Comments 
The cell shape module calculates the length and surface area of the cell across its lifespan. It also keeps track of the cell volume. The cell is approximated to be of a rod shape similar to E. coli, even though M. genitalium is known to have a less uniform flask shape. Initially, the cell is modeled as a cylinder with two hemispherical caps. Once cell pinching commences at the midline of the cell, the shape and size of a septum region is also modeled.
General geometric equations to represent the shape of a cell, and the idea that the density of the cell does not change across the cell cycle are borrowed from Domach et al. (1983). We add the assumption that the width of the cell remains constant during the lifespan of a cell. Thus, the density and cell width are inputs into our model. The cell density of E. coli is used 1100g/L (Baldwin et al., 1995). The cell width is calculated based on the initial cell mass and density and the assumption that the cell is a sphere. The initial cell mass is fit to result in a
cell width of 200nm (Lind et al, 1984).
Our model calculates the mass of the cell at all timesteps. The mass and constant density provide us with the volume at all time points. Volume = [2 hemispheres] + [2 cylinders] + [septum region] The volume of the septum region is calculated as a cylinder of length, 2*septumLength, and width of the cell. Then two cones (height=septum, radius=septum) are subtracted from this cylinder. (This approximation was used in Shuler et al. 1979).
Since we know the volume of the cell from the cell's mass and density, and the septum length from our cytokinesis module, the volume formula gives us the length of the cell at each timestep.
Similarly, we can also calculate the surface area of the cell. Surface Area = [2 hemispheres] + [2 cylinders] + [septum region]. The surface area of the septum region is calculated as a cylinder of length, 2*septum, and width of the cell.
References
Shuler, M.L., Leung, S., Dick, C.C. (1979). A Mathematical Model for the Growth of a Single Bacteria Cell. Annals of the New York Academy of Sciences 326: 3552.
Domach, M.M., Leung, S.K., Cahn, R.E., Cocks, G.G., Shuler, M.L. (1983). Computer model for glucoselimited growth of a single cell of Escherichia coli B/rA. Biotechnology and Bioengineering 26: 203216.
Lind, K., Lindhardt, B., Schutten, H.J., Blom, J., Christiansen, C. (1984). Serological CrossReactions Between Mycoplasma genitalium and Mycoplasma pneumoniae. Journal of Clinical Microbiology 20: 10361043.
Baldwin WW, Myer R, Powell N, Anderson E, Koch AL. (1995). Buoyant density of Escherichia coli is determined solely by the osmolarity of the culture medium. Arch Microbiology 164: 155157.

