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.

Creating a Project

In the Navigator, select Projects.
The folder will expand. Select New Project…

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

Select Create to complete the creation.

Viewing a Project

After you’ve created a new project, or when you select a project from the project listing, you’ll be taken to the project details view:

Editing a Project

You can modify a number of properties of the project, assuming you have the appropriate permissions. The Access field will display the teams that have read and/or write access on this project. If you don’t have write access, you will not be able to modify any property of the project.

The project name is shown in the top section bar. To rename the project, select the Rename button in the top right.
The project description can be modified by hovering your mouse cursor over the description field. An edit button will appear that you can select to modify the description.
Projects can be tagged with custom information by selecting the “+” button in the Tags field.
If you wish to add more complex information than is allowed by a simple tag, you can add a property instead. Select the “+” button in the top right corner of the Property table to do this.

The second section is named Experiments and shows a listing of all experiments that have been added to this project. Initially, this list will be empty.

Creating an Experiment

To create a new Experiment, open a project and select the “New Experiment” button at the top of the Experiments section.

Enter a name for the new experiment and select Create.

Viewing an Experiment

Select an experiment in the project view to open it and see the experiment details and contents.

The experiment view contains two sections:

The first section lists general information about the experiment: its name, ID, creator info, tags and properties.
The second section lists the plates that are contained in the experiment. There are different ways to visualize the plates, depending on which tab you select.

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 result sets.

For each calculated feature, several columns will appear displaying statistics with regards to the feature’s result data.

Heatmaps

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

You can use the selection boxes at the top to switch to a different Feature or Protocol.

Editing an Experiment

If you have the appropriate permissions, 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 plate section, you can add plates using the “New Plate” button. Using the three dots button “…” behind each plate, you can also calculate or delete plates, or perform various other actions on them.

Creating a Plate

To create a new Plate, open an experiment and select the “New Plate” button at the top of the Overview section.

A new section will appear asking you to provide the basic information for the new plate:

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 a plate, select it from the plate list in the Experiment view:

The first section contains the plate barcode, as well as some basic information such as the plate ID, dimensions, and creator information.

The second section contains multiple tabs, which you can toggle by clicking on them:

Layout

This tab shows the plate layout, if available. A plate with no layout information will display “EMPTY” for each well.

Heatmap

Within the Heatmap section the user is able to view the raw feature data from the linked measurement as well as the calculated features from a protocol.

If a user wants to view the heatmap of a raw feature, the user needs to click on the “Active measurement features (raw data)” option and select the feature from the select input list to the right. The list can be filtered for a specific feature in the select input.

If a calculation has been performed on a plate, and a result set is available, the user can view the calculated feature data by clicking on the “Protocol features (calculated data)” option. Similar to the previous option, the user can select a calculated data from the select input to right.

If multiple result sets are available from different Protocols, all the calculated features will be listed in the select input list prefixed by the “[Protocol Name]”.

Well List

To see the well information in a tabular format instead of a grid, you can use the Well List tab.

Measurements

A plate can have one or more measurements linked to it. To see the measurements that are currently linked to the plate, select the Measurements tab.

To link a new measurement to a plate, select the “Link Measurement” button.
If multiple measurements are linked, you can toggle one of them as the active measurement by toggling the Active switch for that measurement. The active measurement is the one that will be used during plate calculations.

Calculations

Select the Calculations tab to get an overview of all calculations that have been performed on this plate.

Editing a Plate

If you have permissions to edit a plate (this depends on the Access settings of the project the plate belongs to), you can modify many of the plate’s properties.

To rename a plate, use the Rename button in the top right.
To change a plate’s description, hover your mouse cursor over the description field. An edit button will appear that you can select to modify the description.
Plates can be tagged with custom information by selecting the “+” button in the Tags field.
If you wish to add more complex information than is allowed by a simple tag, you can add a property instead. Select the “+” button in the top right corner of the Property table to do this.

