Supplementary Data: Macklin et al. (2012)

The supplementary materials on this webpage refer to Macklin et al. (2012), entitled:

Text and other Documents

Supplementary Text: Main text for the supplementary material.
Tutorial: Basic DCIS pathobiology for modelers: Short introduction to biology and pathology of DCIS for modelers, with a collection of references. (This may be updated from time to time.)

The following videos are referenced by the paper and the supplementary material:

Video S1: This is the "baseline" simulation in the paper, plotted in 1.5 mm of duct, from 0 to 45 days.

Legend: In the viable rim, green cells are proliferating (virtual Ki-67 positive), red cells are apoptosing (virtual cleaved Caspase-3 positive, plus estimated undetected portion), and pale blue cells are quiescent / G₀. Dark blue circles are cell nuclei. In the necrotic core, the shade of red denotes the degree of calcification and pyknosis (nuclear degradation). Bright red circles are clinically-detectable calcifications.
Video S2: This shows the unstable perinecrotic boundary (between the viable rim and the necrotic core) resulting from heterogeneous oxygen uptake rates: proliferating cells consume oxygen at a rate 100 times that of non-proliferating tumor cells. Here plotted from 0 to 30 days in 1 mm of duct.

Legend: In the viable rim, green cells are proliferating (virtual Ki-67 positive), red cells are apoptosing (virtual cleaved Caspase-3 positive, plus estimated undetected portion), and pale blue cells are quiescent / G₀. Dark blue circles are cell nuclei. In the necrotic core, the shade of red denotes the degree of calcification and pyknosis (nuclear degradation). Bright red circles are clinically-detectable calcifications.

Please find below computer source code and data referenced by the paper(s) and the supplementary material:

MATLAB configuration script version 1.00 (0.00 MB - coming soon): Configuration script for the model presented in Macklin et al. (2012), using the updated calibration protocol in Hyun and Macklin (2012, in press).
DCIS_benchmark_dataset_1.02.zip (2.08 MB): Simulation data for t = 0, 15, 30, and 45 days, in MultiCellXML format.
Note: Contains a few XML fields for deprecated model features; does not impact results.
MultiCellXML_postprocessing_1.00.zip (109 KB): Code to parse the data file above, for postprocessing as in the paper. Please note that our code is subject to the GPL (GNU General Public License) Version 3.0, as well as standard academic courtesys. Please see the readme.txt file for instructions.
MultiCellXML_visualisation_1.01.zip (173 KB): Code to parse the data file above, for visualization as in the paper. Please note that our code is subject to the GPL (GNU General Public License) Version 3.0, as well as standard academic courtesys. Please see the readme.txt file for instructions.