--- title: "Dose Response (Design Modes)" slug: "dose-response-design-modes" updated: 2026-09-09T13:55:52Z published: 2026-09-09T13:55:52Z canonical: "docs.discngine.com/dose-response-design-modes" --- > ## Documentation Index > Fetch the complete documentation index at: https://docs.discngine.com/llms.txt > Use this file to discover all available pages before exploring further. # Dose Response (Design Modes) ## Scientific Background To select a practical number of compounds that exhibited high activity in the primary screen for follow-up assays, a cutoff value of the primary %Inhibition was applied. The cutoff value was calculated as the sum of the average percent inhibition of all compounds tested and three times their standard deviation. In this case, 48 unique compounds (1.9% of all compounds screened) were selected as hits. As before, the number of unique compounds selected for follow-up screening represents a relatively small sample size and therefore were immediately progressed to individual dose response analysis (ED50 determination). Compounds were "hit-picked" at 10 mM concentration in DMSO and further serially diluted ten times at three-fold dilutions for a total of 10 points per compound. Data was normalized as in the primary assay and curves were plotted and fitted to a four-parameter equation describing a sigmoidal concentration-response curve (for example, the Hill equation). The reported ED50 values are generated from fitted curves by solving for the x-intercept at the 50% activity level of the Y-intercept. Compounds with ED50 values greater than 0.01 micromolar are considered inactive; compounds with ED50 of equal to or less than 0.01 micromolar are considered active. ![Dose Response Analysis with ASSAY](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-well-validation-3.jpg?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) ## Third-Party Software This tutorial was developed using TIBCO Spotfire 11.4. Visualization templates may need adjustments if using older versions of that software. ## Dataset **Prerequisite:** Control Layout `Dose Response` must exist. Six serial dilution plates were used. Minimum and maximum controls were placed in columns 1 and 12, respectively. ![Plate Layout for Dose Response Analysis](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-plate-layout-dose-response.jpg?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) Raw data was generated by an AnalystGT Reader from Molecular Devices. Files to use: - [02-Dose_Response_Assay_p96_Raw_Data](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/discngine-assay-02-dose-response-assay-p96-raw-data.txt?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) - [02-Sample_Mapping_Dose_Response_Assay_p96](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/discngine-assay-02-sample-mapping-dose-response-assay-p96.txt?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) ## Run Creation - To create a new run, click the `New Run` button. - Select Mode as `Design Mode`. - Enter a `Run Name`. - Specify the plate format to use: `96 (8x12)`. - Go to the File Reading step. ![Run Creation](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-run-creation.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) ## File Reading - Select `Analyst GT (TAB)` as a reader. - Select the file `02-Dose_Response_Assay_p96_Raw_Data` in the upload section. The file is automatically uploaded upon selection and listed in the table below. - Go to the Raw Data File step. ![File Reading step: Select a Reader and upload file(s)](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-file-reading.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) ## Raw Data File - The Number of Measurements per Plate (`1`) and the READOUT Alias (`READOUT1`) are already set. - Go to the Plate Mapping step. ![Raw Data File step: Adjust number of measurement and add basic transformations](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-raw-data-file.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) ## Plate Mapping - Click `Edit Control Layouts`. - Select the Control Layout named `Dose_Response` (Minimum control in column 1 and maximum control in column 12). - Click `Save`. Barcode information is not needed in this tutorial. This section allows users to set plate barcodes using a file with two columns (Plate_Index / Barcode). ![Plate Mapping Step: Assign Plate Layout for your analysis](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-plate-mapping-1.jpg?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) - All your plates have the `Dose_Response` layout. ![Plate Mapping Step: Assign Plate Layout for your analysis](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-plate-mapping-2.jpg?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) - Go to the Well Validation step. ## Well Validation Select your visualization tool: If you are using Spotfire Analyst Client, or if only one visualization tool is installed in your environment, this step will be skipped. - TIBCO Spotfire Webplayer (Template: ValidationDefaultTemplate) ![Well Validation step with TIBCO Spotfire tool](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-well-validation-tsw-1.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) - Pipeline Pilot (Template: Well Validation) ![Well Validation step with BIOVIA Pipeline Pilot tool](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-well-validation-pp-1.jpg?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) Results are loaded. Add **Data Normalizations**: - In the left panel, next to the `Data Normalization` summary, click `Edit` to open the Data Normalizations modal. - Look for the `Inhibition Standard` procedure and click `Add`: - Value `READOUT1`, `MIN`, and `MAX` are selected. - Click `Add`. ![Well Validation step: Add normalization(s)](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-data-normalizations-1.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) ![Well Validation step: Add normalization(s)](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-data-normalizations-2.