Documentation: Setting up a Protocol

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

Creating a Protocol

In the Navigator, select Calculation.
The folder will expand. Select New Protocol…

Provide a name for the new protocol, and optionally a description. Also, select the welltype codes that should be used for the well types Low Control and High Control. Finally, choose a starting version number. Note that version numbers must match the pattern “#.#.#” containing three numbers: MajorVersion.MinorVersion.Revision.

When you select Save, the protocol will be created and you will be taken to the Protocol View.

Creating a Protocol using an exported JSON file

Instead of creating a new protocol from scratch, you can also create one as a copy from another protocol, by exporting an existing protocol using the Export button, and then selecting Import… in the protocol creation screen.

Viewing a Protocol

To view a protocol, select Calculation in the Navigator and then select Protocols. A table will be shown, listing all available protocols. Click on the protocol you want to view.

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

The bottom section shows a list of all the features that have been defined in this protocol. Click on view button in the far right column to open a third section containing detailed information about the selected feature.

Editing a Protocol

Rename protocol

To rename the protocol click on the RENAME button:

A “Rename protocol” dialog will appear where you can edit the protocol name:

Edit protocol description

To edit the protocol description click on the edit icon next to the protocol description:

A “Edit description” dialog will appear where you can edit the protocol description:

Add/Delete Tag

To tag the protocol click on the plus icon next to tags label

An “Add tag” dialog will appear similar to “Rename protocol” and “Edit description” where you can input a tag To delete a tag click on the ‘x’ icon next to the tag that you want to delete

Add/Delete Property

Add Feature

To Add a new feature to the protocol click on “ADD FEATURE” button in the upper left corner of the feature list view.

A third section “Add New Feature” will appear with tree main sections: “General Info”, “Calculation” and “Dose-Response Curve”. In the first section the user needs to provide general information like feature’s name, alias, description and format (default is set to #.##).

Because every feature created in a protocol is a calculation feature (meaning the feature executes a function when the protocol is applied a specific plate), the calculation needs to be filled in by the user. The user needs to select a calculation formula and provide a column name (or names depending on number of function inputs) from a specific measurement or name of a other feature from the protocol.

The third section is optional and only needs to be filled in by the user when a dose-response curve needs to be fitted for the new feature.

After all the mandatory information about the new feature is provided, click on the APPLY button in the lower right corner of the new feature section. The newly created feature will appear in the protocol feature list section.

You’ll also notice two new buttons SAVE and RESET have appeared in the feature list section.

Click save if you want to SAVE the feature changes of click RESET to revert the feature changes.

Edit Feature

To edit a specific protocol feature click on the edit button on the far right column in the feature list section.

Alle the other actions are similar to the add new feature action.

Delete Feature

To Delete a specific protocol feature click on the delete button on the far right column in the feature list section.

Everytime you Add, Edit or Delete a protocol feature, the SAVE and RESET buttons will appear. To persist the feature changes you’ll need to click the SAVE button and to discard the feature changes you’ll need to click the RESET button.

Browsing Formulas

To browse the available formulas:

In the Navigator, select Calculation.
The folder will expand. Select Formulas

A table will list the available formulas, showing some basic information for each formula, such as the name, author, scope and language.

To see more detailed information, either click on a formula, or click on the “…” icon and select Details.

The top section will display general information about the formula. The bottom section will display the formula script.

Editing a Formula

To edit a formula, open a formula and select the Edit button in the top right corner.

You can then modify the formula name, description, scope as well as the formula script itself. When you are done making changes, select Save Changes to apply the modifications to the formula.

Creating a New Formula

To create a new formula, open the formula browser and click the NEW FORMULA… button.

A new formula view will appear. The view is split into two sections:

On top is the general information section where the user provides information like:

Name: formula name
Description: description of the formula
Language: the scripting language
Scope: plate level, well level or sub-well level

Below it is the script section where the user provides the script that implements the formula’s function:

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: Importing Measurements

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