During protocol design you can check and verify if during each of the implemented protocol steps / pipetting actions, the correct mixtures of reagents are obtained (theoretically) and which (mixtures of) reagents are present in each labware during each of the protocol steps.
You have several possibilities to check the contents of each of the labware on the virtual bench. There is however a distinction between the “Reagent at start” and the reagent present during each of the protocol steps.
The first way you can check the “Reagent at start”, is by selecting the labware you want to inspect followed by selecting the “Labware info tab” on the right side of your screen (in the Figure here, the middle pink 50 mL Falcon® conical centrifuge tube is selected). On this tab, the name of the reagent that is present in this labware is listed (in the Figure here, Acetonitrile), followed by the volume. The “AUTO calculation” checkbox is by default checked and implies that depending on the pipetting steps during the complete protocol a sufficient amount of starting reagent is added to the labware, without the need to define a specific amount. Alternatively, in case of need, a precise value can be entered, overwriting the default “AUTO calculation” value. Depending on the reagent chosen at the beginning (see the articles “Fill a labware with a reagent” and “Create a new reagent”), this is followed by the concentration (in the Figure here, 1 arbitrary unit) and a description (optional). Note that depending on the reagent, the unit of concentration can be important. Also depending on the application, concentrations can be of minor or major importance.
For example, during a serial dilution the concentrations are followed precisely. In case of the example with acetonitrile, which can be used in its pure form, arbitrary units seem a best fit, while for other reagents, molar units (M), dissolved mass per volume (kg/L), percentage of weight per volume (%w/v), percentage of weight per weight (%w/w) or percentage of volume per volume(%v/v) can be more suitable. By setting the concentration you can easier and quicker implement serial dilutions and normalizations.
As you may see, the selected labware has a black contextual menu bar attached to it, where it is shown that “1 reagent” is present. When you click here, a submenu opens with information about the reagent. You should be aware that the information is the current information, thus it is linked to the protocol step that is selected. If another protocol step is selected, the information is automatically updated:
Here you can see that the predefined volume of 10 mL is present in the labware during protocol step 0 (start). Protocol step 1 involves filling the first column of a 96 well microplate with in each of the wells 100 uL, resulting in a volume in the source labware of 10 mL – 8x100 uL = 9.2 mL, as indicated. At the end of the protocol, during step 5, another 1 mL is transferred to the top 50 mL tube, resulting in 8.2 mL in the source labware. For each of these steps, besides the volume, also all reagents are listed with their concentrations.
You can check and validate any of the labware on the virtual bench, during each of the protocol steps. Below, similar information is displayed for the top 50 mL tube:
Note that in the top left part of the Figure, during protocol step 0, there is only 1 reagent present. During protocol step 5, the top 50 mL tube receives 1 mL from the middle 50 mL tube. Therefore, the black contextual menu bar now states that there are “2 reagents” present (top right part of the Figure). Finally at the bottom left part of the Figure, when you click on “2 reagents”, a submenu appears with the information about the reagents, the total volume and the concentrations in which they are present.
For labware with multiple wells, the black contextual menu bar contains the text “Inspect wells”. When you click here, a zoomed version of the labware is displayed.
You can check each of the individual wells by clicking on it. At the bottom a submenu will open with the following information listed:
- Well location (in the Figure: A1)
- Total volume in this well
- The protocol step (in the Figure: step 5)
- The current reagents that are present with their concentrations (relative to the total amount of liquid).
- The volumes that are present during the start of the experiment (step 0 of the protocol).