, select the source folder. This can be a network location or a directory on your local computer.
Last step is to select a Capture Configuration. The Capture Configuration defines what needs to be done during this Capture Job.
To view the details of the selected capture configuration, click

Browse Measurements

In the Data Capture navigator menu item, select Measurements..
An overview of all previously captured Measurements will be shown

To view the details of a specific measurement, click on the measurement row in the overview:

Upper section of the measurement details view displays general information:
- Barcode: The imported measurement identifier
- Dimensions: The dimension (rows x columns) of the imported measurement
- WellData columns: Number of the imported well data properties aka well features
- SubwellData columns: Number of the imported sub-well data properties aka sub-well features
- Image Channels: In case high content data (images) is imported, number of defined channels (see Manage Image Render Settings)
Lower sections is consists of tree tabs: Well Data, Subwell Data and Image Data

Well Data:

An overview table of all the well data features and their value for the corresponding well

SubWell Data:

With the subwell data view you are able to display a set of user selected subwell feature per user selected well

Image Data:

The third and last view allow the user to visualize the imported images by selecting a specific well

Manage Image Render Settings

In the Data Capture navigator menu item, select Render Settings.
An overview of previously defined Render Settings will be shown

Documentation: Working with Plates

Mon, 01 Jan 0001 00:00:00 +0000

Creating a New Plate

To create a new plate, in the plates Overview section of an experiment, click on the blue + button (Create New Plate) in the top right corner of the table.

Note: Make sure to enter the correct plate dimensions! While you can modify most of the plate’s attributes afterwards, you cannot change a plate’s dimensions after it’s been created.

Viewing a Plate

To view the details of a plate, double-click on it in the Overview section of an experiment.

The top section of the plate view displays general information including the barcode, description, dimensions, validation & approval info, and tags and properties.

The bottom section is organized into multiple tabs, with each tab presenting the plate contents in a different way:

Layout

This tab displays the plate layout, if available. On each well, the Well type is shown, defaulting to “EMPTY” for wells that are neither controls or samples. To display another label, such as the substance or concentration, use the dropdown list in the top right corner of the plate.

Heatmap

In the Heatmap tab, you can view the plate’s feature data presented as a colored heatmap:

To choose which feature (or measurement column) should be displayed on the heatmap, use the Feature Selector which is located in the top right corner of the screen:

The Feature Selector has two buttons to toggle between Measurement Columns (data imported from measurement files) and Features (data calculated by Phaedra).

Note: For more information about features, refer to the Calculation topic.

Well List

Instead of a heatmap or grid, wells can also be listed in a tabular format. The Well List tab presents such a table, where you can sort and filter the wells in a convenient way:

Measurements

Each plate typically has one measurement attached to it, although it is possible to attach multiple measurements to a plate (for example, in the case of a time-lapse assay). The measurements tab lists all the measurements that are attached to the current plate:

To link a different measurement to a plate, click the Link Measurement button and select one of the available measurements.
If multiple measurements are linked to a plate, you can toggle one of them as the active measurement using the Active switch in the first column of the table. The active measurement is the one that will be used by default during plate calculations and for data visualizations.

Note: Manually linking measurements to plates can be a tedious process. Pipelines are designed to automate such tasks and are the recommended way to go, especially in larger projects.

Calculations

The Calculations tab shows a list of all the calculations that took place on the plate, along with information about the outcome of those calculations.

Click on the Details button to see more details about the calculated features and the errors, in the case of a failed calculation.

Dose-Response Curves

If any dose-response curves were calculated on the plate, they will be shown in the Dose-Response Curves tab:

Editing a Plate

Plates can be modified in many different ways, ranging from a simple rename of the barcode, to a full recalculation of all features. Before a plate can be edited, though, two main conditions must be met:

You must have Write permissions on the project
The plate must not be Validated or Invalidated

If these conditions are met, you can edit a plate in the following ways:

In the plate view:

Click the Pencil button next to the plate’s barcode to edit the barcode or description.
Click the Calculator button next to the plate’s barcode to perform a recalculation of the plate.
Click the + button next to the Tags field to add a tag.
Click the + button in the top right corner of the Properties table to add a property.

In the experiment view:

Right-click one or more plates and choose an action to perform:

Clone Plate(s) to create exact copies of the plates
Move Plate(s) to move plates to a different experiment in the same project
Link Measurement to link an available measurement to the plates
Set Plate Layout to apply a plate layout template to the plates
(Re)Calculate Plate to perform a recalculation of the plates
Validation to Validate or Invalidate the plates, or to reset their validation status
Approval to Approve or Disapprove the plates, after the plates have been Validated
Charts to open one of the available charts that can display the plates’ feature data
Scripts to choose and run one of the available scripts (from the Script Catalog) on the plates

Documentation: Phaedra 1 vs Phaedra 2

Mon, 01 Jan 0001 00:00:00 +0000

Users who are familiar with the Phaedra 1 application, may wonder how much different Phaedra 2 is from its predecessor. Given that Phaedra 2 is a complete rewrite from the ground up, there are indeed numerous significant changes. This page lists the most important differences, both conceptually and in the application’s usage.

