The cell cycle tool allows you take a parameter of your data and fit a cell cycle model to it. By doing this you can approximate the percentage of cells in G1, G2, and S phase of the cell cycle. The implementation in Floreada.io is based on the Watson Pragmatic model.
Creating a Cell Cycle Model
To start, select the population you would like to apply the model to, then select the "Cell Cycle" tool from the sidebar. This will bring up a menu where you can choose a parameter to use. The parameter usually is associated with DNA content. The parameter must be on a linear scale. Once you have selected the correct parameter you can click "Apply".
If the model is able to find a good fit, you will see the histogram for the data displayed in black as well as three other curves:
- Modelled G1 phase (Blue)
- Modelled S phase (Green)
- Modelled G2 phase (Red)
In addition, there will be a sidebar displayed with several statistics including:
- The overall percentages of cells in each phase
- The Mean, SD, and CV for the G1 and G2 modelled curves
If the model was not able to find an adequate fit to the data, no additional curves will be displayed and an error will be displayed in the sidebar. You can help the model find a fit by narrowing the range that it looks for the G1 and G2 peaks. You can specify the possible range for the peaks with G1/G2 Bounds tool. Select either G1 Bounds or G2 Bounds for the sidebar and then draw an appropriate range for the associated peak on the plot. The model will then rerun and attempt to fit the model with the new contraints. If it is successful, you will see the modelled curve. If not, try contraining the bounds for the other peak.