We are pleased to announce Joint User-Training Workshop “Developing Multi-Scale,Multi-Cell Developmental and Biomedical Simulations with CompuCell3D and SBW ”. It will focus on teaching the basics of multi-cell, multi-scale modeling using the open-source packages CompuCell3D and SBW. The workshop will be taught by many of the CompuCell3D and SBW developers. In addition to participating in lectures and hands-on exercises, each participant should prepare a 30 min presentation covering her/his area of research. Based on our previous experience such presentations lead to many future collaborations as well as make the workshop more scientifically stimulating event.
JPS
Event Dates: August 2nd - August 13th, 2010.
Location: Biocomplexity Institute, Indiana University
CompuCell3D Workshop page
Date for this half of the course: 2nd August to 7th August
See the PDF file for details
(Schedule)
The following materials will be provided:
Text Book on Enzyme and Gene Regulatory Kinetics (Paper and ebook)
Notes and sample models
Sample Scripts
How to access biomodels from the General Simulation Tool (GST) and simulate it?
Start the script tool in the GST
To access a particular model type:
model = biomodels['BIOMD0000000204']
To get the SBML for the model type:
model.SBML
Load the model into the simulator
LoadSBML (model.SBML)
Carry out the simulation
d = sim.simulateEx(0, 10, 100)
To graph the simulation:
Graph (d)
The following functions are supported by biomodels:
GetModels, GetModelsByChEBI, GetModelsByChEBIId, GetModelsByGo, GetModelsByGoId,
GetModelsByPerson, GetModelsByPublication, GetModelsByTaxonomy, GetModelsByTaxonomyId,
GetModelsByUniprot, GetModelsByUniprotId, GetSBML
How to run a simle stochastic simulation
LoadSBML(
"""p = defn StochasticModel_1
J1: $S1 -> S2; k1*S1;
J2: S2 -> $S3; k2*S2;
end;
p.S1 = 25;
p.S2 = 0;
p.S3 = 0;
p.k1 = 0.26;
p.k2 = 0.15;""")
startTime = 0
endTime = 50
stepSize = 1
gil.loadSBML(sim.getSBML());
gil.setSeed(0)
result = gil.simulate (startTime, endTime, 1);
Graph(result)
How to run a stochastic simulation:
1 def StochSim(sbml, startTime, endTime, stepSize):
2 if (len(sbml)):
3 gil.loadSBML(sbml)
4 gil.setSeed(0)
5 result = gil.simulateOnGrid(startTime, endTime, stepSize)
6 Util.Graph(graph, result)
7 graph.Refresh()
8 else:
9 print "Please load a model first"
11
12 # print "Stochastic Simulation: startTime", 0, " endTime: ", 10, " stepSize: ", 0.01
13 StochSim(host.GetChangedSBML(), 0, 10, 0.01)
How to compute the elasticity of a reaction over a range of concentrations
m = Util.CreateArray(100,2);
sim.reset();
for i in range(100):
m[i,0] = sim.getValue('S1');
m[i,1]= sim.getValue('EE:J1,S1');
print sim.setValue('S1', m[i, 0] + 0.2);
Graph(m);
How to compute the reaction rate/flux through a step
sim.setValue('S1', 0.45);
sim.Instance.model.computeAllRatesOfChange();
flux = sim.getValue ('J1');
How to compute the control coefficient for a reaction
sim.Instance.computeSteadyStateValue('CC:J1,E1');
How to load a Jarnac model
LoadSBML(
"""p = defn NewModel
J1: $S1 -> S2; E1*(k1*S1 - k2*S2);
J2: S2 -> $S3; E2*(k3*S2 - k4*S3);
end;
p.S1 = 1;
p.S2 = 2;
p.S3 = 0;
p.k1 = 0.4;
p.k2 = 3.5;
p.k3 = 0.23;
p.k4 = 0.11;
p.E1 = 1;
p.E2 = 1;""");
How to load a Jarnac file
OpenFile('/path/to/jarnacfile.jan')
or
Open()
Change the plot to Log Plot. For this you could use the following lines of python, after you created the plot:
