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You can export either run calculations (same run across multiple wells) or lineage calculations (same well position across multiple runs). The exporter outputs doubling times and ODs when runs for the selected runs and survivals for each run when lineages is selected.

Figure 1.Select runs for doubling times and ODs, and lineages for survivals.

Doubling Times:

Two calculations are output, each using different algorithms: inflection and interval. They differ only in where on the curve the doubling time is calculated:

  • Inflection algorithm: calculates the doubling time between the two points having the maximum slope in the ln(OD) curve (steepest part of the curve).
  • Interval algorithm: calculates the average doubling time for points having OD > 0.2 and OD < 0.5 (after background is subtracted). This interval has been selected for its consistency across Bioscreen runs for our particular protocol. (Murakami CJ et al., 2008)

The doubling time is calculated as:

doubling time = ln(2) / slope of ln(OD) curve


Optional Doubling Time Correction: The correction option adjusts for the observed increase in doubling time with the time taken to reach a threshold OD of 0.5 for curves where time to reach Od = 0.5 is greater than 500 min.

doubling time corrected = doubling time + 0.0325 * (500 - time to reach OD 0.5)


Survivals:

The program outputs the fraction survival relative to the earliest run selected for each well position (first well in runs, second well in runs, etc...) using the doubling time of the earliest run selected and the time shift between growth curves at OD = 0.3 relative to the earliest run selected.

The survival fractions are calculated as:

survival = 1.0 / 2 ^ (time_shift / doubling_time)



Optional Clean Survival Correction: This correction eliminates any increases (by setting the survival equal to the previous survial) and locks survival = 0 if there are any increases when survival fraction is less than 0.2.


Survival Areas / Survival Integrals (SI): The survival area is calculated by numerical integration (midpoint rule) over survival curves

Relative Measurements: If groups have been named in the well info during upload, relative survival integral (SI) measurements can be computed for each group relative to another (must have grouping set):

  • SI Percent Change: calculates the percent change of a test group versus the reference group: percent change = (test group SI - ref group SI) / ref group SI * 100;
  • SI ln(ratio): calculates the ln(ratio) of a test group versus the reference group: ln(ratio) = ln(test group SI / ref group SI)
  • SI T-Test: calculates the t-statistic and p-value (two-tailed) for the test group versus the reference group assuming equal sample variance (pooled t-test)

Grouping:

If groups were defined in the well info input during upload, this option allows means/medians and standard deviations to be computed for each group.