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Step 1: Choose GR calculation method


Use cell line division times (instead of initial cell count) to calculate GR values.

Use initial (Time 0) cell counts - the measure of cell number in untreated wells grown in parallel until the time of treatment - for GR value calculation.


Step 2: Choose input file format

Case A: Multiple measurements per row

Necessary columns:

  • cell_line = name of the cell line used in the experiment
  • treatment = name of the treatment used in the experiment
  • concentration = concentration value (not log-transformed) of the treatment (all concentrations must be positive numbers)
  • cell_count = treated cell count (end of assay) - measure of cell number in the treated well at the end of the assay
  • cell_count__ctrl - control cell count (end of assay) - measure of cell number in the control well (e.g. untreated or DMSO-treated) from the same plate at the end of the assay

You may use a surrogate of cell number (such as CellTiter-Glo® staining) for the 'cell counts'.

You may include additional columns to be used for grouping the dose-response experiments.

When your file is uploaded, another popup will open in which you can type the division times for the cell lines used as well as the assay duration.

Case A: Multiple measurements per row

Necessary columns:

  • cell_line = name of the cell line used in the experiment
  • treatment = name of the treatment used in the experiment
  • concentration = concentration value (not log-transformed) of the treatment (all concentrations must be positive numbers)
  • cell_count = treated cell count (end of assay) - measure of cell number in the treated well at the end of the assay
  • cell_count__ctrl - control cell count (end of assay) - measure of cell number in the control well (e.g. untreated or DMSO-treated) from the same plate at the end of the assay
  • cell_count__time0 - initial cell count (time of treatment) - measure of cell number at the beginning of the assay. (measure of cells in an untreated well grown in parallel until the time of treatment)

You may use a surrogate of cell number (such as CellTiter-Glo® staining) for the 'cell counts'.

You may include additional columns to be used for grouping the dose-response experiments.

Case B: One measurement per row

Necessary columns:

  • cell_line = name of the cell line used in the experiment
  • treatment = name of the treatment used in the experiment (use a dash “-” for untreated measurements)
  • concentration = concentration value (not log-transformed) of the treatment - use 0 for untreated measurements - concentrations for other measurements must be positive numbers
  • cell_count = measure of cell number
  • time = time of cell number measurement - use 0 for measurements at the beginning of the assay and the length of the assay after treatment, e.g. “72” for a typical 3-day (72 hour) assay, for measurements at the end of the assay (note: time-course calculations have not been implemented yet, all measurements must be at the time of treatment or at the end of the assay.)

You may use a surrogate of cell number (such as CellTiter-Glo® staining) for the 'cell counts'.

You may include additional columns to be used for grouping the dose-response experiments.

Case B: One measurement per row

Necessary columns:

  • cell_line = name of the cell line used in the experiment
  • treatment = name of the treatment used in the experiment (use a dash “-” for untreated measurements)
  • concentration = concentration value (not log-transformed) of the treatment - use 0 for untreated measurements - concentrations for other measurements must be positive numbers
  • cell_count = measure of cell number
  • time = time of cell number measurement - use 0 for measurements at the beginning of the assay and the length of the assay after treatment, e.g. “72” for a typical 3-day (72 hour) assay, for measurements at the end of the assay (note: time-course calculations have not been implemented yet, all measurements must be at the time of treatment or at the end of the assay.)

You may use a surrogate of cell number (such as CellTiter-Glo® staining) for the 'cell counts'.

You may include additional columns to be used for grouping the dose-response experiments.

When your file is uploaded, another popup will open in which you can type the division times for the cell lines used as well as the assay duration.


Step 3: Select file type


Step 4: Upload data file

From your computer:

Or from a URL:


File formatting issues

Your input file is not in the correct format.

Please fix the following issues and re-upload your file.

Add division times and assay duration

Type the length of treatment below. (Do not include units)

Type or copy/paste the time it takes for each (untreated) cell line to undergo one division.

Each line should contain one number (no units), in the order listed.

Note that although units (hours, days, etc.) are not included above, the division times and duration of treatment must all be measured in the same units.

Load Example

Load Example

control values assigned to treated measurements
control values stacked with treated measurements


Working...
  • Getting Started
  • Data Tables
  • Dose-Response by Condition
  • Dose-Response Grid
  • GR Metric Comparison

Update:
GR values may be calculated using cell division times (and assay duration) in place of initial cell counts.
(Click "Import data file" and select "Cell division times" and a case to see more information.)
Recent Changes:
1. Input file must contain columns named "cell_line" and "treatment".
2. "Case C" input format renamed to "Case B".
Report any bugs/questions/feature requests to GR.calculator@gmail.com
For offline computation, analysis, and visualization, see the Bioconductor R package GRmetrics.
For a step-by-step example of using the GRcalculator, see here.

Formatting input files

Input files may be either comma- or tab-separated text files (.csv or .tsv). For more information about the input format, click "Import data file" and make a selection.
For an example input file, click "Load Example" and then "Download Data File" after the file has been loaded.

Instructions

To calculate normalized growth rate inhibition (GR) values and corresponding GR metrics: GR50, GEC50, GRmax, GRinf, GRAOC, and hGR based on cell counts measured in dose-response experiments using this online tool, users must provide a data file in which each row represents a separate treatment condition and the columns specify the keys (variables) that define the treatment condition (e.g. cell line, drug or other perturbagen, perturbagen concentration, treatment time, replicate) and the measured cell counts (or surrogate such as CellTiter-Glo® or other readout). Analogous traditional metrics: IC50, EC50, Emax, Einf, AUC, and h are also computed. Interactive analysis and visualization tools are provided. Detailed instructions can be found below.

Step 1: Load the data file containing cell counts for treated and control cells.

GRcalculator accepts comma-separated (.csv) or tab-separated (.tsv) input files. It can also accept files that use commas as decimal points.

The input files can come in one of two different formats, here called “Case A” and “Case B”. Case A is the simplest format, with treated and control cell counts in different columns. Case B is more general and has treated and control cell counts in the same column. See below for exact descriptions of Case A and Case B.

Click the Load Example button and then click Load Example Case A or Load Example Case B to the left to view a sample data file in the Data Tables tab.

Step 2: Select the grouping variables.

The key variables selected define on which variables the GR values will be averaged before fitting of the dose-response curves. By default, all variables are pre-selected, but, for example, replicates can be averaged by deselecting the proper column header. To deselect a variable, click on it in the grouping variables box and then press the “delete” or “backspace” key. You may repeat this with as many variables as you like.

Step 3: Select additional options and click “Analyze”

Additionally, the user may select Advanced options and choose Cap GR values below 1 and/or Force sigmoidal fit. If Cap GR values below 1 is selected, all calculated GR values that are greater than 1 will be set to 1. If Force sigmoidal fit is selected, the calculator will attempt to “force” a sigmoidal rather than a straight line fit, i.e. it will allow for sigmoidal fits with F-test p-values greater than .05.

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