Added p53 example notebook

Author: vincent-noel

PopMaBoSS_P53.ipynb

@@ -0,0 +1,24 @@
+Node D_b1 {
+  logic = (!D_b1 & !P) | (!D_b1 & P & Papo) | (D_b1 & !D_b2 & !P) | (D_b1 & !D_b2 & P & Papo) | (D_b1 & D_b2);
+  rate_up = @logic ? $u_D_b1 : 0;
+  rate_down = @logic ? 0 : $d_D_b1;
+}
+
+Node D_b2 {
+  logic = (D_b1 & !P) | (D_b1 & P & Papo);
+  rate_up = @logic ? $u_D_b2 : 0;
+  rate_down = @logic ? 0 : $d_D_b2;
+}
+
+Node P {
+  logic = (D_b1);
+  rate_up = @logic ? $u_P : 0;
+  rate_down = @logic ? 0 : $d_P;
+}
+
+Node Papo {
+  logic = (D_b1 & D_b2 & P);
+  rate_up = @logic ? $u_Papo : 0;
+  rate_down = @logic ? 0 : $d_Papo;
+}
+

p53/1782464636474.jpg

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+$u_D_b1 = 2;
+$d_D_b1 = 1;
+$u_D_b2 = 1;
+$d_D_b2 = 1;
+$u_P = 1;
+$d_P = 1;
+$u_Papo = 1;
+$d_Papo = 1;
+
+[D_b1,D_b2].istate = 1 [0,0], 0 [1,0], 0 [1,1];
+[P].istate = 1 [0] , 0 [1];
+[Papo].istate = 1 [0] , 0 [1];
+
+time_tick = 0.5;
+max_time = 30;
+sample_count = 10000;
+discrete_time = 0;
+use_physrandgen = 1;
+seed_pseudorandom = 0;
+display_traj = 0;
+statdist_traj_count = 0;
+statdist_cluster_threshold = 1;
+thread_count = 24;
+statdist_similarity_cache_max_size = 20000;

p53/p53_toy.bnd

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+$u_D_b1 = 2;
+$d_D_b1 = 1;
+$u_D_b2 = 1;
+$d_D_b2 = 1;
+$u_P = 1;
+$d_P = 1;
+$u_Papo = 1;
+$d_Papo = 1;
+$mu = 0.01;
+$K = 100;
+
+[D_b1,D_b2].istate = 1 [0,0], 0 [1,0], 0 [1,1];
+[P].istate = 1 [0] , 0 [1];
+[Papo].istate = 1 [0] , 0 [1];
+
+time_tick = 0.5;
+max_time = 30;
+init_pop = 1;
+sample_count = 1000;
+discrete_time = 0;
+use_physrandgen = 1;
+seed_pseudorandom = 0;
+thread_count = 22;
+

p53/p53_toy.cfg

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+Node D_b1 {
+  logic = (!D_b1 & !P) | (!D_b1 & P & Papo) | (D_b1 & !D_b2 & !P) | (D_b1 & !D_b2 & P & Papo) | (D_b1 & D_b2);
+  rate_up = @logic ? $u_D_b1 * (#cell()/$K) : 0;
+  rate_down = @logic ? 0 : $d_D_b1;
+}
+
+Node D_b2 {
+  logic = (D_b1 & !P) | (D_b1 & P & Papo);
+  rate_up = @logic ? $u_D_b2 : 0;
+  rate_down = @logic ? 0 : $d_D_b2;
+}
+
+Node P {
+  logic = (D_b1);
+  rate_up = @logic ? $u_P : 0;
+  rate_down = @logic ? 0 : $d_P;
+}
+
+Node Papo {
+  logic = (D_b1 & D_b2 & P);
+  rate_up = @logic ? $u_Papo : 0;
+  rate_down = @logic ? 0 : $d_Papo;
+}
+
+# symmetric division
+division {		
+  rate = (!P & !Papo & !D_b1 & !D_b2) ? (1.0 - $mu) : 0.0 ;
+}
+
+# asymmetric division
+division {		
+  rate = (!P & !Papo & !D_b1 & !D_b2) ? $mu : 0.0 ;
+  D_b1.daughter1 = 1;
+  D_b1.daughter2 = 0;
+}
+
+death
+{
+  rate = Papo ? 1.0 : 0.0;
+}