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) The Inhibition Standard normalization is listed in the Data Normalization Summary section. - Repeat this action for **Plate Z'-factor** normalization: - Values `READOUT1`, `MIN`, and `MAX` are selected. - Click `Add`. The Plate Z-factor normalization is listed in the Data Normalization Summary section. - Repeat this action for **Z-Score per Type (Plate)** normalization. - Value `READOUT1` is selected. - Click `Add`. The Z-Score per Type (Plate) normalization is listed in the Data Normalization Summary section. ![Summary of Normalization added](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-data-normalizations-3.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) - Click on `Compute`. You are automatically redirected to the **Well Validation** page. All normalizations are processed. Select another visualization template by clicking on the gears button above the current visualization. ![Well Validation step: Change visualization](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-wv-change-visu-template.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) - Apply the Dose_Response_Template (Spotfire) ![Well Validation step: Apply Dose_Response_Template visualization Template](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-well-validation-tsw-2.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) - Apply the Dose Response Template (Pipeline Pilot) ![Well Validation step: Apply Dose Response Validation Template](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-well-validation-pp-2.jpg?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) - Or create a new one and save it (see ***developer guide*** to register a new Pipeline Pilot Protocol in Assay). For **QC Validation**, select aberrant wells in the visualization and click on the ![Well Validation step: Invalidation button](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-invalidation-button-2-3.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) button. Multiple selection is allowed by holding the Ctrl key. After each invalidation, the normalizations will be relaunched in order to recalculate based on your selection. Plate_ZSCORE_READOUT1 < -2 or Plate_ZSCORE_READOUT1 > 2. (8 wells are invalidated) and all normalizations are recomputed. ![Well Validation step: Invalidate wells based on Plate Z-Score](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-wv-tsw-invalidation.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) ![Well Validation step: Invalidation button](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-invalidation-button.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) The space occupied by the visualization can be optimized to your liking by clicking on the ![full screen icon](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-tsw-full-screen.jpg?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) icon and the icon - Go to the **Sample Mapping** step ## Sample Mapping - Click on `Edit Sample Information` button. - Select filling mode `File` and tick `Sample` and `Dose` for content. - Load the file `02-Sample_Mapping_Dose_Response_Assay_p96`. - Click on `Apply` button. Samples and doses are filled in. ![Sample Mapping step: Mapped from file](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-sample-mapping-1.jpg?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) - Click on `Continue` button. Samples and doses are mapped for all plates. ![Sample Mapping step: Sample and doses are mapped for all plates](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-sample-mapping-2.jpg?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) - Click on `Sample Analysis Settings` button. ## Sample Analysis Settings - Select the parameter to aggregate: `SampleName`. - Select the Series: `PCT_INH_READOUT1`. - Click on `Create Analysis Groups` button: 48 groups are created. ![Sample Analysis step: Groups creation](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-sample-analysis-settings-1.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) - Select the analysis `Dose Response Fitting`, then click on the `Add Sample Analysis` button. - Leave the parameters empty, click on `Save` to apply the method to all series. ![Sample Analysis Step: Set analysis - Robust Dose Response Fit (Advanced)](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-sample-analysis-settings-2.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) - Go to the **Sample Analysis** step. ## Sample Analysis Select your Visualization Tool: - TIBCO Spotfire Webplayer - Pipeline Pilot This step is only available if 2 visualization tools are installed. Otherwise, this step will be skipped. - Apply an existing template - **Dose Response Fitting** (Spotfire Template): ![Dose Response Fitting using Tibco Spotfire](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-sample-analysis-tsw.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) For **Hit Selection**, select points (hits) in the visualization and add them to a list by clicking on the `Add Hits` button. This selection can be exported in CSV format (export button) or used to create a list that can be used in the Sample application. - **Lock** your Analysis using the `Lock Run` button. - Go to Publisher step. ## Publisher Selection & Workflow Template Creation - Select a target publisher (depending on what is installed – None, Warehouse or BIOVIA Project Data). For more information on publishing data see the Publisher guide. ![Selection of a publisher.](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-publisher-1.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) - Save your analysis by clicking on `Save As Run Template`. The template will be used later in the execution mode. ![Save a Run Template.](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-run-template.png?sv=2026-02-06&spr=https&st=2026-11-10T21%3A34%3A37Z&se=2026-11-10T22%3A34%3A37Z&sr=c&sp=r&sig=y3zPkN8AsdrB%2Fbjy%2BxqdbCOX5jm%2BWCgyAZkMpeTRTEU%3D) - Give a name and description to the run template. - Click on `Apply Changes` to save your modifications. Once the run template is saved, the screeners can use it in Execution Mode, following [this tutorial](/public/docs/dose-response-execution-mode)