Starting a Workflow

How to create new experiment and upload its data to the platform

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Last updated 11 months ago

Starting a Workflow

How to create new experiment and upload its data to the platform

Starting a Workflow

Create a new project

A typical workflow begins by creating a new project. This is accomplished by right-clicking on the 'Projects' navigation item. The app can be configured to either use a custom project name or to select one from a project management tool like Harvest, provided that the latter offers an API. Once a project is created, you can click on its name to open the project page, where the project name and details can be edited.

Create a new experiment

A project can contain several experiments, with each experiment typically corresponding to one run. To create a new experiment, right-click on the project name and select 'New Experiment'. This action opens the experiment page, where you can edit the experiment name and details.

controlUpload a Control Plate Layout

Most experiments leverage a control plate to validate measurements and ensure accuracy. The user needs to upload the control plate layout before uploading the echo-output files (otherwise, the QC metrics can not be calculated). The control plate layout must adhere to a specific format, outlined as follows:

File Format: The layout should be in a .csv (comma-separated values) format.
Structure: Each row in the file corresponds to a row on the control plate, with each cell representing a well. For wells containing a compound or DMSO, the compound's name should be specified. For empty wells, use the word null to indicate no compound. Following the rows that represent the control plate layout, include an empty row to signify the end of the section. After this separator, repeat the layout to denote the type of control for each well: P for positive control, N for negative control, and C for the rest of the wells.

You can download an example control plate layout here.

The structure of the .csv file should resemble the following pattern, where Staurosporine, DMSO and other names represent actual compounds, and null denotes empty wells. The layout specifies the content of each well in the first section, followed by an empty row, and then the control designations (P, N, or C) in the repeated layout:

Uploading:

Navigate to the management page, where most data management operations are conducted.
Select the "Import control plate" tab.
In the expandable menu on the left, click on the file name. The name of the file will then be displayed above the action box.
Drag and drop or type the file name into the file name field.
Specify the name of the project. Note: Each project can have several control plate layouts to be used in different experiments.
Specify the plate barcode. This barcode should be unique and correspond to the barcode of the physical control plate used in the experiment and in the echo files.
After uploading, the layout will appear under the project node in the navigation tree. Select 'Well type' in the 'Well content' field in order to see the type of the control plate's wells with a colored background.

Upload Echo Output Files

Navigate to the management page.
Select the "ECHO/M1000" tab and the Echo machine.
In the expandable menu on the left, click on the file name. The name of the file will then be displayed above the action box.
Drag and drop or type the file name into the file name field.
Specify the name of the experiment. Note: experiment names should be unique throughout the entire usage of the app.
If the column names in your echo output files differ from the default ones, you should specify a mapping file.
After uploading, experiment plates will appear in the navigation tree under the corresponding experiment node.

Upload M1000 Output Files

Navigate to the management page.
Select the "ECHO/M1000" tab and the M1000 machine.
In the expandable menu on the left, click on the file name. The name of the file will then be displayed above the action box.
Drag and drop or type the file name into the file name field.
Specify the name of the experiment. Note: experiment names should be unique throughout the entire usage of the app.
You can specify the name of the measurement. If not specified, the default name is "label1". If you have several measurements per file, you can specify the names separated by commas.
After uploading the files, you can see the result heat map on a plate's page. Also, the basic QC metrics are calculated and displayed on the experiment page.

PreviousNavigation Tree NextExperiment page

Last updated 11 months ago

Starting a Workflow

Create a new project

Create a new experiment

controlUpload a Control Plate Layout

File Format: The layout should be in a .csv (comma-separated values) format.
Structure: Each row in the file corresponds to a row on the control plate, with each cell representing a well. For wells containing a compound or DMSO, the compound's name should be specified. For empty wells, use the word null to indicate no compound. Following the rows that represent the control plate layout, include an empty row to signify the end of the section. After this separator, repeat the layout to denote the type of control for each well: P for positive control, N for negative control, and C for the rest of the wells.

You can download an example control plate layout here.

Uploading:

Navigate to the management page, where most data management operations are conducted.
Select the "Import control plate" tab.
In the expandable menu on the left, click on the file name. The name of the file will then be displayed above the action box.
Drag and drop or type the file name into the file name field.
Specify the name of the project. Note: Each project can have several control plate layouts to be used in different experiments.
Specify the plate barcode. This barcode should be unique and correspond to the barcode of the physical control plate used in the experiment and in the echo files.
After uploading, the layout will appear under the project node in the navigation tree. Select 'Well type' in the 'Well content' field in order to see the type of the control plate's wells with a colored background.

Upload Echo Output Files

Navigate to the management page.
Select the "ECHO/M1000" tab and the Echo machine.
In the expandable menu on the left, click on the file name. The name of the file will then be displayed above the action box.
Drag and drop or type the file name into the file name field.
Specify the name of the experiment. Note: experiment names should be unique throughout the entire usage of the app.
If the column names in your echo output files differ from the default ones, you should specify a mapping file.
After uploading, experiment plates will appear in the navigation tree under the corresponding experiment node.

Upload M1000 Output Files

Navigate to the management page.
Select the "ECHO/M1000" tab and the M1000 machine.
In the expandable menu on the left, click on the file name. The name of the file will then be displayed above the action box.
Drag and drop or type the file name into the file name field.
Specify the name of the experiment. Note: experiment names should be unique throughout the entire usage of the app.
You can specify the name of the measurement. If not specified, the default name is "label1". If you have several measurements per file, you can specify the names separated by commas.
After uploading the files, you can see the result heat map on a plate's page. Also, the basic QC metrics are calculated and displayed on the experiment page.