Platform Architecture

As illustrated in the Architecture section, Phaedra 2 is a server-side application. This means that to interact with the application, you won’t use an installed app or a remote desktop session. Instead, you can log in and use the application using your web browser.

This changes offers several advantages:

There is no additional latency because of an intermediate remote desktop server between you and the Phaedra servers
No software installation or computer configuration is needed: the only requirement is a working web browser
You can use multiple browser tabs to access different experiments, or work on multiple projects simultaneously
You can copy the browser address to share pages with colleagues or bookmark them for later use

Plate Model

While the plate model used in Phaedra 2 is largely identical to Phaedra 1, there are some important changes to make note of, listed below. For a full explanation of the plate model, consult the Data Model page.

Measurements

This new entity represents a set of data that is imported into the application (a process also known as data capture). While in Phaedra 1 the imported data was attached directly to a plate entity, in Phaedra 2 the data is imported into a measurement entity, which in turn is linked to a (new or existing) plate.

The main advantage of this change is that there is now a clear distinction between the imported and calculated data of a plate: the imported data of a measurement is strictly read-only and can never be changed. Any plate data that does change (such as calculated features, normalized data, curve fits, etc) is stored in a separate entity called a result set. Furthermore, one measurement can easily be reused in multiple plates, which may be convenient during assay development. You can even inspect and visualize the data of a measurement without creating any plate at all.

Projects

In Phaedra 1, plates were organized into experiments, which were stored under protocols, which in turn were stored under a protocol class. As such, the protocol class served as both the ‘root folder’ of the data, as well as the full ‘blueprint’ of the configuration of the features.

This often caused a complexity in the organization and management of protocol classes, as slight variations of analysis (some extra features, some different normalization, an extra staining channel, …) would require the setup of a new protocol class, even if the plates logically belong to the same project or assay as the plates in the existing protocol class.

Phaedra 2 addresses this issue by separating the protocol class into two distinct entities: the protocol and the project. The protocol takes on the role of the configuration ‘blueprint’: it lists all the features along with their calculation, normalization and other settings. The project takes on the role of the ‘root folder’: it is simply a folder that may contain any number of experiments.

Within a project, you can mix and match multiple protocols. For example, you can use protocol A to calculate normalizations on experiment 1, and then use protocol B to calculate different normalizations on experiment 2. You can even apply multiple protocols on a single plate.

Result Sets

As mentioned earlier, Phaedra 2 no longer attaches data (imported or calculated) directly to plates. Instead, imported data is attached in the form of a measurement, while calculated data is attached in the form of a result set.

Whenever a plate calculation takes place, a new result set is created and all the calculated data is stored in it. The previous result sets remain available though, so you can look back at previously calculated data at any given time: nothing is overwritten or deleted.

Features and Formulas

The role of a feature has been updated in Phaedra 2, with the goal of allowing more flexibility in (chained) calculation. Whereas a Phaedra 1 feature represented both the calculation of a value and the normalization of that value, Phaedra 2 separates these concerns: one feature is responsible for calculating a value, another feature is responsible for calculating a normalization of that value.

In addition, the precise way in which a feature computes a value, is now separated into a formula. The purpose of this change is to allow easier reuse of computation details across features from different protocols. All of the normalization methods that Phaedra provides out of the box are available as formulas that can be used in any feature in any protocol. But a user may also define their own custom normalization formula, which will likewise be available for use by features anywhere in Phaedra.

The User Interface

Since Phaedra 2 is accessed from the web browser rather than an installed app, some differences can be expected in the way you interact with the application. Nonetheless, efforts have been made to make the user experience as close as possible to that of the Phaedra 1 workbench:

The Navigator is the starting point for navigation, giving access to projects, protocols, pipelines, data capture jobs, etc.
In most tables that list entities (experiments, plates, wells, …) rows can be single-clicked to select (highlight) an item. Information or details about the selected item may then appear in any open side-panels; for example a Well Image side-panel may display the image of a selected well.
Likewise, double-clicking an item will open a separate details page for that item; for example double-clicking on a plate will open the Plate Details page.
A right-click on an item will open a context menu with relevant actions you can perform on that item; for example right-clicking on a well will allow you to perform actions such as Accept or Reject Well.