Concentration

Concentration

Overview

In PlateEditor, concentration data can be added to any well by using the Concentration option group provided in the [Menu Panel].
Areas and Concentrations data are defined independently from each other, to facilitate the process of tagging. In cases of dose-response, defining as many areas as doses in the curve would indeed not be satisfying.
Concentrations are defined by two properties, the numerical value by itself, and the physical unit attached to this value.

Units
The unit should be selected from the list provided.

The group of units u/mL, ku/mL (= 1,000 u/mL) and Mu/mL (= 1,000,000 u/mL) are used to represent arbitrary units, or non-dimensional quantities, in particular the number of cells, bacteria or viral particles per unit of volume.
For infection experiments, PlateEditor also provides the MOI, or multiplicity of infection. Dilution factors can also be represented with the "×" sign.

Value
The value can be any valid numerical value. Invalid values will be converted to a number whenever possible, or reset to zero.

Dose-responses

Dose-responses can be prepared quickly using the options provided under the Concentration group of the [Menu Panel].

The first value in the curve is defined by the Value/Unit fields (1d, 1e).
Other values are calculated automatically using the dose-reponse options (2a-f):

• a. Number of doses in the dose-response. This is the total number of doses desired, so the first dose should also be included.
• b. Replicates: how many times the same dose should be repeated before stepping to the next dose.
• c. Operator: mathematical function used for the calculation of the next dose. This function uses the current dose and the indicated factor (d) to compute the next dose. See below for details.
• d. Factor: the numerical value engaged with the operator (c) to yield the next dose. Example for the division operator ("/"): next dose = current dose / factor.
• e. Direction of the dose-response: whether the sequence of doses should be tagged in rows (horizontal) or in columns (vertical).
• f. Use this button to apply the dose-response configured above in the selected wells. Note that, when using the Tag button above (1c), these options are ignored.
  The dose-response will be applied in all the selected wells, occupying as many wells as possible and repeating itself from the begining when the end of the dose-response is reached. Doses will be appended side-by-side (Horizontal direction), or top-to-bottom (vertical direction).

Operator
The operator (2c) should be selected from a drop down list currently allowing the following values:

• "/": division operator. The next dose is calculated from the previous by dividing with the provided factor.
• "×": multiplication operator: The next dose is calculated from the previous by multiplying with the provided factor.
• "+": addition operator. The next dose is calculated from the previous by adding the provided factor.
• "×10^": power operator. The next dose is calculated from the previous by multiplying by 10 to the power of the provided factor. Care should be taken when using this operator, as too high values will result in Infinity. Note that negative values can be used for the factor.

Digits
When computing dose-responses, values can quickly become decimal numbers with a lot of digits. To facilitate the display and reading of the concentrations in the well, PlateEditor allows truncation of the values to remain within a certain number of digits.
This is indicated by the presence of a "~" in front of the number, indicating that the value displayed has been truncated and does not reflect the value calculated and stored in the layout. Only the display is affected.
The cut-off for the number of digits to display can be changed using the Digits dropdown list available in the Options group of the Layout panel.
It is possible to display the stored numbers in full by selecting the "All" value.
Note that PlateEditor will use a scientific or exponential notation when it is appropriate.

Examples

Here are some examples to illustrate the options available for the preparation of dose-responses.

Default options
Using all concentration options to their default values will produce the following output when tagged in a bloc of 10 columns in width:

This corresponds to a dose-response typically used when assessing the activity of a compound, involving 10 doses with a 2-fold dilution factor between each, spreading horizontally.

Vertical with replicates
In this case, the dose-response has 5 doses, each dose should be present in triplicates and stack vertically (in columns).
The configuration and the resulting values are as below:

Note that, because the selection contains 18 wells instead of the 15 needed to append the entire dose-response, a new dose-response is started and left incomplete in the bottom-right corner.