IUPMStats v1.0

Infection Frequency Calculator

This is the development site - See the live app here!





Use this calculator to estimate infection frequencies from limiting dilution assays. In particular, this calculator can be used with an outgrowth assay to measure latent infection in HIV 1, 2. Enter information about your wells in the following order, using a separate line for each well size: number of cells per well, number of replicates of this size, and number of positive outcomes (i.e., wells in which outgrowth was detected). In addition to providing a maximum-likelihood estimate, this calculator returns a 95% confidence interval. Further information about interpreting the output is provided under "About this Calculator."

Enter well size (# cells), Number of replicates for this size, Number of positive outcomes for this size


References

1 Chun, T.-W., Carruth, L., Finzi, D., Shen, X., DiGiuseppe, J. A., Taylor, H., Hermankova, M., Chadwick, K., Margolick, J., Quinn, T. C., Kuo, Y.-H., Brookmeyer, R., Zeiger, M. A., Barditch-Crovo, P., Siliciano, R. F. Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection. Nature 387, 183–188 (1997).

2 Laird G. M., Rosenbloom D. I. S., Lai J., Siliciano R. F., Siliciano J. D. Measuring the frequency of latent HIV-1 in resting CD4+ T cells using a limiting dilution co-culture assay. To appear in HIV Protocols (3rd ed).


Enter Number of Unique Well Sizes, Maximum Well Size (# cells), and Dilution Factor





Enter well size (# cells), Number of replicates for this size, Number of positive outcomes for this size







To upload data for a single patient, create a text file where each row has three numbers: the well size (# cells), the number of replicates for this size, and the number of positive outcomes for this size. The values may be delimited by either white space or commas. For example, your file could look like this:

900,9,1
400,5,2
100,10,2

For multiple patients, simply add rows with a greater-than sign followed by the patient name (in homage to fasta format). For example,

>patient1
900,9,0
100,10,2
>patient2
400,5,2
500,10,1
>patient3
600,10,1
500,4,3
300,5,2

In this mode, the app will produce a graph showing the infection frequencies (IUPM) across the set of patients.

Maximum likelihood


Output Data