clr.AddReference('ZedGraph.dll')
import ZedGraph
graph.GraphPane.YAxis.Type = ZedGraph.AxisType.Log;
graph.Refresh()
// Day 4 Feedback model
// Negative feedback in a metabolic pathway
p = defn feedback
J0: $X0 -> S1; VM1*(X0-S1/Keq1)/(1+X0+S1+S4^h);
J1: S1 -> S2; VM2*(10*S1-2*S2)/(1+S1+S2);
J2: S2 -> S3; VM3*(10*S2-2*S3)/(1+S2+S3);
J3: S3 -> S4; VM4*(10*S3-2*S4)/(1+S3+S4);
J4: S4 -> $X1; VM5*S4/(KS4+S4);
end;
p.X0 = 10;
p.X1 = 0;
p.S1 = 0;
p.S2 = 0;
p.S3 = 0;
p.S4 = 0;
p.VM1 = 10;
p.VM2 = 5;
p.VM3 = 4;
p.VM4 = 2.5;
p.VM5 = 2.5;
p.Keq1 = 10;
p.h = 2;
p.KS4 = 0.5;
p = defn cell
S1 -> S2; k1*S1;
S2 -> S3; k2*S2;
end;
p.S1 = 10;
p.S2 = 0;
p.S3 = 0;
p.k1 = 0.2;
p.k2 = 0.6;
p = defn cell
ext S1, S3;
S1 = sin (time*alpha);
S1 -> S2; k1*S1;
S2 -> S3; k2*S2;
end;
p.S1 = 10;
p.S2 = 0;
p.S3 = 0;
p.k1 = 0.2;
p.k2 = 0.6;
p.alpha = 1.2;
p = defn newModel
$Xo -> S1; v;
S1 -> $X1; k*S1;
at(gt(time,10)): v = 2;
at(gt(time,20)): v = 1;
end;
p.v = 1;
p.k = 0.5;
p.Xo = 0.5;
p = defn NewModel
$alpha -> $S2; Vmax*alpha*(1 + alpha)^(n-1)/((1 + alpha)^n + L*(1 + beta)^n);
end;
p.alpha = 1;
p.beta = 0.1;
p.S2 = 0.1;
p.Inh = 0.1;
p.Vmax = 1;
//p.Km1 = 0.56;
p.n = 4;
p.KI = 0.56;
p.L = 10;
Elasticity calculation, at low S e = 4
p = defn cell
$S1 -> $S2; Vmax*S1^n/(Km + S1^n);
end;
p.S1 = 0.10495;
p.S2 = 0;
p.Vmax = 1;
p.Km = 0.5;
p.n = 4;
Simulate a pulse in S2, observe recovery of state.
LoadSBML(
"""p = defn NewModel
J1: $S1 -> S2; E1*(k1*S1 - k2*S2);
J2: S2 -> $S3; E2*(k3*S2 - k4*S3);
end;
p.S1 = 1;
p.S2 = 2;
p.S3 = 0;
p.k1 = 0.4;
p.k2 = 3.5;
p.k3 = 0.23;
p.k4 = 0.11;
p.E1 = 1;
p.E2 = 1;""");
t = 0
sim.setValue ('S2', 0)
m = Util.CreateArray(100,2)
for i in range(50):
m[i,0] = t
m[i,1]= sim.getValue('S2')
t = sim.oneStep (t, 0.1)
sim.setValue ('S2', 1.2*sim.getValue ('S2'))
t = sim.oneStep (t-0.001, 0.01)
for i in range(50,100):
m[i,0] = t
m[i,1]= sim.getValue('S2')
# t-0.001 is a temporary hack until oneStep is fixed
t = sim.oneStep (t-0.001, 0.01)
Graph(m)
# Rossler Chaotic Model
LoadSBML(
"""p = defn Rossler
var x, y, z;
ext s;
$s -> x; -y-z;
$s -> y; x + a*y;
$s -> z; b + z*(x - c);
end;
// Values for a stable cycle;
//x = 4.59886; #y = -0.00782; #z = 1.54806;
//a = 0.2; #b = 0.2; #c = 2.5;
// Values for a two period stable cycle;
//x = -1.90791; #y = 4.6778; #z = 0.11143;
//a = 0.2; #b = 0.2; #c = 3.5;
// Values for a four (?) period stable cycle;
//x = -3.14657; #y = -1.9551; #z = 0.02726;
//a = 0.2; #b = 0.2; #c = 4;
// Values for a eight (?) period stable cycle;
//x = -6.69015; #y = -4.52629; #z = 0.01666;
//a = 0.2; #b = 0.2; #c = 5;
// And finally values for chaos;
p.x = -6.69015; p.y = -4.52629; p.z = 0.01666;
p.a = 0.2; p.b = 0.2; p.c = 5.7;""")
m = sim.simulateEx (0, 50, 1000);
Graph (m);
# Lorenz Model
LoadSBML(
"""p = defn LorenzODE
$w -> x; sigma*(y - x);
$w -> y; x*(rho - z) - y;
$w -> z; x*y - beta*z;
end;
p.x = 0.96259;
p.y = 2.07272;
p.z = 18.65888;
p.sigma = 10;
p.rho = 28;
p.beta = 2.67;""");
m = sim.simulateEx (0, 30, 1000);
Graph (m);
from System.IO import File, StreamWriter
streamWriter = File.CreateText ('c:/lorenz.txt')
for i in range(1000):
for j in range(3):
streamWriter.Write(m[i,j+1])
streamWriter.Write(', ')
streamWriter.Write ('\n');
streamWriter.Close()
# To plot 3D on gluplot, type
#splot "c:\\lorenz.txt" using 1:2:3 with lines
