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C. elegans

Stem Cell Modeling

A model of stem cell population dynamics:  

in-silico analysis and in-vivo validation

Y. Setty, D. Dalfo, D.Z. Korta, E.J.A. Hubbard, and H. Kugler (2012)

Development, vol. 139, 47-56, 2012.

Supplementary Movies

(Supplementary Movie 1) related to Figures 1,2, and 5: Simulation under baseline design (memory "on", ligand interaction 3CD, and receptor degradation threshold at 16CD, 5:1 division evaluation frequency for larva and adult stages, respectively).

(Supplementary Movie 2) related to Figure 2: Simulation with slow kinetics of proliferative zone loss; baseline design with receptor degradation moved to 8CD. 

(Supplementary Movie 3) related to Figure 2: Simulation with fast kinetics of proliferative zone loss; baseline design with receptor degradation moved to 3CD.

(Supplementary Movie 4) related to Figure 2: Simulation of proliferative zone loss; baseline design with ligand interaction moved to 2CD.

(Supplementary Movie 5) related to Figure 2: Simulation of proliferative zone loss; baseline design with ligand interaction moved to 1CD.

(Supplementary Movie 6) related to Figure 5:  Simulation under baseline design with altered division evaluation frequency of 3.3:1 for larval and adult stages, respectively.

(Supplementary Movie 7) related to Figure 5:  Simulation under baseline design with altered division evaluation frequency of 2.5:2.5 for larval and adult stages, respectively.

(Supplementary Movie 8) related to Figure 5:  Simulation under baseline design with altered division evaluation frequency of 2.5:1 for larval and adult stages, respectively.

(Supplementary Movie 9) related to Figure 5:  Simulation under baseline design with altered division evaluation frequency of 1:1 for larval and adult stages, respectively.

Additional Movies

(Additional Movie 1) related to Figure 1: Simulation under glp-1(gf).

(Additional Movie 2) related to Figure 1: Simulation under glp-1(lf).

(Additional Movie 3) related to Figure 3: Simulation of "temperature shift"; receptor degradation shifted at early adult to 0CD from 12CD. 

(Additional Movie 4) related to Figure 3: Simulation of "temperature shift"; receptor degradation shifted at early adult to 3CD from 12CD.

(Additional Movie 5) related to Figure 3: Simulation of "temperature shift"; receptor degradation shifted at early adult to 8CD from 12CD.

(Additional Movie 6) related to Figure S1: Simulation under lag-2(lf).

Model Source Code

Rhapsody Model 

Statechart C++ Code (Includes files body.h body.cpp cell.h cell.cpp

synchronizer.h synchronizer.cpp worm.h worm.cpp def.h)

Matlab Code related to Figure 4.