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. Author manuscript; available in PMC: 2018 Jan 1.
Published in final edited form as: Methods Mol Biol. 2017;1471:305–323. doi: 10.1007/978-1-4939-6340-9_18

Table 1.

Specification of parameter values for beam-film simulations. Simulations require the user to input values for 15 parameters in the format of a table saved as a comma separated values (.csv) file. Values for different parameters are entered in different columns (as indicated as ‘Input Column’) and parameter values for separate simulations are entered on different rows. The table must contain column headers. Descriptions of the parameters, limits on their possible values and as an example, the parameter values used to simulate the distribution of Mlh1 foci on chromosomes 13–16 of human male meiosis chromosomes (Figure 5) are shown. An example input table is included with the program (simulation_parameters.csv).

Input
Column		 Parameter Description Acceptable
Values		 Example:
simulation of
Human Male
Chr13–16
1 A n Total number of bivalents ≥0 10,000
Precursor Patterning Parameters
2 B N Average number of precursors per bivalent ≥0 30
3 C B Similarity in total precursor number between bivalents 0–11,2 0.9
4 D E Evenness of precursor spacing 0–11 0.6
5 E Bs Left boundary of region of precursor suppression (‘Black Hole’) 0–11,3,4 0.32
6 F Be Right boundary of region of precursor suppression (‘Black Hole’) 0–11,3,4 0.79
7 G Bd Precursor density within the Black Hole, relative to regions outside the Black Hole 0–11 0.15
Crossover Designation Patterning Parameters
8 H Smax Average maximum stress level per bivalent ≥0 5.9
9 I Bsmax Similarity in maximum stress levels between bivalents 0–11 0
10 J A Distribution of precursor sensitivities 1–75 1
11 K L Stress relief distance 0–11,3 0.57
12 L cL Left end clamp 0–11 0.69
13 M cR Right end clamp 0–11 0.69
Crossover Maturation Parameters
14 N M Crossover maturation efficiency 0–11 1
15 O T2prob Probability that a precursor that was not designated to become a crossover will form a Type II crossover 0–11 0
1

Values less than 0 are treated as 0, values greater than 1 are treated as 1.

2

E cannot be greater than 0 when N is less than 1 (or the program will crash).

3

Values are relative to the full length of the bivalent (i.e. a fraction of 1).

4

The maximum size of the Black Hole corresponds to Bs=0.001 and Be=0.999.

5

Other values will result in A=1.