IUPMStats v1.0

Infection Frequency Calculator

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

If you use IUPMStats, please cite the following article:

Daniel I S Rosenbloom, Oliver Elliott, Alison L Hill, Timothy J Henrich, Janet M Siliciano, Robert F Siliciano. Designing and interpreting limiting dilution assays: general principles and applications to the latent reservoir for HIV-1. bioRxiv doi: http://dx.doi.org/10.1101/018911.


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:


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


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

Maximum likelihood

Output Data