v 0.1.9, added lots of JS functionality

biocircuits/__init__.py

@@ -15,4 +15,4 @@
 
 __author__ = """Justin Bois"""
 __email__ = "[email protected]"
-__version__ = "0.1.8"
+__version__ = "0.1.9"

biocircuits/gillespie.py

@@ -49,6 +49,10 @@ def _gillespie_draw(propensity_func, propensities, population, t, args):
     # Sum of propensities
     props_sum = _sum(propensities)
 
+    # Bail if the sum of propensities is zero (no moves to make)
+    if props_sum == 0.0:
+        return -1, -1.0
+
     # Compute time
     time = _draw_time(props_sum)
 
@@ -85,12 +89,16 @@ def _copy_population(population_previous, population):
             # draw the event and time step
             event, dt = draw_fun(propensity_func, propensities, population, t, args)
 
-            # Update the population
-            _copy_population(population_previous, population)
-            population += update[event, :]
+            if event == -1:
+                # Skip to the end of the simulation with the same population
+                t = time_points[-1]
+            else:
+                # Update the population
+                _copy_population(population_previous, population)
+                population += update[event, :]
 
-            # Increment time
-            t += dt
+                # Increment time
+                t += dt
 
         # Update the index (Have to be careful about types for Numba)
         j = np.searchsorted((time_points > t).astype(np.int64), 1)
@@ -105,7 +113,6 @@ def _copy_population(population_previous, population):
     return pop_out, None
 
 
-@numba.njit
 def _gillespie_trajectory_report_time_points(
     propensity_func, update, population_0, time_points, draw_fun, args=()
 ):
@@ -129,12 +136,20 @@ def _gillespie_trajectory_report_time_points(
             # draw the event and time step
             event, dt = draw_fun(propensity_func, propensities, population, t, args)
 
+            if event == -1:
+                # Skip to the end of the simulation with the same population
+                t = time_points[-1]
+            else:
+                # New population
+                population += update[event, :]
+
+                # Increment time
+                t += dt
+
             # Update the population
-            population += update[event, :]
             pop[i, :] = population
 
-            # Increment time
-            t += dt
+            # Updated time
             tp[i] = t
 
             # Increment indexes
@@ -226,6 +241,10 @@ def _draw(propensities, population, t):
             # Sum of propensities
             props_sum = np.sum(propensities)
 
+            # Bail if the sum of propensities is zero
+            if props_sum == 0.0:
+                return -1, -1.0
+
             # Compute time
             time = np.random.exponential(1 / props_sum)
 
@@ -258,12 +277,20 @@ def _traj():
                         # draw the event and time step
                         event, dt = _draw(propensities, population, t)
 
+                        if event == -1:
+                            # Skip to the end of the simulation with the same population
+                            t = time_points[-1]
+                        else:
+                            # New population
+                            population += update[event, :]
+
+                            # Increment time
+                            t += dt
+
                         # Update the population
-                        population += update[event, :]
                         pop[i, :] = population
 
-                        # Increment time
-                        t += dt
+                        # Updated time
                         tp[i] = t
 
                         # Increment indexes
@@ -299,12 +326,16 @@ def _traj():
                         # draw the event and time step
                         event, dt = _draw(propensities, population, t)
 
-                        # Update the population
-                        _copy_population(population_previous, population)
-                        population += update[event, :]
+                        if event == -1:
+                            # Skip to the end of the simulation with the same population
+                            t = time_points[-1]
+                        else:
+                            # Update the population
+                            _copy_population(population_previous, population)
+                            population += update[event, :]
 
-                        # Increment time
-                        t += dt
+                            # Increment time
+                            t += dt
 
                     # Update the index (Be careful about types for Numba)
                     j = np.searchsorted((time_points > t).astype(np.int64), 1)
@@ -321,7 +352,7 @@ def _traj():
     else:
         if return_time_points:
 
-            def traj():
+            def _traj():
                 return _gillespie_trajectory_report_time_points(
                     propensity_func,
                     update,
@@ -371,7 +402,7 @@ def _traj():
 
 
 def _gillespie_multi_fn(args):
-    """Convenient function for multithreading."""
+    """Convenience function for multithreading."""
     return _gillespie_ssa(*args)
 
 

biocircuits/jsfunctions.py

@@ -1616,6 +1616,34 @@
 	cds.change.emit();
 }
 
+""",
+    "simple_binding_sensitivity": """
+function sensitivity(a0, b0, Kd) {
+	let b = a0 - b0 - Kd;
+	let discrim = b * b + 4 * a0 * Kd;
+	let sqrtDiscrim = Math.sqrt(discrim);
+
+	return a0 * (1 - b / sqrtDiscrim) / (sqrtDiscrim - b);
+}
+
+
+function callback() {
+    let b0 = Math.pow(10, b0Slider.value);
+    let KdVals = [0.001, 0.01, 0.1, 1.0, 10.0];        
+    let a0 = cds.data['a0'];
+    
+    for (let i = 0; i < KdVals.length; i++) {
+    	let ind = 's' + i.toString();
+    	for (let j = 0; j < a0.length; j++) {
+    		cds.data[ind][j] = sensitivity(a0[j], b0, KdVals[i]);
+    	}
+    }
+
+    span.location = b0;
+
+    cds.change.emit();
+}
+
 """,
     "toggle_nullclines": """
 function f(x, beta, n) {return beta / (1.0 + Math.pow(x, n));}
@@ -1758,4 +1786,4 @@
     cdsUnstable.change.emit();
 }
 """,
-}
+}