Abstract
Computer program that simulates and plots the dynamics of stem cells, transient amplifying cells, differentiated cells, and mutant cells in normal human colon crypts and early-stage colon cancer. It has been calibrated with measurements of human biopsy specimens. Includes graphical user interface, detailed information text, and annotated code. Experiments can be run from the GUI without knowledge of coding, or from the Behavior Space Tool using example code or modified code. It has been used to simulate human colon cancer initiation, therapy, and prevention. Different chemotherapy or prevention intermittent dose schedules can be input, including combination drug therapy. Chemotherapy of heterogeneous and drug resistant early colon cancers can be simulated. Circadian cell proliferation can be implemented for chronomodulated chemotherapy dose schedules. Simulated output can be saved in spreadsheet format, or as images of plots of cell numbers as function of time.
The model was developed in the application NetLogo version 5.3.1, and revisions made to also run in NetLogo version 6.2.0. The model will not run on the Web version of NetLogo. NetLogo is a multi-agent programmable modeling environment. It is authored by Uri Wilenski and developed at The Center for Connected Learning (CCL) and Computer-Based Modeling. It is multi-platform (Mac, Windows, or Linux) open source application. NetLogo version 6.2.0, can be downloaded at http://ccl.northwestern.edu/netlogo/download.shtml.
Versions of the model and its use have been described in the following publications: Theoret Biol Med Model. 2013;10:66-89, Cancer Chemother Pharmcol 2017;79:889-898, Converg Sci Phys Oncol 2017;3:035004, Cancer Inform 2019;18:1-8, JCO Clin Cancer Inform 2020;4:514-520 Cancer Inform 2022;21:1-8. A forthcoming publication will describe results of combination chemotherapy of multidrug resistant early-stage colon cancer.